Aaron Zhang Leigh Carmody Peter Robinson An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations. Medical Action Ontology 2020-12-10 definition definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition IAO:0000116 uberon editor_note true editor_note editor note editor note term replaced by Add as annotation triples in the granting ontology Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive abbreviation Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. uberon dc-creator true dc-creator An entity primarily responsible for making the content of the resource. Creator Creator creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. uberon dc-description true dc-description An account of the content of the resource. Description Description description Typically, a Title will be a name by which the resource is formally known. uberon dc-title true dc-title A name given to the resource. Title Title title Mark Miller 2018-05-11T13:47:29Z uberon dcterms-license true dcterms-license license has broad synonym has_broad_synonym database cross reference database_cross_reference has_exact_synonym has narrow synonym has_narrow_synonym has_related_synonym has_synonym_type is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external human_stages_ontology protein quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 chebi_ontology external protein quality uberon has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. PATOC:CJM realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after human_stages_ontology uberon preceded_by preceded_by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 external occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t BFO:0000067 uberon contains_process contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process contains process x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer cjm 2009-07-31T02:15:46Z BSPO:0000096 uberon anterior_to anterior_to anterior_to x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 uberon distal_to distal_to distal_to x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 uberon dorsal_to dorsal_to dorsal_to x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. BSPO:0000099 caudal_to uberon posterior_to posterior_to posterior_to x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. x proximal_to y iff x is closer to the point of attachment with the body than y. BSPO:0000100 uberon proximal_to proximal_to proximal_to x proximal_to y iff x is closer to the point of attachment with the body than y. x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 uberon ventral_to ventral_to ventral_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 uberon deep_to deep_to deep_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:0000120 uberon in_left_side_of in_left_side_of in_left_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:PATO_mtg_2009 X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:0000121 uberon in_right_side_of in_right_side_of in_right_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:PATO_mtg_2009 X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:0000122 uberon in_posterior_side_of in_posterior_side_of in_posterior_side_of X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:PATO_mtg_2009 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:0000123 uberon in_anterior_side_of in_anterior_side_of in_anterior_side_of X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:PATO_mtg_2009 X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in_proximal_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:PATO_mtg_2009 X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of in_distal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:PATO_mtg_2009 X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure BSPO:0000126 uberon in_lateral_side_of in_lateral_side_of in_lateral_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost_part_of X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y This relation holds when both the deep_to and ajdacent_to relationship similarly hold. BSPO:0001107 uberon immediately_deep_to immediately_deep_to immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost_part_of X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001113 uberon preaxialmost_part_of preaxialmost_part_of preaxialmost_part_of X intersects_median_plane of iff X crosses the midine plane of Y. BSPO:0005001 uberon intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects_midsagittal_plane_of BSPO:0015101 uberon in_dorsal_side_of in_dorsal_side_of in_dorsal_side_of A defining ingredient defines what a food is principally categorized as, rather than an ingredient listed by percentage of weight or volume. A food may have more than one defining ingredient. Damion Dooley FoodOn For example, 'bean soup' has a defining ingredient of some 'bean (whole)'. Similarly, spicy chicken wings require a defining ingredient of (usually minute) amounts of chilli. A soup may 'has ingredient' some bean, but that doesn't make it a 'bean soup', i.e. there should be no inference to that category. However, some classes may have that simple ingredient "necessary and sufficient" equivalency. has defining ingredient A relation attaching between a food material and another food material that has been added to it at some point in its history. Damion Dooley FoodOn has ingredient This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by 2020-01-28T19:01:13Z avoided behavior 2019-06-12T14:23:27Z avoided medical action 2019-07-12T14:23:27Z avoided food has_specified_input has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in RO:0000052 inheres_in inheres_in inheres in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 uberon bearer_of bearer_of bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 protein uberon participates_in false participates_in participates in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role RO:0000087 chebi_ontology protein has_role false false has_role has role has role has_role a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity derives from is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of RO:0001015 uberon location_of location_of location of location_of contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): Intended meaning: domain: material entity range: spatial region or site (immaterial continuant) contained_in contained in contains RO:0001019 uberon contains contains contains contains located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 protein uberon located_in located_in located in located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of RO:0002000 uberon boundary_of boundary_of 2D boundary of boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. David Osumi-Sutherland has boundary has_2D_boundary RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by nerve supply FMA:85999 X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland RO:0002007 uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of bounding layer of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. dos 2017-07-19T17:30:36Z has ligand dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of human_stages_ontology uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps overlaps true Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. David Osumi-Sutherland <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002134 uberon innervates innervates http://code.google.com/p/obo-relations/issues/detail?id=6 innervates innervates X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) RO:0002150 uberon continuous_with continuous_with continuous with continuous_with FMA:85972 two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. Consider obsoleting and merging with child relation, 'in homology relationship with' RO:0002158 uberon homologous_to homologous_to VBO calls this homologous_to homologous_to shares ancestor with lactation SubClassOf 'only in taxon' some 'Mammalia' S only_in_taxon T iff: S SubClassOf in_taxon only T U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon. x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall RO:0002160 never_outside_taxon specific_to specific_to_taxon protein uberon only_in_taxon false only_in_taxon Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species. only in taxon only_in_taxon S only_in_taxon T iff: S SubClassOf in_taxon only T U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon. ROC:Waclaw x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Chris Mungall Jennifer Deegan RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 uberon attaches_to_part_of attaches_to_part_of attached to part of attaches_to_part_of true true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. relation between an artery and the structure is supplies with blood. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies supplies arterial supply of FMA:86003 Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure RO:0002179 drains blood from drains from uberon drains drains source: Wikipedia drains drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 protein uberon has_component false has_component has component has component has_component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops from develops_from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops_into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor FBbt RO:0002207 uberon directly_develops_from directly_develops_from TODO - add child relations from DOS directly develops from directly_develops_from inverse of directly develops from developmental precursor of directly develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates regulates regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) RO:0002215 protein uberon capable_of false capable_of capable of capable of capable_of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x actively participates in y if and only if x participates in y and x realizes some active role Chris Mungall agent in actively participates in 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent obsolete has active participant true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y Chris Mungall RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded_by x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. x adjacent_to y iff: x and y share a boundary This relation acts as a join point with BSPO Chris Mungall RO:0002220 uberon adjacent_to adjacent_to adjacent to adjacent_to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. inverse of surrounded by inverse of surrounded_by Chris Mungall RO:0002221 uberon surrounds surrounds surrounds surrounds inverse of surrounded_by Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Relation between occurrents, shares a start boundary with. inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Relation between occurrents, shares a start boundary with. Allen:starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall RO:0002225 uberon develops_from_part_of develops_from_part_of develops from part of develops_from_part_of x develops_in y if x is located in y whilst x is developing Chris Mungall EHDAA2 Jonathan Bard, EHDAA2 RO:0002226 uberon develops_in develops_in This relation take from EHDAA2 - precise semantics yet to be defined develops in develops_in Relation between occurrents, shares an end boundary with. inverse of ends with Chris Mungall RO:0002229 finishes uberon ends ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by RO:0002230 uberon ends_with ends_with ends with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y Chris Mungall starts with process that occurs in has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. has output Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from Chris Mungall RO:0002255 uberon developmentally_contributes_to developmentally_contributes_to developmentally contributes to developmentally_contributes_to t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T Chris Mungall David Osumi-Sutherland Melissa Haendel induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induced by developmentally_induced_by t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. GO:0001759 Inverse of developmentally induced by Chris Mungall developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue Chris Mungall part of developmental precursor of cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall RO:0002314 inheres_in_part_of inheres_in_part_of inheres in part of inheres in part of true A relationship that holds via some environmental process Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of RO:0002331 protein involved_in false involved_in involved in involved_in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO RO:0002350 uberon member_of member_of member of member of has member is a mereological relation between a collection and an item. SIO RO:0002351 uberon has_member has_member has member has member inverse of has input Chris Mungall RO:0002352 uberon input_of input_of input of input of inverse of has output output of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attaches_to m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002372 uberon has_muscle_origin has_muscle_origin The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles has muscle origin has_muscle_origin We need to import uberon muscle to create a stricter domain constraint m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Chris Mungall Wikipedia:Insertion_(anatomy) RO:0002373 uberon has_muscle_insertion has_muscle_insertion The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles has muscle insertion has_muscle_insertion We need to import uberon muscle into RO to use as a stricter domain constraint m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. Chris Mungall drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) RO:0002376 uberon drains into tributary_of tributary_of tributary of tributary_of http://en.wikipedia.org/wiki/Tributary drains into dbpowl:drainsTo A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location Chris Mungall This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve Chris Mungall RO:0002380 uberon branching_part_of branching_part_of branching part of branching_part_of FMA:85994 x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y Chris Mungall has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall RO:0002388 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. Chris Mungall executes activity in enables activity in is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/MI_0914 https://github.com/oborel/obo-relations/wiki/InteractionRelations An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls activity directly regulates activity of directly regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits inhibits molecularly decreases activity of activity directly negatively regulates activity of directly negatively regulates activity of Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré activates directly activates molecularly increases activity of activity directly positively regulates activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. x composed_primarily_of y iff: more than half of the mass of x is made from parts of y Chris Mungall RO:0002473 uberon RO:0002473 composed_primarily_of composed_primarily_of composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in true Chris Mungall is kinase activity Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage relation between structure and stage Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). Chris Mungall RO:0002488 begins_to_exist_during uberon RO:0002488 existence_starts_during existence_starts_during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. Relation between continuant and occurrent, such that c comes into existence at the start of p. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). Chris Mungall RO:0002489 uberon existence_starts_with existence_starts_with existence starts with Relation between continuant and occurrent, such that c comes into existence at the start of p. x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x existence starts and ends during y if and only if the start of x is part of y and the end of x is part of y. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) Chris Mungall RO:0002491 uberon existence_starts_and_ends_during existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). Chris Mungall RO:0002492 ceases_to_exist_during uberon RO:0002492 existence_ends_during existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. Relation between continuant and occurrent, such that c ceases to exist at the end of p. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). Chris Mungall RO:0002493 uberon existence_ends_with existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with Relation between continuant and occurrent, such that c ceases to exist at the end of p. x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall RO:0002494 transforms from uberon transformation_of transformation_of transformation of transforms from SIO:000657 x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of direct_transformation_of immediately transforms from SIO:000658 x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). Chris Mungall RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. Chris Mungall RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. Chris Mungall RO:0002503 towards towards towards The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causal relation between material entities Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall causally influenced by (entity-centric) causally influenced by (material entity to material entity) causally influenced by Chris Mungall interaction relation helper property https://github.com/oborel/obo-relations/wiki/InteractionRelations Chris Mungall molecular interaction relation helper property Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences (material entity to material entity) causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. Chris Mungall Wikipedia:Antagonist_(muscle) RO:0002568 uberon has_muscle_antagonist has_muscle_antagonist has muscle antagonist has_muscle_antagonist m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. inverse of branching part of Chris Mungall RO:0002569 uberon has_branching_part has_branching_part has branching part x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. Chris Mungall GOC:cjm RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall RO:0002572 uberon luminal_space_of luminal_space_of luminal space of A relation that holds between an attribute or a qualifier and another attribute. Chris Mungall This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. RO:0002180 qualifier qualifier placeholder relation to indicate normality/abnormality. has modifier inverse of has skeleton Chris Mungall RO:0002576 uberon skeleton_of skeleton_of skeleton of Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel RO:0003000 uberon produces produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel RO:0003001 uberon produced_by produced_by produced by produced_by Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. Damion Dooley has substance added The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of chebi_ontology has_functional_parent false false has functional parent chebi_ontology has_parent_hydride false false has parent hydride chebi_ontology is_conjugate_acid_of true false is conjugate acid of chebi_ontology is_conjugate_base_of true false is conjugate base of chebi_ontology is_enantiomer_of true false is enantiomer of chebi_ontology is_substituent_group_from false false is substituent group from chebi_ontology is_tautomer_of true is tautomer of q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. uberon anteriorly_connected_to anteriorly connected to x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to distally connected to x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon existence_starts_and_ends_during existence starts and ends during uberon extends_fibers_into extends_fibers_into Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s add to RO uberon indirectly_supplies indirectly_supplies uberon layer_part_of layer part of x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon sexually_homologous_to sexually_homologous_to uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of . uberon transitively_anteriorly_connected_to transitively anteriorly connected to . uberon transitively_connected_to transitively_connected to . uberon transitively_distally_connected_to transitively distally connected to . . uberon transitively_proximally_connected_to transitively proximally connected to . uberon trunk_part_of trunk_part_of A planned process that has specified output a software product and that involves the creation of source code. Mathias Brochhausen William R. Hogan http://en.wikipedia.org/wiki/Software_development A planned process resulting in a software product involving the creation of source code. software development creating a data set A planned process that has a data set as its specified output. William R. Hogan data set creation dataset creation dataset creating entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] spatial region process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] bfo BFO:0000015 process process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] quality Quality quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] bfo BFO:0000019 quality quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] bfo BFO:0000030 object gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] bfo BFO:0000040 material entity material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] immaterial entity anatomical entity connected anatomical structure material anatomical entity immaterial anatomical entity cell part (CARO) cell part multi-cell-part structure neuron projection bundle organism or virus or viroid multicellular anatomical structure biological entity Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. -1 0.000548579903 0.0 KEGG:C05359 PMID:21614077 Wikipedia:Electron electron chebi_ontology Elektron beta beta(-) beta-particle e e(-) e- negatron CHEBI:10545 electron PMID:21614077 Europe PMC electron ChEBI electron IUPAC electron KEGG_COMPOUND Elektron ChEBI beta IUPAC beta(-) ChEBI beta-particle IUPAC e IUPAC e(-) UniProt e- KEGG_COMPOUND negatron IUPAC The conjugate base of gamma-amino-beta-hydroxybutyric acid arising from deprotonation of the carboxy group. -1 C4H8NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8)/p-1 YQGDEPYYFWUPGO-UHFFFAOYSA-M 118.11126 118.05097 NCC(O)CC([O-])=O CAS:352-21-6 KEGG:C03678 4-Amino-3-hydroxybutanoate chebi_ontology CHEBI:11955 4-amino-3-hydroxybutanoate CAS:352-21-6 KEGG COMPOUND KEGG:C03678 ChEBI 4-Amino-3-hydroxybutanoate KEGG_COMPOUND Any bacterial metabolite produced during a metabolic reaction in Mycoplasma genitalium. chebi_ontology Mycoplasma genitalium metabolites CHEBI:131604 Mycoplasma genitalium metabolite Mycoplasma genitalium metabolites ChEBI A steroid compound with a structure based on a 27-carbon (cholestane) skeleton. chebi_ontology C27-steroids CHEBI:131619 C27-steroid C27-steroids ChEBI A steroid compound with a structure based on a 24-carbon (cholane) skeleton. chebi_ontology C24-steroids CHEBI:131620 C24-steroid C24-steroids ChEBI Any steroid (or derivative) based on a cholane skeleton. chebi_ontology cholane derivatives CHEBI:131657 cholane derivative cholane derivatives ChEBI Any steroid acid anion based on a cholanic acid skeleton. PMID:1527482 chebi_ontology cholanic acid anions cholanoic acid anion cholanoic acid anions CHEBI:131878 cholanic acid anion PMID:1527482 SUBMITTER cholanic acid anions ChEBI cholanoic acid anion SUBMITTER cholanoic acid anions ChEBI A class of carbonyl compound encompassing dicarboxylic acids and any derivatives obtained by substitution of either one or both of the carboxy hydrogens. chebi_ontology dicarboxylic acids and derivatives CHEBI:131927 dicarboxylic acids and O-substituted derivatives dicarboxylic acids and derivatives ChEBI Any member of the class of benzoquinones that is 1,4-benzoquinone or its C-substituted derivatives. 0 C6O2R4 104.063 103.98983 O=C1C(*)=C(*)C(=O)C(*)=C1* chebi_ontology a quinone p-benzoquinones para-benzoquinones CHEBI:132124 1,4-benzoquinones a quinone UniProt p-benzoquinones ChEBI para-benzoquinones ChEBI Any quinone in which one or more of the carbons making up the quinone moiety is substituted by a hydroxy group. chebi_ontology hydroxyquinones CHEBI:132130 hydroxyquinone hydroxyquinones ChEBI Any polyunsaturated fatty acid containing 22 carbons and 6 double bonds. 0 C22H32O2 328.48830 328.24023 C(=O)(O)* chebi_ontology FA 22:6 FA(22:6) free fatty acid 22:6 CHEBI:132544 fatty acid 22:6 FA 22:6 ChEBI FA(22:6) ChEBI free fatty acid 22:6 ChEBI A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of oxalic acid. chebi_ontology ethanedioic acid anion ethanedioic acid anions oxalate anion oxalate anions oxalates oxalic acid anion oxalic acid anions CHEBI:132952 oxalate ethanedioic acid anion ChEBI ethanedioic acid anions ChEBI oxalate anion ChEBI oxalate anions ChEBI oxalates ChEBI oxalic acid anion ChEBI oxalic acid anions ChEBI Any organic compound having an initial boiling point less than or equal to 250 degreeC (482 degreeF) measured at a standard atmospheric pressure of 101.3 kPa. Wikipedia:Volatile_organic_compound chebi_ontology VOC VOCs volatile organic compounds CHEBI:134179 volatile organic compound VOC ChEBI VOCs ChEBI volatile organic compounds ChEBI An N-oxide where there are three organic groups bonded to the nitrogen atom. 0 NOR3 30.006 29.99799 *[N+](*)([O-])* Patent:EP0545208 Patent:EP0757983 Patent:EP0866058 Patent:EP1068179 Patent:US4206204 Patent:WO9950236 chebi_ontology tertiary amine oxides CHEBI:134363 tertiary amine oxide tertiary amine oxides ChEBI A compound that, on administration, undergoes conversion by biochemical (enzymatic), chemical (possibly following an enzymatic step), or physical (e.g. photochemical) activation processes before becoming the active agent for which it is a pro-agent. PMID:26449612 chebi_ontology pro-agents proagent proagents CHEBI:136859 pro-agent PMID:26449612 Europe PMC pro-agents ChEBI proagent ChEBI proagents ChEBI Any steroid that has beta-configuration at position 5. chebi_ontology 5beta steroids 5beta-steroid 5beta-steroids CHEBI:136889 5beta steroid 5beta steroids ChEBI 5beta-steroid ChEBI 5beta-steroids ChEBI A cardiovascular drug that tends to raise reduced blood pressure. Wikipedia:Antihypotensive_agent chebi_ontology antihypotensive agents pressor pressors vasopressor agent vasopressor agents CHEBI:137431 antihypotensive agent antihypotensive agents ChEBI pressor ChEBI pressors ChEBI vasopressor agent ChEBI vasopressor agents ChEBI An organic cation obtained by protonation of the amino group of any tertiary amino compound. +1 HNR3 15.015 15.01090 [NH+](*)(*)* chebi_ontology a tertiary amine tertiary amine(1+) tertiary ammonium ions CHEBI:137982 tertiary ammonium ion a tertiary amine UniProt tertiary amine(1+) ChEBI tertiary ammonium ions ChEBI A quaternary ammonium ion obtained by methylation of any tertiary amine +1 CH3NR3 29.041 29.02655 [N+](C)(*)(*)* chebi_ontology a methylated tertiary amine CHEBI:137983 methylated tertiary amine a methylated tertiary amine UniProt Any compound that can disrupt the functions of the endocrine (hormone) system PMID:27929035 PMID:28356401 PMID:28526231 Wikipedia:Endocrine_disruptor chebi_ontology endocrine disrupting chemical endocrine disrupting chemicals endocrine disrupting compound endocrine disrupting compounds endocrine disruptors endocrine-disrupting chemical endocrine-disrupting chemicals hormonally active agent hormonally active agents CHEBI:138015 endocrine disruptor PMID:27929035 Europe PMC PMID:28356401 Europe PMC PMID:28526231 Europe PMC endocrine disrupting chemical ChEBI endocrine disrupting chemicals ChEBI endocrine disrupting compound ChEBI endocrine disrupting compounds ChEBI endocrine disruptors ChEBI endocrine-disrupting chemical ChEBI endocrine-disrupting chemicals ChEBI hormonally active agent ChEBI hormonally active agents ChEBI A Bronsted acid derived from one or more inorganic compounds. Inorganic acids (also known as mineral acids) form hydrons and conjugate base ions when dissolved in water. Wikipedia:Mineral_acid chebi_ontology inorganic acids mineral acid mineral acids CHEBI:138103 inorganic acid inorganic acids ChEBI mineral acid ChEBI mineral acids ChEBI Any member of a group of hydroxy steroids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration, while in lower vertebrates, some bile acids, known as allo-bile acids, have 5alpha-configuration. chebi_ontology CHEBI:138366 bile acids Any main group molecular entity that is gaseous at standard temperature and pressure (STP; 0degreeC and 100 kPa). Wikipedia:https://en.wikipedia.org/wiki/Gas chebi_ontology gas molecular entities gaseous molecular entities gaseous molecular entity CHEBI:138675 gas molecular entity gas molecular entities ChEBI gaseous molecular entities ChEBI gaseous molecular entity ChEBI Any carotenoid derivative with an beta-end group 0 C19H27R 255.418 255.21128 C1(=C(CCCC1(C)C)C)/C=C/C(=C/C=C/C(=C/*)/C)/C MetaCyc:Carotenoid-beta-end-group chebi_ontology a carotenoid beta-end derivative CHEBI:139120 carotenoid beta-end group MetaCyc:Carotenoid-beta-end-group SUBMITTER a carotenoid beta-end derivative UniProt -1 CH2NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)/p-1 KXDHJXZQYSOELW-UHFFFAOYSA-M 60.03212 60.00910 NC([O-])=O Beilstein:3903503 CAS:302-11-4 Gmelin:239604 carbamate chebi_ontology Carbamat Karbamat carbamate ion carbamic acid, ion(1-) CHEBI:13941 carbamate Beilstein:3903503 Beilstein CAS:302-11-4 ChemIDplus Gmelin:239604 Gmelin carbamate IUPAC carbamate UniProt Carbamat ChEBI Karbamat ChEBI carbamate ion ChemIDplus carbamic acid, ion(1-) ChemIDplus An alpha-oxyketone that has a hydroxy group as the alpha-oxy moiety. PMID:15326516 PMID:19908854 PMID:20382022 PMID:23295224 chebi_ontology alpha-hydroxy ketones alpha-hydroxy-ketone alpha-hydroxy-ketones alpha-hydroxyketone alpha-hydroxyketones CHEBI:139588 alpha-hydroxy ketone PMID:15326516 Europe PMC PMID:19908854 Europe PMC PMID:20382022 Europe PMC PMID:23295224 Europe PMC alpha-hydroxy ketones ChEBI alpha-hydroxy-ketone ChEBI alpha-hydroxy-ketones ChEBI alpha-hydroxyketone ChEBI alpha-hydroxyketones ChEBI An alpha-hydroxy ketone in which the carbonyl group and the hydroxy group are linked by a carbon bearing two organyl groups. 0 C2HO2R3 57.028 56.99765 C(C(=O)*)(O)(*)* chebi_ontology tertiary alpha-hydroxy ketones tertiary alpha-hydroxy-ketone tertiary alpha-hydroxy-ketones tertiary alpha-hydroxyketone tertiary alpha-hydroxyketones CHEBI:139592 tertiary alpha-hydroxy ketone tertiary alpha-hydroxy ketones ChEBI tertiary alpha-hydroxy-ketone ChEBI tertiary alpha-hydroxy-ketones ChEBI tertiary alpha-hydroxyketone ChEBI tertiary alpha-hydroxyketones ChEBI Any saturated fatty acid containing 4 carbons. 0 CHO2R 45.017 44.99765 *C(O)=O chebi_ontology CHEBI:140601 fatty acid 4:0 0 C62H88CoN13O14PR 1329.350 1328.56433 [Co-3]1234(N5C6=C(C7=[N+]4C(=CC8=[N+]3C(=C(C9=[N+]2[C@@]([C@]5([C@@H]([C@@]6(C)CCC(=O)NC[C@H](OP(O[C@@H]%10[C@H](O[C@H](N%11C=[N+]1C%12=CC(=C(C=C%12%11)C)C)[C@@H]%10O)CO)(=O)[O-])C)CC(=O)N)[H])([C@]([C@@H]9CCC(N)=O)(CC(=O)N)C)C)C)[C@](C)([C@@H]8CCC(=O)N)CC(N)=O)C([C@@H]7CCC(=O)N)(C)C)C)* MetaCyc:CPD-20938 chebi_ontology an alkylcob(III)alamin CHEBI:140785 alkylcob(III)alamin MetaCyc:CPD-20938 SUBMITTER an alkylcob(III)alamin UniProt An organic anion arising from deprotonation of the hydroxy group of an enol. -1 C2OR3 40.021 39.99491 [O-]C(=C(*)*)* chebi_ontology enolate anion enolate anions enolates CHEBI:142839 enolate enolate anion ChEBI enolate anions ChEBI enolates ChEBI An alpha-amino-acid anion that is the conjugate base of glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1 WHUUTDBJXJRKMK-UHFFFAOYSA-M 146.12136 146.04588 [NH3+]C(CCC([O-])=O)C([O-])=O Gmelin:327908 glutamate(1-) hydrogen glutamate chebi_ontology 2-ammoniopentanedioate glutamate glutamic acid monoanion CHEBI:14321 glutamate(1-) Gmelin:327908 Gmelin glutamate(1-) JCBN hydrogen glutamate IUPAC 2-ammoniopentanedioate IUPAC glutamate UniProt glutamic acid monoanion JCBN 0 C21H17N2O7R5 409.370 409.10358 C12=C(C=C(C(=C1C(C=3[C@]([C@@H]([C@]4([C@@H](C([O-])=C(C([C@@]4(O)C3O)=O)C(N)=O)[NH+](C)C)[H])*)(C2(*)*)[H])=O)O)*)* chebi_ontology a tetracycline CHEBI:144644 a tetracycline zwittterion a tetracycline UniProt A cardiovascular drug that prevents atherosclerosis (a disease in which the inside of an artery narrows due to the build up of plaque). Compare with antiatherogenic agent. antiatherosclerotic agent chebi_ontology anti-atherosclerotic agent anti-atherosclerotic agents anti-atherosclerotic drug anti-atherosclerotic drugs antiatherosclerotic agents antiatherosclerotic drug antiatherosclerotic drugs CHEBI:145947 antiatherosclerotic agent antiatherosclerotic agent ChEBI anti-atherosclerotic agent ChEBI anti-atherosclerotic agents ChEBI anti-atherosclerotic drug ChEBI anti-atherosclerotic drugs ChEBI antiatherosclerotic agents ChEBI antiatherosclerotic drug ChEBI antiatherosclerotic drugs ChEBI Any EC 3.4.17.* (metallocarboxypeptidase) inhibitor that inhibits the action of angiotensin-converting enzyme 2 (EC 3.4.17.23). Wikipedia:Angiotensin-converting_enzyme_2 EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitor chebi_ontology ACE-2 inhibitor ACE-2 inhibitors ACE2 inhibitor ACE2 inhibitors EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitors EC 3.4.17.23 inhibitor EC 3.4.17.23 inhibitors angiotensin converting enzyme 2 inhibitor angiotensin converting enzyme 2 inhibitors angiotensin converting enzyme-2 inhibitor angiotensin converting enzyme-2 inhibitors angiotensin-converting enzyme 2 inhibitor angiotensin-converting enzyme 2 inhibitors hACE2 inhibitor hACE2 inhibitors CHEBI:147289 EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitor EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitor ChEBI ACE-2 inhibitor ChEBI ACE-2 inhibitors ChEBI ACE2 inhibitor ChEBI ACE2 inhibitors ChEBI EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitors ChEBI EC 3.4.17.23 inhibitor ChEBI EC 3.4.17.23 inhibitors ChEBI angiotensin converting enzyme 2 inhibitor ChEBI angiotensin converting enzyme 2 inhibitors ChEBI angiotensin converting enzyme-2 inhibitor ChEBI angiotensin converting enzyme-2 inhibitors ChEBI angiotensin-converting enzyme 2 inhibitor ChEBI angiotensin-converting enzyme 2 inhibitors ChEBI hACE2 inhibitor ChEBI hACE2 inhibitors ChEBI Any EC 3.4.* (hydrolases acting on peptide bond) inhibitor that inhibits the action of a metallocarboxypeptidase (EC 3.4.17.*). EC 3.4.17* (metallocarboxypeptidase) inhibitor chebi_ontology EC 3.4.17* (metallocarboxypeptidase) inhibitors EC 3.4.17.* inhibitor EC 3.4.17.* inhibitors metallocarboxypeptidase inhibitor metallocarboxypeptidase inhibitors CHEBI:147290 EC 3.4.17* (metallocarboxypeptidase) inhibitor EC 3.4.17* (metallocarboxypeptidase) inhibitor ChEBI EC 3.4.17* (metallocarboxypeptidase) inhibitors ChEBI EC 3.4.17.* inhibitor ChEBI EC 3.4.17.* inhibitors ChEBI metallocarboxypeptidase inhibitor ChEBI metallocarboxypeptidase inhibitors ChEBI Any agent that induces nausea and vomiting. chebi_ontology emetics CHEBI:149552 emetic emetics ChEBI A molecular entity that can accept an electron, a pair of electrons, an atom or a group from another molecular entity. CHEBI:13699 CHEBI:2377 KEGG:C00028 KEGG:C16722 Acceptor chebi_ontology A Akzeptor Hydrogen-acceptor Oxidized donor accepteur CHEBI:15339 acceptor Acceptor KEGG_COMPOUND A KEGG_COMPOUND Akzeptor ChEBI Hydrogen-acceptor KEGG_COMPOUND Oxidized donor KEGG_COMPOUND accepteur ChEBI A choline that is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function. +1 C5H14NO InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1 OEYIOHPDSNJKLS-UHFFFAOYSA-N 104.17080 104.10699 C[N+](C)(C)CCO CHEBI:13985 CHEBI:23212 CHEBI:3665 CHEBI:41524 Beilstein:1736748 CAS:62-49-7 DrugBank:DB00122 Drug_Central:3097 ECMDB:ECMDB00097 Gmelin:324597 HMDB:HMDB0000097 KEGG:C00114 KEGG:D07690 KNApSAcK:C00007298 MetaCyc:CHOLINE PDBeChem:CHT PMID:10930630 PMID:12826235 PMID:12946691 PMID:14972364 PMID:16210714 PMID:17087106 PMID:17283071 PMID:17344490 PMID:18204095 PMID:18230680 PMID:18786517 PMID:18786520 PMID:19246089 PMID:20038853 PMID:20446114 PMID:22770225 PMID:22961562 PMID:23095202 PMID:23616508 PMID:23637565 PMID:23733158 PMID:6420466 PMID:7590654 PMID:9517478 Reaxys:1736748 Wikipedia:Choline YMDB:YMDB00227 2-hydroxy-N,N,N-trimethylethanaminium Choline choline chebi_ontology Bilineurine CHOLINE ION N,N,N-trimethylethanol-ammonium N-trimethylethanolamine trimethylethanolamine CHEBI:15354 choline Beilstein:1736748 Beilstein CAS:62-49-7 ChemIDplus CAS:62-49-7 KEGG COMPOUND Drug_Central:3097 DrugCentral Gmelin:324597 Gmelin PMID:10930630 Europe PMC PMID:12826235 Europe PMC PMID:12946691 Europe PMC PMID:14972364 Europe PMC PMID:16210714 Europe PMC PMID:17087106 Europe PMC PMID:17283071 Europe PMC PMID:17344490 Europe PMC PMID:18204095 Europe PMC PMID:18230680 Europe PMC PMID:18786517 Europe PMC PMID:18786520 Europe PMC PMID:19246089 Europe PMC PMID:20038853 Europe PMC PMID:20446114 Europe PMC PMID:22770225 Europe PMC PMID:22961562 Europe PMC PMID:23095202 Europe PMC PMID:23616508 Europe PMC PMID:23637565 Europe PMC PMID:23733158 Europe PMC PMID:6420466 Europe PMC PMID:7590654 Europe PMC PMID:9517478 Europe PMC Reaxys:1736748 Reaxys 2-hydroxy-N,N,N-trimethylethanaminium IUPAC Choline KEGG_COMPOUND choline UniProt Bilineurine KEGG_COMPOUND CHOLINE ION PDBeChem N,N,N-trimethylethanol-ammonium ChEBI N-trimethylethanolamine ChEBI trimethylethanolamine ChEBI A sulfur-containing amino acid that is propanoic acid with an amino group at position 2 and a sulfanyl group at position 3. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) XUJNEKJLAYXESH-UHFFFAOYSA-N 121.15922 121.01975 NC(CS)C(O)=O CHEBI:14061 CHEBI:23508 CHEBI:4050 Beilstein:1721406 CAS:3374-22-9 Gmelin:2933 KEGG:C00736 KNApSAcK:C00001351 KNApSAcK:C00007323 PMID:17439666 PMID:25181601 Reaxys:1721406 Wikipedia:Cysteine Cysteine cysteine chebi_ontology 2-Amino-3-mercaptopropionic acid 2-amino-3-mercaptopropanoic acid 2-amino-3-sulfanylpropanoic acid C Cys Cystein Hcys Zystein cisteina CHEBI:15356 cysteine Beilstein:1721406 Beilstein CAS:3374-22-9 ChemIDplus CAS:3374-22-9 KEGG COMPOUND CAS:3374-22-9 NIST Chemistry WebBook Gmelin:2933 Gmelin PMID:17439666 Europe PMC PMID:25181601 Europe PMC Reaxys:1721406 Reaxys Cysteine KEGG_COMPOUND cysteine ChEBI cysteine IUPAC 2-Amino-3-mercaptopropionic acid KEGG_COMPOUND 2-amino-3-mercaptopropanoic acid JCBN 2-amino-3-sulfanylpropanoic acid IUPAC C ChEBI Cys ChEBI Cystein ChEBI Hcys IUPAC Zystein ChEBI cisteina ChEBI A 2-oxo monocarboxylic acid anion that is the conjugate base of pyruvic acid, arising from deprotonation of the carboxy group. -1 C3H3O3 InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)/p-1 LCTONWCANYUPML-UHFFFAOYSA-M 87.05412 87.00877 CC(=O)C([O-])=O CHEBI:14987 CHEBI:26462 Beilstein:3587721 CAS:57-60-3 Gmelin:2502 KEGG:C00022 PMID:17190852 PMID:21603897 PMID:21823181 PMID:21854850 PMID:22006570 PMID:22016370 PMID:22215378 PMID:22311625 PMID:22451307 PMID:22458763 Reaxys:3587721 UM-BBD_compID:c0159 2-oxopropanoate pyruvate chebi_ontology 2-oxopropanoate 2-oxopropanoic acid, ion(1-) CHEBI:15361 pyruvate Beilstein:3587721 Beilstein CAS:57-60-3 ChemIDplus Gmelin:2502 Gmelin PMID:17190852 Europe PMC PMID:21603897 Europe PMC PMID:21823181 Europe PMC PMID:21854850 Europe PMC PMID:22006570 Europe PMC PMID:22016370 Europe PMC PMID:22215378 Europe PMC PMID:22311625 Europe PMC PMID:22451307 Europe PMC PMID:22458763 Europe PMC Reaxys:3587721 Reaxys UM-BBD_compID:c0159 UM-BBD 2-oxopropanoate IUPAC pyruvate UniProt 2-oxopropanoate ChEBI 2-oxopropanoic acid, ion(1-) ChemIDplus A simple monocarboxylic acid containing two carbons. 0 C2H4O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4) QTBSBXVTEAMEQO-UHFFFAOYSA-N 60.05200 60.02113 CC(O)=O CHEBI:22169 CHEBI:2387 CHEBI:40486 Beilstein:506007 CAS:64-19-7 Drug_Central:4211 Gmelin:1380 HMDB:HMDB0000042 KEGG:C00033 KEGG:D00010 KNApSAcK:C00001176 LIPID_MAPS_instance:LMFA01010002 MetaCyc:ACET PDBeChem:ACT PDBeChem:ACY PMID:12005138 PMID:15107950 PMID:16630552 PMID:16774200 PMID:17190852 PMID:19416101 PMID:19469536 PMID:22153255 PMID:22173419 PPDB:1333 Reaxys:506007 Wikipedia:Acetic_acid ACETIC ACID Acetic acid acetic acid chebi_ontology AcOH CH3-COOH CH3CO2H E 260 E-260 E260 Essigsaeure Ethanoic acid Ethylic acid HOAc INS No. 260 MeCO2H MeCOOH Methanecarboxylic acid acide acetique ethoic acid CHEBI:15366 acetic acid Beilstein:506007 Beilstein CAS:64-19-7 ChemIDplus CAS:64-19-7 KEGG COMPOUND CAS:64-19-7 NIST Chemistry WebBook Drug_Central:4211 DrugCentral Gmelin:1380 Gmelin LIPID_MAPS_instance:LMFA01010002 LIPID MAPS PMID:12005138 Europe PMC PMID:15107950 Europe PMC PMID:16630552 Europe PMC PMID:16774200 Europe PMC PMID:17190852 Europe PMC PMID:19416101 Europe PMC PMID:19469536 Europe PMC PMID:22153255 Europe PMC PMID:22173419 Europe PMC Reaxys:506007 Reaxys ACETIC ACID PDBeChem Acetic acid KEGG_COMPOUND acetic acid IUPAC AcOH ChEBI CH3-COOH IUPAC CH3CO2H ChEBI E 260 ChEBI E-260 ChEBI E260 ChEBI Essigsaeure ChEBI Ethanoic acid KEGG_COMPOUND Ethylic acid ChemIDplus HOAc ChEBI INS No. 260 ChEBI MeCO2H ChEBI MeCOOH ChEBI Methanecarboxylic acid ChemIDplus acide acetique ChemIDplus ethoic acid ChEBI A sulfonium compound that is the S-adenosyl derivative of L-methionine. It is an intermediate in the metabolic pathway of methionine. +1 C15H23N6O5S InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8+,10+,11+,14+,27?/m0/s1 MEFKEPWMEQBLKI-AIRLBKTGSA-O 399.44500 399.14452 C[S+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 CHEBI:10786 CHEBI:10833 CHEBI:12742 CHEBI:12757 CHEBI:12760 CHEBI:22036 CHEBI:45607 CHEBI:527887 CHEBI:8946 Beilstein:3576439 CAS:29908-03-0 COMe:MOL000172 DrugBank:DB00118 HMDB:HMDB0001185 KEGG:C00019 KNApSAcK:C00007347 MetaCyc:S-ADENOSYLMETHIONINE PMID:11017945 PMID:17439666 Reaxys:3919754 Wikipedia:S-Adenosyl_methionine S-Adenosyl-L-methionine S-adenosyl-L-methionine [(3S)-3-amino-3-carboxypropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium chebi_ontology (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt Acylcarnitine AdoMet S-(5'-deoxyadenosin-5'-yl)-L-methionine S-Adenosylmethionine S-adenosylmethionine SAM SAMe [1-(adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium CHEBI:15414 S-adenosyl-L-methionine Beilstein:3576439 Beilstein CAS:29908-03-0 ChemIDplus CAS:29908-03-0 KEGG COMPOUND PMID:11017945 Europe PMC PMID:17439666 Europe PMC Reaxys:3919754 Reaxys S-Adenosyl-L-methionine KEGG_COMPOUND S-adenosyl-L-methionine ChEBI [(3S)-3-amino-3-carboxypropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium IUPAC (3S)-5'-[(3-amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt ChemIDplus Acylcarnitine KEGG_COMPOUND AdoMet JCBN S-(5'-deoxyadenosin-5'-yl)-L-methionine JCBN S-Adenosylmethionine KEGG_COMPOUND S-adenosylmethionine ChEBI SAM JCBN SAMe ChemIDplus [1-(adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium IUPAC The simplest (and the only achiral) proteinogenic amino acid, with a hydrogen atom as its side chain. glycine http://langual.org 0 C2H5NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N 75.06664 75.03203 NCC(O)=O CHEBI:10792 CHEBI:14344 CHEBI:24368 CHEBI:42964 CHEBI:5460 Beilstein:635782 CAS:56-40-6 Codex::640 DrugBank:DB00145 Drug_Central:1319 ECMDB:ECMDB00123 Europe::640 Gmelin:1808 HMDB:HMDB0000123 KEGG:C00037 KEGG:D00011 KNApSAcK:C00001361 MetaCyc:GLY PDBeChem:GLY PMID:10930630 PMID:11019925 PMID:11174716 PMID:11542461 PMID:11806864 PMID:12631515 PMID:12754315 PMID:12770151 PMID:12921899 PMID:15331688 PMID:15388434 PMID:15710237 PMID:16105183 PMID:16151895 PMID:16214212 PMID:16417482 PMID:16444815 PMID:16664855 PMID:16901953 PMID:16918424 PMID:16986325 PMID:16998855 PMID:17154252 PMID:17383967 PMID:17582620 PMID:17970719 PMID:18079355 PMID:18396796 PMID:18440992 PMID:18593588 PMID:18816054 PMID:18840508 PMID:19028609 PMID:19120667 PMID:19449910 PMID:19526731 PMID:19544666 PMID:19738917 PMID:19916621 PMID:19924257 PMID:21751272 PMID:22044190 PMID:22079563 PMID:22234938 PMID:22264337 PMID:22293292 PMID:22401276 PMID:22434786 Reaxys:635782 Wikipedia:Glycine YMDB:YMDB00016 http://www.langual.org/langual_thesaurus.asp?termid=B3110 GLYCINE Glycine aminoacetic acid glycine chebi_ontology Aminoacetic acid Aminoessigsaeure G Gly Glycin Glycocoll Glykokoll Glyzin H2N-CH2-COOH Hgly Leimzucker aminoethanoic acid CHEBI:15428 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): flavour enhancer. glycine Beilstein:635782 Beilstein CAS:56-40-6 ChemIDplus CAS:56-40-6 KEGG COMPOUND CAS:56-40-6 NIST Chemistry WebBook Drug_Central:1319 DrugCentral Gmelin:1808 Gmelin PMID:10930630 Europe PMC PMID:11019925 Europe PMC PMID:11174716 Europe PMC PMID:11542461 Europe PMC PMID:11806864 Europe PMC PMID:12631515 Europe PMC PMID:12754315 Europe PMC PMID:12770151 Europe PMC PMID:12921899 Europe PMC PMID:15331688 Europe PMC PMID:15388434 Europe PMC PMID:15710237 Europe PMC PMID:16105183 Europe PMC PMID:16151895 Europe PMC PMID:16214212 Europe PMC PMID:16417482 Europe PMC PMID:16444815 Europe PMC PMID:16664855 Europe PMC PMID:16901953 Europe PMC PMID:16918424 Europe PMC PMID:16986325 Europe PMC PMID:16998855 Europe PMC PMID:17154252 Europe PMC PMID:17383967 Europe PMC PMID:17582620 Europe PMC PMID:17970719 Europe PMC PMID:18079355 Europe PMC PMID:18396796 Europe PMC PMID:18440992 Europe PMC PMID:18593588 Europe PMC PMID:18816054 Europe PMC PMID:18840508 Europe PMC PMID:19028609 Europe PMC PMID:19120667 Europe PMC PMID:19449910 Europe PMC PMID:19526731 Europe PMC PMID:19544666 Europe PMC PMID:19738917 Europe PMC PMID:19916621 Europe PMC PMID:19924257 Europe PMC PMID:21751272 Europe PMC PMID:22044190 Europe PMC PMID:22079563 Europe PMC PMID:22234938 Europe PMC PMID:22264337 Europe PMC PMID:22293292 Europe PMC PMID:22401276 Europe PMC PMID:22434786 Europe PMC Reaxys:635782 Reaxys GLYCINE PDBeChem Glycine KEGG_COMPOUND aminoacetic acid IUPAC glycine IUPAC Aminoacetic acid KEGG_COMPOUND Aminoessigsaeure ChEBI G ChEBI Gly KEGG_COMPOUND Glycin ChemIDplus Glycocoll ChemIDplus Glykokoll ChEBI Glyzin ChEBI H2N-CH2-COOH IUPAC Hgly IUPAC Leimzucker ChemIDplus aminoethanoic acid ChEBI aminoethanoic acid JCBN +1 C15H23N6O5S InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8-,10-,11-,14-,27?/m1/s1 MEFKEPWMEQBLKI-XCPQSEKJSA-O 399.450 399.14452 [S+](C[C@H]1O[C@@H](N2C3=NC=NC(N)=C3N=C2)[C@H](O)[C@@H]1O)(CC[C@@H](N)C(O)=O)C chebi_ontology CHEBI:156255 S-adenosyl-D-methionine Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals. 0 C2H4O2(CH2O)n CHEBI:13755 CHEBI:22305 CHEBI:2561 KEGG:C01370 Wikipedia:Aldose Aldose chebi_ontology aldoses an aldose CHEBI:15693 aldose Aldose KEGG_COMPOUND aldoses ChEBI an aldose UniProt Any alpha-amino acid having L-configuration at the alpha-carbon. 0 C2H4NO2R 74.05870 74.02420 N[C@@H]([*])C(O)=O CHEBI:13072 CHEBI:13243 CHEBI:13797 CHEBI:21224 CHEBI:6175 KEGG:C00151 L-alpha-amino acid L-alpha-amino acids chebi_ontology L-2-Amino acid L-Amino acid L-alpha-amino acids CHEBI:15705 L-alpha-amino acid L-alpha-amino acid IUPAC L-alpha-amino acids IUPAC L-2-Amino acid KEGG_COMPOUND L-Amino acid KEGG_COMPOUND L-alpha-amino acids ChEBI A tertiary amine oxide resulting from the oxidation of the amino group of trimethylamine. 0 C3H9NO InChI=1S/C3H9NO/c1-4(2,3)5/h1-3H3 UYPYRKYUKCHHIB-UHFFFAOYSA-N 75.110 75.06841 C[N+](C)([O-])C CHEBI:15262 CHEBI:15263 CHEBI:27126 CHEBI:9733 Beilstein:1734787 CAS:1184-78-7 Gmelin:1839 HMDB:HMDB0000925 KEGG:C01104 MetaCyc:TRIMENTHLAMINE-N-O PDBeChem:TMO PMID:12683801 PMID:1453985 PMID:17697669 PMID:19425246 PMID:22770225 PMID:3170512 PMID:3674879 Reaxys:1734787 Wikipedia:Trimethylamine_oxide N,N-dimethylmethanamine oxide Trimethylamine N-oxide trimethylamine N-oxide chebi_ontology (CH3)3NO Me3N(+)O(-) Me3N(O) N(CH3)3O TMAO Trimethylaminoxid trimethylamine oxide trimethyloxamine CHEBI:15724 trimethylamine N-oxide Beilstein:1734787 Beilstein CAS:1184-78-7 ChemIDplus CAS:1184-78-7 KEGG COMPOUND CAS:1184-78-7 NIST Chemistry WebBook Gmelin:1839 Gmelin PMID:12683801 Europe PMC PMID:1453985 Europe PMC PMID:17697669 Europe PMC PMID:19425246 Europe PMC PMID:22770225 Europe PMC PMID:3170512 Europe PMC PMID:3674879 Europe PMC Reaxys:1734787 Reaxys N,N-dimethylmethanamine oxide IUPAC Trimethylamine N-oxide KEGG_COMPOUND trimethylamine N-oxide UniProt (CH3)3NO IUPAC Me3N(+)O(-) ChEBI Me3N(O) ChEBI N(CH3)3O ChEBI TMAO NIST_Chemistry_WebBook Trimethylaminoxid ChEBI trimethylamine oxide NIST_Chemistry_WebBook trimethyloxamine ChemIDplus A primary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has either three hydrogen atoms attached to it or only one other carbon atom and two hydrogen atoms attached to it. 0 CH3OR 31.034 31.01839 *C(O)([H])[H] CHEBI:13676 CHEBI:14887 CHEBI:26262 CHEBI:57489 CHEBI:8406 KEGG:C00226 Primary alcohol chebi_ontology 1-Alcohol a primary alcohol primary alcohols CHEBI:15734 primary alcohol Primary alcohol KEGG_COMPOUND 1-Alcohol KEGG_COMPOUND a primary alcohol UniProt primary alcohols ChEBI A straight-chain, sixteen-carbon, saturated long-chain fatty acid. 0 C16H32O2 InChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18) IPCSVZSSVZVIGE-UHFFFAOYSA-N 256.42410 256.24023 CCCCCCCCCCCCCCCC(O)=O CHEBI:14730 CHEBI:233028 CHEBI:24540 CHEBI:24541 CHEBI:24542 CHEBI:24550 CHEBI:29889 CHEBI:35978 CHEBI:44952 Beilstein:607489 CAS:57-10-3 DrugBank:DB03796 Gmelin:190200 HMDB:HMDB0000220 KEGG:C00249 KEGG:D05341 KNApSAcK:C00001233 KNApSAcK:C00030479 LIPID_MAPS_instance:LMFA01010001 MetaCyc:PALMITATE PDBeChem:PLM PMID:12492626 PMID:15357969 PMID:1589452 PMID:16509590 PMID:16884313 PMID:17439666 PMID:17502136 PMID:20001317 PMID:22735334 PMID:25584012 PMID:28600633 PPDB:1336 Reaxys:607489 Wikipedia:Palmitic_acid hexadecanoic acid chebi_ontology 1-Pentadecanecarboxylic acid 1-hexyldecanoic acid 16:00 C16 C16 fatty acid C16:0 CH3-[CH2]14-COOH FA 16:0 Hexadecanoate Hexadecylic acid Hexaectylic acid PALMITIC ACID Palmitate Palmitic acid Palmitinic acid Palmitinsaeure Pentadecanecarboxylic acid cetylic acid hexadecoic acid n-hexadecanoic acid n-hexadecoic acid palmitic acid CHEBI:15756 hexadecanoic acid Beilstein:607489 Beilstein CAS:57-10-3 ChemIDplus CAS:57-10-3 KEGG COMPOUND CAS:57-10-3 NIST Chemistry WebBook Gmelin:190200 Gmelin LIPID_MAPS_instance:LMFA01010001 LIPID MAPS PMID:12492626 Europe PMC PMID:15357969 ChEMBL PMID:1589452 Europe PMC PMID:16509590 ChEMBL PMID:16884313 ChEMBL PMID:17439666 Europe PMC PMID:17502136 ChEMBL PMID:20001317 Europe PMC PMID:22735334 Europe PMC PMID:25584012 Europe PMC PMID:28600633 Europe PMC Reaxys:607489 Reaxys hexadecanoic acid IUPAC 1-Pentadecanecarboxylic acid ChemIDplus 1-hexyldecanoic acid HMDB 16:00 ChEBI C16 ChEBI C16 fatty acid HMDB C16:0 LIPID_MAPS CH3-[CH2]14-COOH IUPAC FA 16:0 ChEBI Hexadecanoate KEGG_COMPOUND Hexadecylic acid HMDB Hexadecylic acid KEGG_COMPOUND Hexaectylic acid HMDB PALMITIC ACID PDBeChem Palmitate KEGG_COMPOUND Palmitic acid KEGG_COMPOUND Palmitinic acid HMDB Palmitinsaeure ChEBI Pentadecanecarboxylic acid ChemIDplus cetylic acid KEGG_COMPOUND hexadecoic acid ChEBI n-hexadecanoic acid NIST_Chemistry_WebBook n-hexadecoic acid NIST_Chemistry_WebBook palmitic acid ChEBI Any N-acyl-amino acid in which the amino acid moiety has D configuration. 0 C3H3NO3R2 101.06080 101.01129 OC(=O)[C@@H]([*])NC([*])=O CHEBI:12474 CHEBI:21631 CHEBI:7224 chebi_ontology CHEBI:15778 N-acyl-D-amino acid +1 C62H90CoN13O15P InChI=1S/C62H90N13O14P.Co.H2O/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;1H2/q;+3;/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 YOZNUFWCRFCGIH-WZHZPDAFSA-L 1347.36310 1346.57434 [H][O+]([H])[Co-3]1234N5C6=C(C)C7=[N+]1C(=CC1=[N+]2C(=C(C)C2=[N+]3[C@@](C)([C@@]5([H])[C@H](CC(N)=O)[C@@]6(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@@H]3[C@@H](CO)O[C@@H]([C@@H]3O)n3c[n+]4c4cc(C)c(C)cc34)[C@@](C)(CC(N)=O)[C@@H]2CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]1CCC(N)=O)C(C)(C)[C@@H]7CCC(N)=O CHEBI:13851 CHEBI:22589 CHEBI:2794 CAS:13422-52-1 KEGG:C00992 Aquacob(III)alamin Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-aquacobamide aquacob(III)alamin chebi_ontology Aquacobalamin aquacobalamin vitamin B-12a CHEBI:15852 aquacob(III)alamin CAS:13422-52-1 ChemIDplus CAS:13422-52-1 KEGG COMPOUND Aquacob(III)alamin KEGG_COMPOUND Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-aquacobamide IUPAC aquacob(III)alamin UniProt Aquacobalamin KEGG_COMPOUND aquacobalamin CBN vitamin B-12a CBN Any 3-hydroxy steroid whose skeleton is closely related to cholestan-3-ol (additional carbon atoms may be present in the side chain). 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCC(C4)O)C CHEBI:13688 CHEBI:15114 CHEBI:26771 CHEBI:9266 KEGG:C00370 LIPID_MAPS_class:LMST01 MetaCyc:Sterols Wikipedia:Sterol Sterol sterols chebi_ontology 3-hydroxysteroids a sterol CHEBI:15889 sterol LIPID_MAPS_class:LMST01 LIPID MAPS Sterol KEGG_COMPOUND sterols IUPAC 3-hydroxysteroids ChEBI a sterol UniProt A fatty acid with a chain length ranging from C13 to C22. 0 CHO2R 45.017 44.99765 OC([*])=O CHEBI:13655 CHEBI:14529 CHEBI:25075 CHEBI:6528 KEGG:C00638 Long-chain fatty acid chebi_ontology Higher fatty acid LCFA LCFAs long-chain fatty acids CHEBI:15904 long-chain fatty acid Long-chain fatty acid KEGG_COMPOUND Higher fatty acid KEGG_COMPOUND LCFA ChEBI LCFAs ChEBI long-chain fatty acids ChEBI A pyridinemonocarboxylic acid that is pyridine in which the hydrogen at position 3 is replaced by a carboxy group. niacin nicotinic acid http://langual.org 0 C6H5NO2 InChI=1S/C6H5NO2/c8-6(9)5-2-1-3-7-4-5/h1-4H,(H,8,9) PVNIIMVLHYAWGP-UHFFFAOYSA-N 123.10944 123.03203 OC(=O)c1cccnc1 CHEBI:25538 CHEBI:44319 CHEBI:7559 Beilstein:109591 CAS:59-67-6 DrugBank:DB00627 Drug_Central:2835 Gmelin:3340 HMDB:HMDB0001488 KEGG:C00253 KEGG:D00049 KNApSAcK:C00000208 LINCS:LSM-4676 MetaCyc:NIACINE PDBeChem:NIO PMID:12563315 PMID:12789870 PMID:15037193 PMID:15183629 PMID:15205990 PMID:15311728 PMID:15627518 PMID:16018787 PMID:16172771 PMID:16400392 PMID:16449845 PMID:16767301 PMID:16877271 PMID:16945375 PMID:18037924 PMID:18993152 PMID:18996527 PMID:19369827 PMID:19592242 PMID:19678716 PMID:19779335 PMID:20979384 PMID:21632263 PMID:22116693 PMID:22155410 PMID:22229411 PMID:22366213 PMID:22458880 PMID:22770225 PMID:24568240 PMID:24675661 PMID:24848081 PMID:24975217 PMID:25040591 PMID:25241762 PMID:25429652 PMID:4259917 Reaxys:109591 Wikipedia:Niacin http://www.langual.org/langual_thesaurus.asp?termid=B3757 http://www.langual.org/langual_thesaurus.asp?termid=B3772 NICOTINIC ACID Nicotinic acid nicotinic acid pyridine-3-carboxylic acid chebi_ontology 3-Pyridinecarboxylic acid 3-Pyridylcarboxylic acid 3-carboxypyridine Niacin Nikotinsaeure P.P. factor PP factor acide nicotinique acido nicotinico acidum nicotinicum anti-pellagra vitamin beta-pyridinecarboxylic acid m-pyridinecarboxylic acid nicotinic acid pellagra preventive factor pyridine-beta-carboxylic acid vitamin B3 CHEBI:15940 nicotinic acid Beilstein:109591 Beilstein CAS:59-67-6 ChemIDplus CAS:59-67-6 KEGG COMPOUND CAS:59-67-6 NIST Chemistry WebBook Drug_Central:2835 DrugCentral Gmelin:3340 Gmelin PMID:12563315 Europe PMC PMID:12789870 Europe PMC PMID:15037193 Europe PMC PMID:15183629 Europe PMC PMID:15205990 Europe PMC PMID:15311728 Europe PMC PMID:15627518 Europe PMC PMID:16018787 Europe PMC PMID:16172771 Europe PMC PMID:16400392 Europe PMC PMID:16449845 Europe PMC PMID:16767301 Europe PMC PMID:16877271 Europe PMC PMID:16945375 Europe PMC PMID:18037924 Europe PMC PMID:18993152 Europe PMC PMID:18996527 Europe PMC PMID:19369827 Europe PMC PMID:19592242 Europe PMC PMID:19678716 Europe PMC PMID:19779335 Europe PMC PMID:20979384 Europe PMC PMID:21632263 Europe PMC PMID:22116693 Europe PMC PMID:22155410 Europe PMC PMID:22229411 Europe PMC PMID:22366213 Europe PMC PMID:22458880 Europe PMC PMID:22770225 Europe PMC PMID:24568240 Europe PMC PMID:24675661 Europe PMC PMID:24848081 Europe PMC PMID:24975217 Europe PMC PMID:25040591 Europe PMC PMID:25241762 Europe PMC PMID:25429652 Europe PMC PMID:4259917 Europe PMC Reaxys:109591 Reaxys NICOTINIC ACID PDBeChem Nicotinic acid KEGG_COMPOUND nicotinic acid IUPAC pyridine-3-carboxylic acid IUPAC 3-Pyridinecarboxylic acid KEGG_COMPOUND 3-Pyridylcarboxylic acid HMDB 3-carboxypyridine NIST_Chemistry_WebBook Niacin KEGG_COMPOUND Nikotinsaeure ChEBI P.P. factor NIST_Chemistry_WebBook PP factor NIST_Chemistry_WebBook acide nicotinique WHO_MedNet acido nicotinico WHO_MedNet acidum nicotinicum WHO_MedNet anti-pellagra vitamin NIST_Chemistry_WebBook beta-pyridinecarboxylic acid ChEBI m-pyridinecarboxylic acid NIST_Chemistry_WebBook nicotinic acid WHO_MedNet pellagra preventive factor NIST_Chemistry_WebBook pyridine-beta-carboxylic acid NIST_Chemistry_WebBook vitamin B3 ChEBI An optically active form of glutamic acid having D-configuration. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m1/s1 WHUUTDBJXJRKMK-GSVOUGTGSA-N 147.12930 147.05316 N[C@H](CCC(O)=O)C(O)=O CHEBI:21023 CHEBI:4183 Beilstein:1723800 CAS:6893-26-1 DrugBank:DB02517 Gmelin:201189 HMDB:HMDB0003339 KEGG:C00217 KNApSAcK:C00019577 MetaCyc:D-GLT PDBeChem:DGL Reaxys:1723800 (2R)-2-aminopentanedioic acid D-Glutamic acid D-glutamic acid chebi_ontology (R)-2-aminopentanedioic acid D-2-Aminoglutaric acid D-Glutaminic acid D-Glutaminsaeure DGL glutamic acid D-form CHEBI:15966 D-glutamic acid (R)-2-aminopentanedioic acid ChEBI D-2-Aminoglutaric acid KEGG_COMPOUND D-Glutaminic acid KEGG_COMPOUND D-Glutaminsaeure ChEBI DGL PDBeChem glutamic acid D-form ChemIDplus Beilstein:1723800 Beilstein CAS:6893-26-1 ChemIDplus CAS:6893-26-1 KEGG COMPOUND CAS:6893-26-1 NIST Chemistry WebBook Gmelin:201189 Gmelin Reaxys:1723800 Reaxys (2R)-2-aminopentanedioic acid IUPAC D-Glutamic acid KEGG_COMPOUND D-glutamic acid IUPAC An optically active form of glutamic acid having L-configuration. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1 WHUUTDBJXJRKMK-VKHMYHEASA-N 147.12930 147.05316 N[C@@H](CCC(O)=O)C(O)=O CHEBI:21304 CHEBI:42825 CHEBI:6224 BPDB:2297 Beilstein:1723801 CAS:56-86-0 DrugBank:DB00142 Drug_Central:1310 Gmelin:3502 HMDB:HMDB0000148 KEGG:C00025 KEGG:D00007 KNApSAcK:C00001358 LINCS:LSM-36375 MetaCyc:GLT PDBeChem:GLU_LFOH PMID:15739367 PMID:15930465 PMID:16719819 PMID:16892196 PMID:19581495 PMID:22219301 PMID:22735334 Reaxys:1723801 Wikipedia:L-Glutamic_Acid (2S)-2-aminopentanedioic acid L-Glutamic acid L-glutamic acid chebi_ontology (S)-2-aminopentanedioic acid (S)-glutamic acid E GLUTAMIC ACID Glu Glutamate L-Glu L-Glutaminic acid L-Glutaminsaeure acide glutamique acido glutamico acidum glutamicum glutamic acid CHEBI:16015 L-glutamic acid Beilstein:1723801 Beilstein CAS:56-86-0 ChemIDplus CAS:56-86-0 KEGG COMPOUND CAS:56-86-0 NIST Chemistry WebBook Drug_Central:1310 DrugCentral Gmelin:3502 Gmelin PMID:15739367 Europe PMC PMID:15930465 Europe PMC PMID:16719819 Europe PMC PMID:16892196 Europe PMC PMID:19581495 Europe PMC PMID:22219301 Europe PMC PMID:22735334 Europe PMC Reaxys:1723801 Reaxys (2S)-2-aminopentanedioic acid IUPAC L-Glutamic acid KEGG_COMPOUND L-glutamic acid IUPAC (S)-2-aminopentanedioic acid ChEBI (S)-glutamic acid NIST_Chemistry_WebBook E ChEBI GLUTAMIC ACID PDBeChem Glu ChEBI Glutamate KEGG_COMPOUND L-Glu ChEBI L-Glutaminic acid KEGG_COMPOUND L-Glutaminsaeure ChEBI acide glutamique ChEBI acido glutamico ChEBI acidum glutamicum ChEBI glutamic acid ChEBI A monoatomic monoanion resulting from the addition of an electron to any halogen atom. -1 X 0.0 0.0 [*-] CHEBI:14384 CHEBI:5605 KEGG:C00462 halide ions chebi_ontology HX Halide a halide anion halide anions halide(1-) halides halogen anion CHEBI:16042 halide anion halide ions IUPAC HX KEGG_COMPOUND Halide KEGG_COMPOUND a halide anion UniProt halide anions ChEBI halide(1-) ChEBI halides ChEBI halogen anion ChEBI A gamma-amino acid comprising 4-aminobutyric acid having a 2-hydroxy substituent. 0 C4H9NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8) YQGDEPYYFWUPGO-UHFFFAOYSA-N 119.11920 119.05824 NCC(O)CC(O)=O CHEBI:1780 CHEBI:20311 Beilstein:1721708 Beilstein:1752568 CAS:352-21-6 Drug_Central:1263 KEGG:C03678 KEGG:D00174 4-amino-3-hydroxybutanoic acid gamma-Amino-beta-hydroxybutyric acid chebi_ontology 3-hydroxy-GABA 4-Amino-3-hydroxybutanoic acid 4-amino-3-hydroxybutyric acid GABOB CHEBI:16080 gamma-amino-beta-hydroxybutyric acid Beilstein:1721708 Beilstein Beilstein:1752568 Beilstein CAS:352-21-6 ChemIDplus CAS:352-21-6 KEGG COMPOUND Drug_Central:1263 DrugCentral 4-amino-3-hydroxybutanoic acid IUPAC gamma-Amino-beta-hydroxybutyric acid KEGG_COMPOUND 3-hydroxy-GABA ChemIDplus 4-Amino-3-hydroxybutanoic acid KEGG_COMPOUND 4-amino-3-hydroxybutyric acid ChemIDplus GABOB KEGG_COMPOUND A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. 0 C27H46O InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1 HVYWMOMLDIMFJA-DPAQBDIFSA-N 386.655 386.35487 C1[C@@]2([C@]3(CC[C@]4([C@]([C@@]3(CC=C2C[C@H](C1)O)[H])(CC[C@@]4([C@H](C)CCCC(C)C)[H])[H])C)[H])C CHEBI:13982 CHEBI:23204 CHEBI:3659 CHEBI:41564 Beilstein:2060565 CAS:57-88-5 DrugBank:DB04540 Gmelin:550297 HMDB:HMDB0000067 KEGG:C00187 KEGG:D00040 KNApSAcK:C00003648 LIPID_MAPS_instance:LMST01010001 MetaCyc:CHOLESTEROL PDBeChem:CLR PMID:10901445 PMID:11412894 PMID:16341241 PMID:24287311 PMID:25308664 PMID:25451949 PMID:25522988 PMID:25658343 PMID:25977713 PMID:4696527 PMID:8838010 Reaxys:2060565 Wikipedia:Cholesterol CHOLESTEROL Cholesterol cholest-5-en-3beta-ol cholesterol chebi_ontology (3beta,14beta,17alpha)-cholest-5-en-3-ol Cholest-5-en-3beta-ol Cholesterin CHEBI:16113 cholesterol Beilstein:2060565 Beilstein CAS:57-88-5 ChemIDplus CAS:57-88-5 KEGG COMPOUND CAS:57-88-5 NIST Chemistry WebBook Gmelin:550297 Gmelin LIPID_MAPS_instance:LMST01010001 LIPID MAPS PMID:10901445 Europe PMC PMID:11412894 Europe PMC PMID:16341241 Europe PMC PMID:24287311 Europe PMC PMID:25308664 Europe PMC PMID:25451949 Europe PMC PMID:25522988 Europe PMC PMID:25658343 Europe PMC PMID:25977713 Europe PMC PMID:4696527 Europe PMC PMID:8838010 Europe PMC Reaxys:2060565 Reaxys CHOLESTEROL PDBeChem Cholesterol KEGG_COMPOUND cholest-5-en-3beta-ol IUPAC cholesterol UniProt (3beta,14beta,17alpha)-cholest-5-en-3-ol IUPAC Cholest-5-en-3beta-ol KEGG_COMPOUND Cholesterin NIST_Chemistry_WebBook An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. 0 H3N InChI=1S/H3N/h1H3 QGZKDVFQNNGYKY-UHFFFAOYSA-N 17.03056 17.02655 [H]N([H])[H] CHEBI:13405 CHEBI:13406 CHEBI:13407 CHEBI:13771 CHEBI:22533 CHEBI:44269 CHEBI:44284 CHEBI:44404 CHEBI:7434 Beilstein:3587154 CAS:7664-41-7 Drug_Central:4625 Gmelin:79 HMDB:HMDB0000051 KEGG:C00014 KEGG:D02916 KNApSAcK:C00007267 MetaCyc:AMMONIA MolBase:930 PDBeChem:NH3 PMID:110589 PMID:11139349 PMID:11540049 PMID:11746427 PMID:11783653 PMID:13753780 PMID:14663195 PMID:15092448 PMID:15094021 PMID:15554424 PMID:15969015 PMID:16008360 PMID:16050680 PMID:16348008 PMID:16349403 PMID:16614889 PMID:16664306 PMID:16842901 PMID:17025297 PMID:17439666 PMID:17569513 PMID:17737668 PMID:18670398 PMID:22002069 PMID:22081570 PMID:22088435 PMID:22100291 PMID:22130175 PMID:22150211 PMID:22240068 PMID:22290316 PMID:22342082 PMID:22385337 PMID:22443779 PMID:22560242 Reaxys:3587154 Wikipedia:Ammonia AMMONIA Ammonia ammonia azane chebi_ontology Ammoniak NH3 R-717 [NH3] ammoniac amoniaco spirit of hartshorn CHEBI:16134 ammonia Beilstein:3587154 Beilstein CAS:7664-41-7 ChemIDplus CAS:7664-41-7 KEGG COMPOUND CAS:7664-41-7 NIST Chemistry WebBook Drug_Central:4625 DrugCentral Gmelin:79 Gmelin PMID:110589 Europe PMC PMID:11139349 Europe PMC PMID:11540049 Europe PMC PMID:11746427 Europe PMC PMID:11783653 Europe PMC PMID:13753780 Europe PMC PMID:14663195 Europe PMC PMID:15092448 Europe PMC PMID:15094021 Europe PMC PMID:15554424 Europe PMC PMID:15969015 Europe PMC PMID:16008360 Europe PMC PMID:16050680 Europe PMC PMID:16348008 Europe PMC PMID:16349403 Europe PMC PMID:16614889 Europe PMC PMID:16664306 Europe PMC PMID:16842901 Europe PMC PMID:17025297 Europe PMC PMID:17439666 Europe PMC PMID:17569513 Europe PMC PMID:17737668 Europe PMC PMID:18670398 Europe PMC PMID:22002069 Europe PMC PMID:22081570 Europe PMC PMID:22088435 Europe PMC PMID:22100291 Europe PMC PMID:22130175 Europe PMC PMID:22150211 Europe PMC PMID:22240068 Europe PMC PMID:22290316 Europe PMC PMID:22342082 Europe PMC PMID:22385337 Europe PMC PMID:22443779 Europe PMC PMID:22560242 Europe PMC Reaxys:3587154 Reaxys AMMONIA PDBeChem Ammonia KEGG_COMPOUND ammonia IUPAC azane IUPAC Ammoniak ChemIDplus NH3 IUPAC NH3 KEGG_COMPOUND NH3 UniProt R-717 ChEBI [NH3] MolBase ammoniac ChEBI amoniaco ChEBI spirit of hartshorn ChemIDplus A carbonyl group with two C-bound amine groups. The commercially available fertilizer has an analysis of 46-0-0 (N-P2O5-K2O). 0 CH4N2O InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4) XSQUKJJJFZCRTK-UHFFFAOYSA-N 60.05534 60.03236 NC(N)=O CHEBI:15292 CHEBI:27218 CHEBI:46379 CHEBI:9888 Beilstein:635724 CAS:57-13-6 DrugBank:DB03904 Drug_Central:4264 ECMDB:ECMDB04172 Gmelin:1378 HMDB:HMDB0000294 KEGG:C00086 KEGG:D00023 KNApSAcK:C00007314 MetaCyc:UREA PDBeChem:URE PMID:18037357 PMID:22770225 PPDB:1728 Reaxys:635724 UM-BBD_compID:c0165 Wikipedia:Urea YMDB:YMDB00003 UREA Urea urea chebi_ontology 1728 Carbamide E927b H2NC(O)NH2 Harnstoff Karbamid carbamide carbonyldiamide ur uree CHEBI:16199 urea Beilstein:635724 Beilstein CAS:57-13-6 ChemIDplus CAS:57-13-6 KEGG COMPOUND CAS:57-13-6 NIST Chemistry WebBook Drug_Central:4264 DrugCentral Gmelin:1378 Gmelin PMID:18037357 Europe PMC PMID:22770225 Europe PMC Reaxys:635724 Reaxys UM-BBD_compID:c0165 UM-BBD UREA PDBeChem Urea KEGG_COMPOUND urea IUPAC urea UniProt 1728 PPDB Carbamide KEGG_COMPOUND E927b ChEBI H2NC(O)NH2 ChEBI Harnstoff NIST_Chemistry_WebBook Karbamid ChEBI carbamide ChEBI carbonyldiamide NIST_Chemistry_WebBook ur IUPAC uree ChEBI A branched-chain saturated fatty acid consisting of hexadecanoic acid carrying methyl substituents at positions 3, 7, 11 and 15. 0 C20H40O2 InChI=1S/C20H40O2/c1-16(2)9-6-10-17(3)11-7-12-18(4)13-8-14-19(5)15-20(21)22/h16-19H,6-15H2,1-5H3,(H,21,22) RLCKHJSFHOZMDR-UHFFFAOYSA-N 312.53040 312.30283 CC(C)CCCC(C)CCCC(C)CCCC(C)CC(O)=O CHEBI:26111 CHEBI:8189 Beilstein:1789963 CAS:14721-66-5 KEGG:C01607 LIPID_MAPS_instance:LMFA01020251 PMID:12187408 PMID:17956237 PMID:9819701 Reaxys:1789963 3,7,11,15-tetramethylhexadecanoic acid Phytanic acid chebi_ontology 3,7,11,15-Tetramethyl-hexadecansaeure 3,7,11,15-tetramethyl hexadecanoic acid 3,7,11,15-tetramethyl-hexadecanoic acid CHEBI:16285 phytanic acid Beilstein:1789963 Beilstein CAS:14721-66-5 ChemIDplus CAS:14721-66-5 KEGG COMPOUND LIPID_MAPS_instance:LMFA01020251 LIPID MAPS PMID:12187408 Europe PMC PMID:17956237 Europe PMC PMID:9819701 Europe PMC Reaxys:1789963 Reaxys 3,7,11,15-tetramethylhexadecanoic acid IUPAC Phytanic acid KEGG_COMPOUND 3,7,11,15-Tetramethyl-hexadecansaeure ChEBI 3,7,11,15-tetramethyl hexadecanoic acid ChEBI 3,7,11,15-tetramethyl-hexadecanoic acid LIPID_MAPS An optically active form of cysteine having D-configuration. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-N 121.15922 121.01975 N[C@H](CS)C(O)=O CHEBI:12919 CHEBI:20921 CHEBI:4111 CHEBI:41887 Beilstein:1721407 CAS:921-01-7 DrugBank:DB03201 ECMDB:ECMDB03417 Gmelin:363236 HMDB:HMDB0003417 KEGG:C00793 KNApSAcK:C00007323 PDBeChem:DCY PMID:13761469 PMID:23340406 PMID:24800864 Reaxys:1721407 YMDB:YMDB00913 D-CYSTEINE D-Cysteine D-cysteine chebi_ontology (2S)-2-amino-3-mercaptopropanoic acid (2S)-2-amino-3-sulfanylpropanoic acid (S)-2-amino-3-mercaptopropanoic acid D-Amino-3-mercaptopropionic acid D-Cystein D-Zystein DCY CHEBI:16375 D-cysteine Beilstein:1721407 Beilstein CAS:921-01-7 ChemIDplus CAS:921-01-7 KEGG COMPOUND Gmelin:363236 Gmelin PMID:13761469 Europe PMC PMID:23340406 Europe PMC PMID:24800864 Europe PMC Reaxys:1721407 Reaxys D-CYSTEINE PDBeChem D-Cysteine KEGG_COMPOUND D-cysteine IUPAC (2S)-2-amino-3-mercaptopropanoic acid JCBN (2S)-2-amino-3-sulfanylpropanoic acid IUPAC (S)-2-amino-3-mercaptopropanoic acid ChEBI D-Amino-3-mercaptopropionic acid KEGG_COMPOUND D-Cystein ChEBI D-Zystein ChEBI DCY PDBeChem Any benzoquinone derived from 2,3-dimethoxy-5-methylbenzoquinone; one of a group of naturally occurring homologues. The redox-active quinoid moiety usually carries a polyprenoid side chain at position 6, the number of isoprenoid units in which is species-specific. Ubiquinones are involved in the control of mitochondrial electron transport, and are also potent anti-oxidants. 0 C9H10O4(C5H8)n CHEBI:15279 CHEBI:27186 CHEBI:9852 CAS:1339-63-5 KEGG:C00399 PMID:15788391 PMID:7599208 Ubiquinones chebi_ontology CoQ Coenzym Q Coenzyme Q Koenzym Q Q Ubichinon Ubiquinone a ubiquinone coenzyme Q coenzymes Q mitochondrial ubiquinone mitochondrial ubiquinones mitoquinones CHEBI:16389 ubiquinones CAS:1339-63-5 ChemIDplus CAS:1339-63-5 KEGG COMPOUND PMID:15788391 Europe PMC PMID:7599208 Europe PMC Ubiquinones ChemIDplus CoQ KEGG_COMPOUND Coenzym Q ChEBI Coenzyme Q KEGG_COMPOUND Koenzym Q ChEBI Q KEGG_COMPOUND Ubichinon ChEBI Ubiquinone KEGG_COMPOUND a ubiquinone UniProt coenzyme Q ChEBI coenzymes Q ChEBI mitochondrial ubiquinone ChEBI mitochondrial ubiquinones ChEBI mitoquinones ChEBI The R-enantiomer of serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-N 105.09262 105.04259 N[C@H](CO)C(O)=O CHEBI:13019 CHEBI:143888 CHEBI:21090 CHEBI:42262 CHEBI:4245 Beilstein:1721403 CAS:312-84-5 DrugBank:DB03929 ECMDB:ECMDB03406 Gmelin:1041392 HMDB:HMDB0003406 KEGG:C00740 MetaCyc:D-SERINE PDBeChem:DSN PMID:11864625 PMID:12850593 PMID:19212759 PMID:19217074 PMID:21295046 PMID:21914633 PMID:21956571 PMID:22117694 PMID:22128843 PMID:22266400 PMID:22280157 PMID:22362148 PMID:22369458 PMID:22445805 PMID:22465696 PMID:22486999 Reaxys:1721403 YMDB:YMDB00284 D-SERINE D-Serine D-serine chebi_ontology (2R)-2-amino-3-hydroxypropanoic acid (R)-2-Amino-3-hydroxy-propionic acid (R)-2-amino-3-hydroxypropanoic acid D-Serin DSN CHEBI:16523 D-serine Beilstein:1721403 Beilstein CAS:312-84-5 ChemIDplus CAS:312-84-5 KEGG COMPOUND CAS:312-84-5 NIST Chemistry WebBook Gmelin:1041392 Gmelin PMID:11864625 Europe PMC PMID:12850593 Europe PMC PMID:19212759 Europe PMC PMID:19217074 Europe PMC PMID:21295046 Europe PMC PMID:21914633 Europe PMC PMID:21956571 Europe PMC PMID:22117694 Europe PMC PMID:22128843 Europe PMC PMID:22266400 Europe PMC PMID:22280157 Europe PMC PMID:22362148 Europe PMC PMID:22369458 Europe PMC PMID:22445805 Europe PMC PMID:22465696 Europe PMC PMID:22486999 Europe PMC Reaxys:1721403 Reaxys D-SERINE PDBeChem D-Serine KEGG_COMPOUND D-serine IUPAC (2R)-2-amino-3-hydroxypropanoic acid IUPAC (R)-2-Amino-3-hydroxy-propionic acid ChEMBL (R)-2-amino-3-hydroxypropanoic acid ChEBI D-Serin ChEBI DSN PDBeChem The L-enantiomer of methionine. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1 FFEARJCKVFRZRR-BYPYZUCNSA-N 149.21238 149.05105 CSCC[C@H](N)C(O)=O CHEBI:13141 CHEBI:21360 CHEBI:43990 CHEBI:6271 CAS:63-68-3 DrugBank:DB00134 Drug_Central:3347 ECMDB:ECMDB00696 Gmelin:26935 HMDB:HMDB0000696 KEGG:C00073 KEGG:D00019 KNApSAcK:C00001379 MetaCyc:MET PDBeChem:MET_LFOH PMID:16575097 PMID:21683740 PMID:21946918 PMID:22200379 PMID:22370952 PMID:22448874 PMID:22517898 PMID:24126240 PMID:24939187 PMID:5764336 Reaxys:1722294 YMDB:YMDB00318 L-Methionine L-methionine chebi_ontology (2S)-2-amino-4-(methylsulfanyl)butanoic acid (S)-2-amino-4-(methylthio)butanoic acid (S)-2-amino-4-(methylthio)butyric acid (S)-methionine L-(-)-methionine L-Methionin L-alpha-amino-gamma-methylmercaptobutyric acid M METHIONINE Met Methionine CHEBI:16643 L-methionine CAS:63-68-3 ChemIDplus CAS:63-68-3 KEGG COMPOUND CAS:63-68-3 NIST Chemistry WebBook Drug_Central:3347 DrugCentral Gmelin:26935 Gmelin PMID:16575097 Europe PMC PMID:21683740 Europe PMC PMID:21946918 Europe PMC PMID:22200379 Europe PMC PMID:22370952 Europe PMC PMID:22448874 Europe PMC PMID:22517898 Europe PMC PMID:24126240 Europe PMC PMID:24939187 Europe PMC PMID:5764336 Europe PMC Reaxys:1722294 Reaxys L-Methionine KEGG_COMPOUND L-methionine IUPAC (2S)-2-amino-4-(methylsulfanyl)butanoic acid IUPAC (S)-2-amino-4-(methylthio)butanoic acid ChemIDplus (S)-2-amino-4-(methylthio)butyric acid ChemIDplus (S)-methionine ChEBI L-(-)-methionine NIST_Chemistry_WebBook L-Methionin ChEBI L-alpha-amino-gamma-methylmercaptobutyric acid NIST_Chemistry_WebBook M ChEBI METHIONINE PDBeChem Met ChEBI Methionine KEGG_COMPOUND Methionine KEGG_DRUG Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. CHEBI:15131 CHEBI:23008 CHEBI:9318 Wikipedia:Carbohydrate carbohydrate carbohydrates chebi_ontology Kohlenhydrat Kohlenhydrate carbohidrato carbohidratos glucide glucides glucido glucidos hydrates de carbone saccharide saccharides saccharidum CHEBI:16646 carbohydrate carbohydrate IUPAC carbohydrates IUPAC Kohlenhydrat ChEBI Kohlenhydrate ChEBI carbohidrato IUPAC carbohidratos IUPAC glucide ChEBI glucides ChEBI glucido ChEBI glucidos ChEBI hydrates de carbone ChEBI saccharide IUPAC saccharides IUPAC saccharidum ChEBI peptide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide A methylated tertiary amine that is trimethylammonium in which the hydrogen attached to the nitrogen is replaced by a hydroxy group. +1 C3H10NO InChI=1S/C3H10NO/c1-4(2,3)5/h5H,1-3H3/q+1 LGHYUXIXXNHKSE-UHFFFAOYSA-N 76.118 76.07569 C[N+](C)(C)O hydroxy(trimethyl)ammonium chebi_ontology (CH3)3NOH hydroxy(trimethyl)azanium hydroxytrimethylazanium CHEBI:166856 hydroxytrimethylaminium hydroxy(trimethyl)ammonium IUPAC (CH3)3NOH ChEBI hydroxy(trimethyl)azanium IUPAC hydroxytrimethylazanium IUPAC A ribonucleoside composed of a molecule of uracil attached to a ribofuranose moiety via a beta-N(1)-glycosidic bond. 0 C9H12N2O6 InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1 DRTQHJPVMGBUCF-XVFCMESISA-N 244.20146 244.06954 OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1ccc(=O)[nH]c1=O CHEBI:15296 CHEBI:27227 CHEBI:46386 CHEBI:46391 CHEBI:46460 CHEBI:9893 Beilstein:754904 CAS:58-96-8 DrugBank:DB02745 ECMDB:ECMDB00296 Gmelin:397474 HMDB:HMDB0000296 KEGG:C00299 KNApSAcK:C00019674 MetaCyc:URIDINE PDBeChem:URI PMID:12084455 PMID:15621516 PMID:16839635 PMID:17190852 PMID:22392515 PMID:22770225 Reaxys:754904 Wikipedia:Uridine YMDB:YMDB00127 URIDINE Uridine uridine chebi_ontology 1-beta-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione 1-beta-D-ribofuranosyluracil Urd Uridin beta-Uridine u CHEBI:16704 uridine Beilstein:754904 Beilstein CAS:58-96-8 ChemIDplus CAS:58-96-8 KEGG COMPOUND Gmelin:397474 Gmelin PMID:12084455 Europe PMC PMID:15621516 Europe PMC PMID:16839635 Europe PMC PMID:17190852 Europe PMC PMID:22392515 Europe PMC PMID:22770225 Europe PMC Reaxys:754904 Reaxys URIDINE PDBeChem Uridine KEGG_COMPOUND uridine IUPAC uridine UniProt 1-beta-D-ribofuranosylpyrimidine-2,4(1H,3H)-dione ChEBI 1-beta-D-ribofuranosyluracil HMDB Urd CBN Uridin ChemIDplus beta-Uridine HMDB u ChEBI A penicillanic acid compound having a (6R)-amino substituent. The active nucleus common to all penicillins, it may be substituted at the 6-amino position to form the semisynthetic penicillins, resulting in a variety of antibacterial and pharmacologic characteristics. 0 C8H12N2O3S InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/t3-,4+,6-/m1/s1 NGHVIOIJCVXTGV-ALEPSDHESA-N 216.260 216.05686 C([C@H]1C(S[C@@]2([C@@H](C(N12)=O)N)[H])(C)C)(O)=O CHEBI:20705 CHEBI:2172 Beilstein:15080 Beilstein:959078 CAS:551-16-6 Gmelin:1876702 KEGG:C02954 PDBeChem:X1E PMID:12569987 PMID:1384868 PMID:14687482 PMID:1701026 PMID:20970923 PMID:21614893 PMID:24293403 PMID:24389703 PMID:24631718 PMID:25057428 PMID:26852849 PMID:26986755 PMID:6166603 Patent:US2941995 Reaxys:15080 Wikipedia:6-APA 6-Aminopenicillanic acid 6-amino-2,2-dimethylpenam-3alpha-carboxylic acid chebi_ontology (+)-6-aminopenicillanic acid (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid 6-APA 6-Aminopenicillamine acid 6-Aminopenicillanate 6-Apa 6-Aps 6beta-aminopenicillanic acid Aminopenicillanic acid Penicin Penin Phenacyl 6-aminopenicillinate CHEBI:16705 6-aminopenicillanic acid Beilstein:15080 Beilstein Beilstein:959078 Beilstein CAS:551-16-6 ChemIDplus CAS:551-16-6 KEGG COMPOUND Gmelin:1876702 Gmelin PMID:12569987 Europe PMC PMID:1384868 Europe PMC PMID:14687482 Europe PMC PMID:1701026 Europe PMC PMID:20970923 Europe PMC PMID:21614893 Europe PMC PMID:24293403 Europe PMC PMID:24389703 Europe PMC PMID:24631718 Europe PMC PMID:25057428 Europe PMC PMID:26852849 Europe PMC PMID:26986755 Europe PMC PMID:6166603 Europe PMC Reaxys:15080 Reaxys 6-Aminopenicillanic acid KEGG_COMPOUND 6-amino-2,2-dimethylpenam-3alpha-carboxylic acid IUPAC (+)-6-aminopenicillanic acid ChEBI (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid IUPAC 6-APA ChEBI 6-Aminopenicillamine acid ChemIDplus 6-Aminopenicillanate KEGG_COMPOUND 6-Apa ChemIDplus 6-Aps ChemIDplus 6beta-aminopenicillanic acid ChEBI Aminopenicillanic acid ChemIDplus Penicin ChemIDplus Penin ChemIDplus Phenacyl 6-aminopenicillinate ChemIDplus A hydroxymethylpyridine with hydroxymethyl groups at positions 4 and 5, a hydroxy group at position 3 and a methyl group at position 2. The 4-methanol form of vitamin B6, it is converted intoto pyridoxal phosphate which is a coenzyme for synthesis of amino acids, neurotransmitters, sphingolipids and aminolevulinic acid. 0 C8H11NO3 InChI=1S/C8H11NO3/c1-5-8(12)7(4-11)6(3-10)2-9-5/h2,10-12H,3-4H2,1H3 LXNHXLLTXMVWPM-UHFFFAOYSA-N 169.17788 169.07389 Cc1ncc(CO)c(CO)c1O CHEBI:14981 CHEBI:26429 CHEBI:8671 Beilstein:139854 CAS:65-23-6 DrugBank:DB00165 Drug_Central:2836 Gmelin:563676 HMDB:HMDB0000239 KEGG:C00314 KEGG:D08454 KNApSAcK:C00001551 LINCS:LSM-5324 PMID:24035968 PMID:2580028 Reaxys:139854 Wikipedia:Pyridoxine 4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol Pyridoxine pyridoxine chebi_ontology 2-methyl-3-hydroxy-4,5-dihydroxymethylpyridine 3-hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine 3-hydroxy-4,5-dimethylol-alpha-picoline 5-hydroxy-6-methyl-3,4-pyridinedimethanol Pyridoxol vitamin B6 CHEBI:16709 pyridoxine Beilstein:139854 Beilstein CAS:65-23-6 ChemIDplus CAS:65-23-6 KEGG COMPOUND CAS:65-23-6 NIST Chemistry WebBook Drug_Central:2836 DrugCentral Gmelin:563676 Gmelin PMID:24035968 Europe PMC PMID:2580028 Europe PMC Reaxys:139854 Reaxys 4,5-bis(hydroxymethyl)-2-methylpyridin-3-ol IUPAC Pyridoxine KEGG_COMPOUND pyridoxine UniProt 2-methyl-3-hydroxy-4,5-dihydroxymethylpyridine NIST_Chemistry_WebBook 3-hydroxy-4,5-bis(hydroxymethyl)-2-methylpyridine ChEBI 3-hydroxy-4,5-dimethylol-alpha-picoline NIST_Chemistry_WebBook 5-hydroxy-6-methyl-3,4-pyridinedimethanol NIST_Chemistry_WebBook Pyridoxol KEGG_COMPOUND vitamin B6 NIST_Chemistry_WebBook A six-carbon aromatic annulene in which each carbon atom donates one of its two 2p electrons into a delocalised pi system. A toxic, flammable liquid byproduct of coal distillation, it is used as an industrial solvent. Benzene is a carcinogen that also damages bone marrow and the central nervous system. 0 C6H6 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N 78.11184 78.04695 c1ccccc1 CHEBI:13876 CHEBI:22703 CHEBI:3025 CHEBI:41187 Beilstein:969212 CAS:71-43-2 Gmelin:1671 HMDB:HMDB0001505 KEGG:C01407 PDBeChem:BNZ PMID:11684179 PMID:11993966 PMID:12857942 PMID:14677922 PMID:15468289 PMID:15935818 PMID:16161967 PMID:17373369 PMID:18072742 PMID:18407866 PMID:18409691 PMID:18836923 PMID:19228219 PMID:21325737 PMID:23088855 PMID:23222815 PMID:23534829 PMID:6353911 PMID:8124204 Reaxys:969212 UM-BBD_compID:c0142 Wikipedia:Benzene BENZENE Benzene benzene chebi_ontology Benzen Benzine Benzol Bicarburet of hydrogen Coal naphtha Mineral naphtha Phene Pyrobenzol Pyrobenzole [6]annulene benzole cyclohexatriene phenyl hydride CHEBI:16716 benzene Beilstein:969212 Beilstein CAS:71-43-2 ChemIDplus CAS:71-43-2 KEGG COMPOUND CAS:71-43-2 NIST Chemistry WebBook Gmelin:1671 Gmelin PMID:11684179 Europe PMC PMID:11993966 Europe PMC PMID:12857942 Europe PMC PMID:14677922 Europe PMC PMID:15468289 Europe PMC PMID:15935818 Europe PMC PMID:16161967 Europe PMC PMID:17373369 Europe PMC PMID:18072742 Europe PMC PMID:18407866 Europe PMC PMID:18409691 Europe PMC PMID:18836923 Europe PMC PMID:19228219 Europe PMC PMID:21325737 Europe PMC PMID:23088855 Europe PMC PMID:23222815 Europe PMC PMID:23534829 Europe PMC PMID:6353911 Europe PMC PMID:8124204 Europe PMC Reaxys:969212 Reaxys UM-BBD_compID:c0142 UM-BBD BENZENE PDBeChem Benzene KEGG_COMPOUND benzene ChEBI benzene IUPAC benzene UniProt Benzen IUPAC Benzine UM-BBD Benzol ChemIDplus Bicarburet of hydrogen ChemIDplus Coal naphtha ChemIDplus Mineral naphtha ChemIDplus Phene ChemIDplus Pyrobenzol ChemIDplus Pyrobenzole ChemIDplus [6]annulene NIST_Chemistry_WebBook benzole NIST_Chemistry_WebBook cyclohexatriene UM-BBD phenyl hydride UM-BBD 0 C2H4NO2R 74.05870 74.02420 N[C@H]([*])C(O)=O CHEBI:12909 CHEBI:13625 CHEBI:20906 CHEBI:4097 KEGG:C00405 D-alpha-amino acid D-alpha-amino acids chebi_ontology D-Amino acid D-alpha-amino acids CHEBI:16733 D-alpha-amino acid D-alpha-amino acid ChEBI D-alpha-amino acids IUPAC D-Amino acid KEGG_COMPOUND D-alpha-amino acids ChEBI A dihydroxy-5beta-cholanic acid that is (5beta)-cholan-24-oic acid substituted by hydroxy groups at positions 3 and 7 respectively. 0 C24H40O4 InChI=1S/C24H40O4/c1-14(4-7-21(27)28)17-5-6-18-22-19(9-11-24(17,18)3)23(2)10-8-16(25)12-15(23)13-20(22)26/h14-20,22,25-26H,4-13H2,1-3H3,(H,27,28)/t14-,15+,16-,17-,18+,19+,20-,22+,23+,24-/m1/s1 RUDATBOHQWOJDD-BSWAIDMHSA-N 392.57200 392.29266 [H][C@@]12C[C@H](O)CC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])[C@H](O)C2)[C@H](C)CCC(O)=O CHEBI:23094 CHEBI:3588 CHEBI:3593 Beilstein:3219887 CAS:474-25-9 DrugBank:DB06777 Drug_Central:4361 HMDB:HMDB0000518 KEGG:C02528 KEGG:D00163 LINCS:LSM-5353 LIPID_MAPS_instance:LMST04010032 PDBeChem:JN3 PMID:11530998 PMID:16037564 PMID:24448653 PMID:24464484 Reaxys:3219887 Wikipedia:Chenodiol 3alpha,7alpha-dihydroxy-5beta-cholan-24-oic acid Chenodeoxycholic acid chebi_ontology 3alpha,7alpha-Dihydroxy-5beta-cholanic acid 7alpha-hydroxylithocholic acid CDCA Chenix Chenodiol anthropodeoxycholic acid anthropodesoxycholic acid chenic acid gallodesoxycholic acid CHEBI:16755 chenodeoxycholic acid Beilstein:3219887 Beilstein CAS:474-25-9 ChemIDplus CAS:474-25-9 KEGG COMPOUND Drug_Central:4361 DrugCentral LIPID_MAPS_instance:LMST04010032 LIPID MAPS PMID:11530998 Europe PMC PMID:16037564 Europe PMC PMID:24448653 Europe PMC PMID:24464484 Europe PMC Reaxys:3219887 Reaxys 3alpha,7alpha-dihydroxy-5beta-cholan-24-oic acid IUPAC Chenodeoxycholic acid KEGG_COMPOUND 3alpha,7alpha-Dihydroxy-5beta-cholanic acid KEGG_COMPOUND 7alpha-hydroxylithocholic acid ChemIDplus CDCA IUPHAR Chenix ChemIDplus Chenodiol KEGG_COMPOUND anthropodeoxycholic acid ChemIDplus anthropodesoxycholic acid ChemIDplus chenic acid ChemIDplus gallodesoxycholic acid ChemIDplus A sulfur-containing amino acid that is butyric acid bearing an amino substituent at position 2 and a methylthio substituent at position 4. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8) FFEARJCKVFRZRR-UHFFFAOYSA-N 149.21238 149.05105 CSCCC(N)C(O)=O CHEBI:14590 CHEBI:25229 CHEBI:6829 Beilstein:636185 CAS:59-51-8 Gmelin:3117 KEGG:C01733 KEGG:D04983 PMID:16702333 PMID:22264337 PMID:2543976 Reaxys:636185 UM-BBD_compID:c0094 Wikipedia:Methionine Methionine methionine chebi_ontology 2-Amino-4-(methylthio)butyric acid 2-amino-4-(methylsulfanyl)butanoic acid 2-amino-4-(methylthio)butanoic acid DL-Methionine Hmet M Met Methionin Racemethionine alpha-amino-gamma-methylmercaptobutyric acid metionina CHEBI:16811 methionine Beilstein:636185 Beilstein CAS:59-51-8 ChemIDplus CAS:59-51-8 KEGG COMPOUND CAS:59-51-8 NIST Chemistry WebBook Gmelin:3117 Gmelin PMID:16702333 Europe PMC PMID:22264337 Europe PMC PMID:2543976 Europe PMC Reaxys:636185 Reaxys UM-BBD_compID:c0094 UM-BBD Methionine KEGG_COMPOUND methionine ChEBI methionine IUPAC 2-Amino-4-(methylthio)butyric acid KEGG_COMPOUND 2-amino-4-(methylsulfanyl)butanoic acid IUPAC 2-amino-4-(methylthio)butanoic acid JCBN DL-Methionine KEGG_DRUG Hmet IUPAC M ChEBI Met ChEBI Methionin ChEBI Racemethionine KEGG_DRUG alpha-amino-gamma-methylmercaptobutyric acid NIST_Chemistry_WebBook metionina ChEBI An optically active form of methionine having D-configuration. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1 FFEARJCKVFRZRR-SCSAIBSYSA-N 149.21238 149.05105 CSCC[C@@H](N)C(O)=O CHEBI:13005 CHEBI:21065 CHEBI:4215 CHEBI:44071 Beilstein:1722293 CAS:348-67-4 DrugBank:DB02893 ECMDB:ECMDB21203 Gmelin:26934 KEGG:C00855 MetaCyc:CPD-218 PDBeChem:MED PMID:15375647 PMID:20431016 PMID:20872028 PMID:21480759 PMID:21750343 PMID:21924333 PMID:22192214 PMID:22304623 PMID:318639 Reaxys:1722293 YMDB:YMDB00816 D-METHIONINE D-Methionine D-methionine chebi_ontology (2R)-2-amino-4-(methylsulfanyl)butanoic acid (R)-2-amino-4-(methylthio)butanoic acid (R)-methionine D-2-Amino-4-(methylthio)butyric acid D-Methionin MED CHEBI:16867 D-methionine Beilstein:1722293 Beilstein CAS:348-67-4 ChemIDplus CAS:348-67-4 KEGG COMPOUND CAS:348-67-4 NIST Chemistry WebBook Gmelin:26934 Gmelin PMID:15375647 Europe PMC PMID:20431016 Europe PMC PMID:20872028 Europe PMC PMID:21480759 Europe PMC PMID:21750343 Europe PMC PMID:21924333 Europe PMC PMID:22192214 Europe PMC PMID:22304623 Europe PMC PMID:318639 Europe PMC Reaxys:1722293 Reaxys D-METHIONINE PDBeChem D-Methionine KEGG_COMPOUND D-methionine IUPAC (2R)-2-amino-4-(methylsulfanyl)butanoic acid IUPAC (R)-2-amino-4-(methylthio)butanoic acid JCBN (R)-methionine ChemIDplus D-2-Amino-4-(methylthio)butyric acid KEGG_COMPOUND D-Methionin ChEBI MED PDBeChem A glycine derivative having methyl and amidino groups attached to the nitrogen. 0 C4H9N3O2 InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9) CVSVTCORWBXHQV-UHFFFAOYSA-N 131.13328 131.06948 CN(CC(O)=O)C(N)=N CHEBI:14028 CHEBI:23404 CHEBI:3909 CHEBI:41678 Beilstein:907175 CAS:57-00-1 DrugBank:DB00148 Drug_Central:4661 Gmelin:240513 HMDB:HMDB0000064 KEGG:C00300 MetaCyc:CREATINE PDBeChem:CRN PMID:11356982 PMID:11483809 PMID:11867929 PMID:12085493 PMID:12184144 PMID:12878267 PMID:16445883 PMID:17190852 PMID:17253521 PMID:18555535 PMID:19082141 PMID:19651674 PMID:19741514 PMID:19968328 PMID:21556832 PMID:21660517 PMID:21698493 PMID:22038587 PMID:22101931 PMID:22196490 PMID:22252611 PMID:22347384 PMID:22386973 PMID:22422801 PMID:22429992 PMID:22465051 PMID:22521466 PMID:7752905 Reaxys:907175 Wikipedia:Creatine Creatine N-[amino(imino)methyl]-N-methylglycine chebi_ontology ((amino(imino)methyl)(methyl)amino)acetic acid (N-methylcarbamimidamido)acetic acid (alpha-methylguanido)acetic acid Creatin Kreatin Methylglycocyamine N-(aminoiminomethyl)-N-methylglycine N-Methyl-N-guanylglycine N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE N-amidinosarcosine N-carbamimidoyl-N-methylglycine N-methyl-N-guanylglycine alpha-Methylguanidino acetic acid CHEBI:16919 creatine Beilstein:907175 Beilstein CAS:57-00-1 ChemIDplus CAS:57-00-1 KEGG COMPOUND CAS:57-00-1 NIST Chemistry WebBook Drug_Central:4661 DrugCentral Gmelin:240513 Gmelin PMID:11356982 Europe PMC PMID:11483809 Europe PMC PMID:11867929 Europe PMC PMID:12085493 Europe PMC PMID:12184144 Europe PMC PMID:12878267 Europe PMC PMID:16445883 Europe PMC PMID:17190852 Europe PMC PMID:17253521 Europe PMC PMID:18555535 Europe PMC PMID:19082141 Europe PMC PMID:19651674 Europe PMC PMID:19741514 Europe PMC PMID:19968328 Europe PMC PMID:21556832 Europe PMC PMID:21660517 Europe PMC PMID:21698493 Europe PMC PMID:22038587 Europe PMC PMID:22101931 Europe PMC PMID:22196490 Europe PMC PMID:22252611 Europe PMC PMID:22347384 Europe PMC PMID:22386973 Europe PMC PMID:22422801 Europe PMC PMID:22429992 Europe PMC PMID:22465051 Europe PMC PMID:22521466 Europe PMC PMID:7752905 Europe PMC Reaxys:907175 Reaxys Creatine KEGG_COMPOUND N-[amino(imino)methyl]-N-methylglycine IUPAC ((amino(imino)methyl)(methyl)amino)acetic acid HMDB (N-methylcarbamimidamido)acetic acid ChEBI (alpha-methylguanido)acetic acid HMDB (alpha-methylguanido)acetic acid NIST_Chemistry_WebBook Creatin ChemIDplus Kreatin ChemIDplus Methylglycocyamine KEGG_COMPOUND N-(aminoiminomethyl)-N-methylglycine NIST_Chemistry_WebBook N-Methyl-N-guanylglycine HMDB N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE PDBeChem N-amidinosarcosine ChemIDplus N-carbamimidoyl-N-methylglycine PDBeChem N-methyl-N-guanylglycine ChemIDplus alpha-Methylguanidino acetic acid KEGG_COMPOUND An alpha,omega-dicarboxylic acid that is ethane substituted by carboxyl groups at positions 1 and 2. 0 C2H2O4 InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6) MUBZPKHOEPUJKR-UHFFFAOYSA-N 90.03490 89.99531 OC(=O)C(O)=O CHEBI:25730 CHEBI:44583 CHEBI:7811 Beilstein:385686 CAS:144-62-7 DrugBank:DB03902 Gmelin:2208 HMDB:HMDB0002329 KEGG:C00209 KNApSAcK:C00001198 LIPID_MAPS_instance:LMFA01170031 MetaCyc:OXALATE PDBeChem:OXD PMID:15587083 PMID:22735334 Reaxys:385686 Wikipedia:Oxalic_acid OXALIC ACID Oxalic acid oxalic acid chebi_ontology Ethandisaeure Ethanedioic acid H2ox HOOCCOOH Oxalsaeure ethane-1,2-dioic acid CHEBI:16995 oxalic acid Beilstein:385686 Beilstein CAS:144-62-7 ChemIDplus CAS:144-62-7 KEGG COMPOUND CAS:144-62-7 NIST Chemistry WebBook Gmelin:2208 Gmelin LIPID_MAPS_instance:LMFA01170031 LIPID MAPS PMID:15587083 Europe PMC PMID:22735334 Europe PMC Reaxys:385686 Reaxys OXALIC ACID PDBeChem Oxalic acid KEGG_COMPOUND oxalic acid IUPAC Ethandisaeure ChEBI Ethanedioic acid KEGG_COMPOUND H2ox IUPAC HOOCCOOH NIST_Chemistry_WebBook Oxalsaeure ChEBI ethane-1,2-dioic acid NIST_Chemistry_WebBook D-Ribitol in which the hydroxy group at position 5 is substituted by a 7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl moiety. It is a nutritional factor found in milk, eggs, malted barley, liver, kidney, heart, and leafy vegetables, but the richest natural source is yeast. The free form occurs only in the retina of the eye, in whey, and in urine; its principal forms in tissues and cells are as flavin mononucleotide and flavin-adenine dinucleotide. riboflavin vitamin b2 http://langual.org 0 C17H20N4O6 InChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/t11-,12+,14-/m0/s1 AUNGANRZJHBGPY-SCRDCRAPSA-N 376.36390 376.13828 Cc1cc2nc3c(nc(=O)[nH]c3=O)n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C CHEBI:15044 CHEBI:27299 CHEBI:45214 CHEBI:529204 CHEBI:8843 Beilstein:97831 CAS:83-88-5 Codex::101(i) DrugBank:DB00140 Drug_Central:2834 Europe::101 HMDB:HMDB0000244 KEGG:C00255 KEGG:D00050 KNApSAcK:C00001552 LINCS:LSM-4084 MetaCyc:RIBOFLAVIN PDBeChem:RBF PMID:16658098 PMID:22770225 PMID:24643482 PMID:25108762 Patent:US2807611 Patent:US2876169 Reaxys:97831 Wikipedia:Riboflavin http://www.langual.org/langual_thesaurus.asp?termid=B3233 http://www.langual.org/langual_thesaurus.asp?termid=B3756 5-deoxy-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol Riboflavin riboflavin chebi_ontology 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol 6,7-dimethyl-9-D-ribitylisoalloxazine 7,8-Dimethyl-10-ribitylisoalloxazine 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)benzo[g]pteridine-2,4(3H,10H)-dione 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)isoalloxazine E101 Lactoflavin RIBOFLAVINE Vitamin B2 riboflavin riboflavina riboflavine riboflavinum vitamin B2 vitamin G riboflavin, synthetic CHEBI:17015 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): colour. riboflavin Beilstein:97831 Beilstein CAS:83-88-5 ChemIDplus CAS:83-88-5 KEGG COMPOUND CAS:83-88-5 NIST Chemistry WebBook Drug_Central:2834 DrugCentral PMID:16658098 Europe PMC PMID:22770225 Europe PMC PMID:24643482 Europe PMC PMID:25108762 Europe PMC Reaxys:97831 Reaxys 5-deoxy-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-D-ribitol IUPAC Riboflavin KEGG_COMPOUND riboflavin ChEMBL 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol NIST_Chemistry_WebBook 6,7-dimethyl-9-D-ribitylisoalloxazine ChemIDplus 7,8-Dimethyl-10-ribitylisoalloxazine KEGG_COMPOUND 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)benzo[g]pteridine-2,4(3H,10H)-dione ChEBI 7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)isoalloxazine ChemIDplus E101 ChEBI Lactoflavin KEGG_COMPOUND RIBOFLAVINE PDBeChem Vitamin B2 KEGG_COMPOUND riboflavin ChemIDplus riboflavina ChemIDplus riboflavine ChemIDplus riboflavinum ChemIDplus vitamin B2 ChEBI vitamin G DrugBank -1 F InChI=1S/FH/h1H/p-1 KRHYYFGTRYWZRS-UHFFFAOYSA-M 18.99840 18.99895 [F-] CHEBI:14271 CHEBI:49593 CHEBI:5113 CAS:16984-48-8 Gmelin:14905 KEGG:C00742 PDBeChem:F Fluoride fluoride fluoride(1-) chebi_ontology F(-) F- FLUORIDE ION Fluoride ion Fluorine anion CHEBI:17051 fluoride CAS:16984-48-8 ChemIDplus CAS:16984-48-8 NIST Chemistry WebBook Gmelin:14905 Gmelin Fluoride KEGG_COMPOUND fluoride IUPAC fluoride UniProt fluoride(1-) IUPAC F(-) IUPAC F- KEGG_COMPOUND FLUORIDE ION PDBeChem Fluoride ion KEGG_COMPOUND Fluorine anion NIST_Chemistry_WebBook 0 CH4NR 30.04920 30.03437 NC[*] CHEBI:13431 CHEBI:8749 KEGG:C00375 chebi_ontology RCH2NH2 primary aliphatic amines CHEBI:17062 primary aliphatic amine RCH2NH2 ChEBI RCH2NH2 KEGG_COMPOUND primary aliphatic amines ChEBI A compound in which a carbonyl group is bonded to two carbon atoms: R2C=O (neither R may be H). 0 COR2 28.010 27.99491 [*]C([*])=O CHEBI:13427 CHEBI:13646 CHEBI:24974 CHEBI:6127 CHEBI:8742 KEGG:C01450 Wikipedia:Ketone Ketone ketones chebi_ontology Keton R-CO-R' a ketone cetone ketones CHEBI:17087 ketone Ketone KEGG_COMPOUND ketones IUPAC Keton ChEBI R-CO-R' KEGG_COMPOUND a ketone UniProt cetone ChEBI ketones ChEBI The L-enantiomer of serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-N 105.09262 105.04259 N[C@@H](CO)C(O)=O CHEBI:13167 CHEBI:21387 CHEBI:45440 CHEBI:45451 CHEBI:45590 CHEBI:45597 CHEBI:45677 CHEBI:6301 Beilstein:1721404 CAS:56-45-1 DrugBank:DB00133 Drug_Central:4127 ECMDB:ECMDB00187 Gmelin:2570 HMDB:HMDB0000187 KEGG:C00065 KEGG:D00016 KNApSAcK:C00001393 MetaCyc:SER PDBeChem:SER PMID:1650428 PMID:17439666 PMID:19062365 PMID:21956576 PMID:22265470 PMID:22393170 PMID:22547037 PMID:22566084 PMID:22566694 Reaxys:1721404 Wikipedia:L-serine YMDB:YMDB00112 L-Serine L-serine chebi_ontology (2S)-2-amino-3-hydroxypropanoic acid (S)-(-)-serine (S)-2-amino-3-hydroxypropanoic acid (S)-alpha-Amino-beta-hydroxypropionic acid (S)-serine L-(-)-serine L-2-Amino-3-hydroxypropionic acid L-3-Hydroxy-2-aminopropionic acid L-3-Hydroxy-alanine L-Ser L-Serin S SERINE Ser Serine beta-Hydroxy-L-alanine beta-Hydroxyalanine CHEBI:17115 L-serine Beilstein:1721404 Beilstein CAS:56-45-1 ChemIDplus CAS:56-45-1 KEGG COMPOUND CAS:56-45-1 NIST Chemistry WebBook Drug_Central:4127 DrugCentral Gmelin:2570 Gmelin PMID:1650428 Europe PMC PMID:17439666 Europe PMC PMID:19062365 Europe PMC PMID:21956576 Europe PMC PMID:22265470 Europe PMC PMID:22393170 Europe PMC PMID:22547037 Europe PMC PMID:22566084 Europe PMC PMID:22566694 Europe PMC Reaxys:1721404 Reaxys L-Serine KEGG_COMPOUND L-serine IUPAC (2S)-2-amino-3-hydroxypropanoic acid IUPAC (S)-(-)-serine NIST_Chemistry_WebBook (S)-2-amino-3-hydroxypropanoic acid NIST_Chemistry_WebBook (S)-alpha-Amino-beta-hydroxypropionic acid HMDB (S)-serine ChemIDplus L-(-)-serine NIST_Chemistry_WebBook L-2-Amino-3-hydroxypropionic acid KEGG_COMPOUND L-3-Hydroxy-2-aminopropionic acid HMDB L-3-Hydroxy-alanine KEGG_COMPOUND L-Ser DrugBank L-Serin ChEBI S ChEBI SERINE PDBeChem Ser ChEBI Serine KEGG_COMPOUND beta-Hydroxy-L-alanine HMDB beta-Hydroxyalanine HMDB A short-chain fatty acid anion that is the conjugate base of hexanoic acid (also known as caproic acid). -1 C6H11O2 InChI=1S/C6H12O2/c1-2-3-4-5-6(7)8/h2-5H2,1H3,(H,7,8)/p-1 FUZZWVXGSFPDMH-UHFFFAOYSA-M 115.15034 115.07645 CCCCCC([O-])=O CHEBI:14398 CHEBI:24569 Beilstein:3601453 CAS:151-33-7 ECMDB:ECMDB21229 Gmelin:326340 KEGG:C01585 MetaCyc:HEXANOATE hexanoate chebi_ontology 1-hexanoate 1-pentacarboxylate 1-pentanecarboxylate CH3-[CH2]4-COO(-) butylacetate caproate capronate hexoate hexylate n-caproate n-hexanoate n-hexoate n-hexylate nPnCO2 anion pentanecarboxylate pentylformate CHEBI:17120 hexanoate Beilstein:3601453 Beilstein CAS:151-33-7 Beilstein Gmelin:326340 Gmelin hexanoate IUPAC hexanoate UniProt 1-hexanoate ChEBI 1-pentacarboxylate ChEBI 1-pentanecarboxylate ChEBI CH3-[CH2]4-COO(-) IUPAC butylacetate ChEBI caproate ChEBI capronate ChEBI hexoate ChEBI hexylate ChEBI n-caproate ChEBI n-hexanoate ChEBI n-hexoate ChEBI n-hexylate ChEBI nPnCO2 anion NIST_Chemistry_WebBook pentanecarboxylate ChEBI pentylformate ChEBI An amino-acid betaine that is butanoate substituted with a hydroxy group at position C-3 and a trimethylammonium group at C-4. 0 C7H15NO3 InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3 PHIQHXFUZVPYII-UHFFFAOYSA-N 161.19894 161.10519 C[N+](C)(C)CC(O)CC([O-])=O CHEBI:11817 CHEBI:13947 CHEBI:20047 CHEBI:23038 Beilstein:1866665 CAS:461-06-3 DrugBank:DB02648 KEGG:C00487 MetaCyc:DL-CARNITINE PMID:22770225 PMID:23868375 Patent:US4255449 Patent:US4315944 Reaxys:1866665 Wikipedia:Carnitine 3-hydroxy-4-(trimethylammonio)butanoate carnitine chebi_ontology D,L-carnitine CHEBI:17126 carnitine Beilstein:1866665 Beilstein CAS:461-06-3 ChemIDplus PMID:22770225 Europe PMC PMID:23868375 Europe PMC Reaxys:1866665 Reaxys 3-hydroxy-4-(trimethylammonio)butanoate IUPAC carnitine UniProt D,L-carnitine MetaCyc -1 HO3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-1 LSNNMFCWUKXFEE-UHFFFAOYSA-M 81.07214 80.96519 OS([O-])=O CHEBI:13367 CHEBI:5598 CAS:15181-46-1 Gmelin:1455 KEGG:C11481 PDBeChem:SO3 hydrogen(trioxidosulfate)(1-) hydrogensulfite(1-) hydrogentrioxosulfate(1-) hydrogentrioxosulfate(IV) hydroxidodioxidosulfate(1-) monohydrogentrioxosulfate chebi_ontology Bisulfite HSO3(-) HSO3- Hydrogen sulfite [SO2(OH)](-) bisulfite bisulphite hydrogen sulfite(1-) hydrosulfite anion CHEBI:17137 hydrogensulfite CAS:15181-46-1 ChemIDplus CAS:15181-46-1 KEGG COMPOUND Gmelin:1455 Gmelin hydrogen(trioxidosulfate)(1-) IUPAC hydrogensulfite(1-) IUPAC hydrogentrioxosulfate(1-) IUPAC hydrogentrioxosulfate(IV) IUPAC hydroxidodioxidosulfate(1-) IUPAC monohydrogentrioxosulfate IUPAC Bisulfite KEGG_COMPOUND HSO3(-) IUPAC HSO3- KEGG_COMPOUND Hydrogen sulfite KEGG_COMPOUND [SO2(OH)](-) IUPAC bisulfite ChemIDplus bisulphite ChemIDplus hydrogen sulfite(1-) ChemIDplus hydrosulfite anion ChemIDplus Any 3beta-hydroxy-steroid that contains a double bond between positions 5 and 6. 0 C19H29OR 273.434 273.22184 C12C(C3C(C(CC3)*)(C)CC1)CC=C4C2(CC[C@@H](C4)O)C CHEBI:13608 CHEBI:136845 CHEBI:20245 KEGG:C03836 MetaCyc:3b-hydroxy-D5-steroids chebi_ontology 3beta-hydroxy Delta(5)-steroids 3beta-hydroxy-Delta(5)-steroids a 3beta-hydroxy-Delta(5)-steroid CHEBI:1722 3beta-hydroxy-Delta(5)-steroid 3beta-hydroxy Delta(5)-steroids ChEBI 3beta-hydroxy-Delta(5)-steroids ChEBI a 3beta-hydroxy-Delta(5)-steroid UniProt glucose An aldohexose used as a source of energy and metabolic intermediate. 0 C6H12O6 180.15588 180.06339 CHEBI:14313 CHEBI:24277 CHEBI:33929 CHEBI:5418 CAS:50-99-7 KEGG:C00293 Wikipedia:Glucose Glucose gluco-hexose glucose chebi_ontology DL-glucose Glc Glukose CHEBI:17234 glucose CAS:50-99-7 KEGG COMPOUND Glucose KEGG_COMPOUND gluco-hexose IUPAC glucose IUPAC DL-glucose ChEBI Glc JCBN Glukose ChEBI The conjugate base of propionic acid; a key precursor in lipid biosynthesis. -1 C3H5O2 InChI=1S/C3H6O2/c1-2-3(4)5/h2H2,1H3,(H,4,5)/p-1 XBDQKXXYIPTUBI-UHFFFAOYSA-M 73.07060 73.02950 CCC([O-])=O CHEBI:14903 CHEBI:26290 Beilstein:3587503 CAS:72-03-7 Gmelin:1820 KEGG:C00163 PMID:17951291 PMID:18375549 PMID:2647392 UM-BBD_compID:c0277 propanoate propionate chebi_ontology CH3-CH2-COO(-) EtCO2 anion carboxylatoethane ethanecarboxylate ethylformate metacetonate methylacetate propanate propanoate propanoic acid, ion(1-) pseudoacetate CHEBI:17272 propionate Beilstein:3587503 Beilstein CAS:72-03-7 ChemIDplus CAS:72-03-7 NIST Chemistry WebBook Gmelin:1820 Gmelin PMID:17951291 Europe PMC PMID:18375549 Europe PMC PMID:2647392 Europe PMC UM-BBD_compID:c0277 UM-BBD propanoate IUPAC propionate IUPAC CH3-CH2-COO(-) IUPAC EtCO2 anion NIST_Chemistry_WebBook carboxylatoethane ChEBI ethanecarboxylate ChEBI ethylformate ChEBI metacetonate ChEBI methylacetate ChEBI propanate ChEBI propanoate UniProt propanoic acid, ion(1-) ChemIDplus pseudoacetate ChEBI Any member of the group of substituted penams containing two methyl substituents at position 2, a carboxylate substituent at position 3 and a carboxamido group at position 6. 0 C9H11N2O4SR 243.26000 243.04395 [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC([*])=O)C(O)=O CHEBI:14742 CHEBI:25869 CHEBI:7961 KEGG:C00395 PMID:11851248 PMID:12833570 PMID:1502708 PMID:16033609 PMID:7061385 PMID:7798534 Wikipedia:Penicillin Penicillin penicillins chebi_ontology penicillins CHEBI:17334 penicillin PMID:11851248 Europe PMC PMID:12833570 Europe PMC PMID:1502708 Europe PMC PMID:16033609 Europe PMC PMID:7061385 Europe PMC PMID:7798534 Europe PMC Penicillin KEGG_COMPOUND penicillins IUPAC penicillins ChEBI A sulfur oxoanion that is the conjugate base of hydrogen sulfite (H2SO3). -2 O3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3)/p-2 LSNNMFCWUKXFEE-UHFFFAOYSA-L 80.06420 79.95791 [O-]S([O-])=O CHEBI:15139 CHEBI:45548 CAS:14265-45-3 Gmelin:1449 PDBeChem:SO3 sulfite trioxidosulfate(2-) trioxosulfate(2-) trioxosulfate(IV) chebi_ontology SO3 SO3(2-) SULFITE ION [SO3](2-) sulphite CHEBI:17359 sulfite CAS:14265-45-3 ChemIDplus Gmelin:1449 Gmelin sulfite IUPAC sulfite UniProt trioxidosulfate(2-) IUPAC trioxosulfate(2-) IUPAC trioxosulfate(IV) IUPAC SO3 ChEBI SO3(2-) IUPAC SULFITE ION PDBeChem [SO3](2-) IUPAC sulphite ChEBI A straight-chain saturated fatty acid containing five carbon atoms. 0 C5H10O2 InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7) NQPDZGIKBAWPEJ-UHFFFAOYSA-N 102.13170 102.06808 CCCCC(O)=O CHEBI:113448 CHEBI:27263 CHEBI:27264 CHEBI:43606 CHEBI:44803 CHEBI:7980 Beilstein:969454 CAS:109-52-4 DrugBank:DB02406 Gmelin:26714 HMDB:HMDB0000892 KEGG:C00803 KNApSAcK:C00001208 LIPID_MAPS_instance:LMFA01010005 PDBeChem:LEA PMID:20507156 PPDB:3130 Reaxys:969454 Wikipedia:Valeric_acid Valeric acid pentanoic acid chebi_ontology 1-butanecarboxylic acid CH3-[CH2]3-COOH PENTANOIC ACID Pentanoate Pentanoic acid Valerate Valerianic acid Valeriansaeure n-BuCOOH n-Pentanoate n-Valeric acid n-pentanoic acid n-valeric acid pentoic acid propylacetic acid valeric acid, normal CHEBI:17418 valeric acid Beilstein:969454 Beilstein CAS:109-52-4 ChemIDplus CAS:109-52-4 KEGG COMPOUND CAS:109-52-4 NIST Chemistry WebBook Gmelin:26714 Gmelin LIPID_MAPS_instance:LMFA01010005 LIPID MAPS PMID:20507156 Europe PMC Reaxys:969454 Reaxys Valeric acid KEGG_COMPOUND pentanoic acid IUPAC 1-butanecarboxylic acid ChemIDplus 1-butanecarboxylic acid NIST_Chemistry_WebBook CH3-[CH2]3-COOH IUPAC PENTANOIC ACID PDBeChem Pentanoate KEGG_COMPOUND Pentanoic acid KEGG_COMPOUND Valerate KEGG_COMPOUND Valerianic acid KEGG_COMPOUND Valeriansaeure ChEBI n-BuCOOH ChEBI n-Pentanoate KEGG_COMPOUND n-Valeric acid KEGG_COMPOUND n-pentanoic acid ChemIDplus n-valeric acid ChemIDplus pentoic acid ChEBI propylacetic acid ChemIDplus valeric acid, normal ChemIDplus A complex cob(III)alamin in which cobalt is positioned in the centre of a planar corrin tetrapyrrole ring and bound axially to a 5,6-dimethylbenzimidazole moiety and a cyano group. It is one of several forms of the vitamin known as vitamin B12. cyanocobalamin http://langual.org 0 C63H88CoN14O14P InChI=1S/C62H90N13O14P.CN.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;1-2;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;/q;;+2/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 RMRCNWBMXRMIRW-WZHZPDAFSA-L 1355.36520 1354.56740 [H][C@@]1(C)CNC(=O)CC[C@]2(C)[C@@H](CC(N)=O)[C@@]3([H])N4C2=C(C)C2=[N+]5C(=CC6=[N+]7C(=C(C)C8=[N+]([C@]3(C)[C@@](C)(CC(N)=O)[C@@H]8CCC(N)=O)[Co-3]457(C#N)[n+]3cn([C@H]4O[C@H](CO)[C@@H](OP([O-])(=O)O1)[C@H]4O)c1cc(C)c(C)cc31)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O)C(C)(C)[C@@H]2CCC(N)=O CHEBI:14041 CHEBI:23435 CHEBI:3979 CHEBI:48820 CHEBI:60496 CAS:68-19-9 DrugBank:DB00115 Gmelin:249901 Gmelin:457955 KEGG:C02823 KEGG:D00166 KNApSAcK:C00001534 PDBeChem:CNC PMID:29286160 http://www.langual.org/langual_thesaurus.asp?termid=B3779 Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-cyanocobamide Cyanocob(III)alamin cyanocob(III)alamin chebi_ontology CN-Cbl CO-CYANOCOBALAMIN Dicopac Vitamin B12 complex cyanocobalamin vitamin B-12 CHEBI:17439 cyanocob(III)alamin CAS:68-19-9 ChemIDplus CAS:68-19-9 KEGG COMPOUND Gmelin:249901 Gmelin Gmelin:457955 Gmelin PMID:29286160 Europe PMC Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-cyanocobamide IUPAC Cyanocob(III)alamin KEGG_COMPOUND cyanocob(III)alamin IUPAC cyanocob(III)alamin UniProt CN-Cbl CBN CO-CYANOCOBALAMIN PDBeChem Dicopac KEGG_COMPOUND Vitamin B12 complex KEGG_COMPOUND cyanocobalamin KEGG_DRUG vitamin B-12 CBN A carbohydrate that is an acyclic polyol having the general formula HOCH2[CH(OH)]nCH2OH (formally derivable from an aldose by reduction of the carbonyl group). 0 (CH2O)nC2H6O2 CHEBI:13754 CHEBI:22298 CHEBI:2556 KEGG:C00717 Wikipedia:Glycerin Alditol alditol chebi_ontology Glycitol Sugar alcohol alditols CHEBI:17522 alditol Alditol KEGG_COMPOUND alditol UniProt Glycitol KEGG_COMPOUND Sugar alcohol KEGG_COMPOUND alditols ChEBI The carbon oxoanion resulting from the removal of a proton from carbonic acid. -1 CHO3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-1 BVKZGUZCCUSVTD-UHFFFAOYSA-M 61.01684 60.99312 OC([O-])=O CHEBI:13363 CHEBI:22863 CHEBI:40961 CHEBI:5589 Beilstein:3903504 CAS:71-52-3 Gmelin:49249 HMDB:HMDB0000595 KEGG:C00288 MetaCyc:HCO3 PDBeChem:BCT PMID:17215880 PMID:17505962 PMID:18439416 PMID:28732801 PMID:29150416 PMID:29460248 PMID:29466234 PMID:4208463 Wikipedia:Bicarbonate Hydrogencarbonate hydrogen(trioxidocarbonate)(1-) hydrogencarbonate hydrogencarbonate(1-) hydrogentrioxocarbonate(1-) hydrogentrioxocarbonate(IV) hydroxidodioxidocarbonate(1-) chebi_ontology Acid carbonate BICARBONATE ION Bicarbonate HCO3(-) HCO3- [CO2(OH)](-) hydrogen carbonate CHEBI:17544 hydrogencarbonate Beilstein:3903504 Beilstein CAS:71-52-3 ChemIDplus Gmelin:49249 Gmelin PMID:17215880 Europe PMC PMID:17505962 Europe PMC PMID:18439416 Europe PMC PMID:28732801 Europe PMC PMID:29150416 Europe PMC PMID:29460248 Europe PMC PMID:29466234 Europe PMC PMID:4208463 Europe PMC Hydrogencarbonate KEGG_COMPOUND hydrogen(trioxidocarbonate)(1-) IUPAC hydrogencarbonate IUPAC hydrogencarbonate UniProt hydrogencarbonate(1-) IUPAC hydrogentrioxocarbonate(1-) IUPAC hydrogentrioxocarbonate(IV) IUPAC hydroxidodioxidocarbonate(1-) IUPAC Acid carbonate KEGG_COMPOUND BICARBONATE ION PDBeChem Bicarbonate KEGG_COMPOUND HCO3(-) IUPAC HCO3- KEGG_COMPOUND [CO2(OH)](-) IUPAC hydrogen carbonate PDBeChem An optically active form of cysteine having L-configuration. 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-N 121.15800 121.01975 N[C@@H](CS)C(O)=O CHEBI:13095 CHEBI:21261 CHEBI:41227 CHEBI:41700 CHEBI:41768 CHEBI:41781 CHEBI:41811 CHEBI:6207 Beilstein:1721408 CAS:52-90-4 DrugBank:DB00151 Drug_Central:769 ECMDB:ECMDB00574 Gmelin:49991 HMDB:HMDB0000574 KEGG:C00097 KEGG:D00026 KNApSAcK:C00001351 MetaCyc:CYS PDBeChem:CYS PMID:11732994 PMID:13761469 PMID:22735334 Reaxys:1721408 Wikipedia:Cysteine YMDB:YMDB00046 L-Cysteine L-cysteine chebi_ontology (2R)-2-amino-3-mercaptopropanoic acid (2R)-2-amino-3-sulfanylpropanoic acid (R)-2-amino-3-mercaptopropanoic acid C CYSTEINE Cys E 920 E-920 E920 FREE CYSTEINE L-2-Amino-3-mercaptopropionic acid L-Cystein L-Zystein CHEBI:17561 L-cysteine Beilstein:1721408 Beilstein CAS:52-90-4 ChemIDplus CAS:52-90-4 KEGG COMPOUND CAS:52-90-4 NIST Chemistry WebBook Drug_Central:769 DrugCentral Gmelin:49991 Gmelin PMID:11732994 Europe PMC PMID:13761469 Europe PMC PMID:22735334 Europe PMC Reaxys:1721408 Reaxys L-Cysteine KEGG_COMPOUND L-cysteine IUPAC (2R)-2-amino-3-mercaptopropanoic acid JCBN (2R)-2-amino-3-sulfanylpropanoic acid IUPAC (R)-2-amino-3-mercaptopropanoic acid NIST_Chemistry_WebBook C ChEBI CYSTEINE PDBeChem Cys ChEBI E 920 ChEBI E-920 ChEBI E920 ChEBI FREE CYSTEINE PDBeChem L-2-Amino-3-mercaptopropionic acid KEGG_COMPOUND L-Cystein ChEBI L-Zystein ChEBI A common and naturally occurring pyrimidine nucleobase in which the pyrimidine ring is substituted with two oxo groups at positions 2 and 4. Found in RNA, it base pairs with adenine and replaces thymine during DNA transcription. 0 C4H4N2O2 InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) ISAKRJDGNUQOIC-UHFFFAOYSA-N 112.08684 112.02728 O=c1cc[nH]c(=O)[nH]1 CHEBI:15288 CHEBI:27210 CHEBI:46375 CHEBI:9882 Beilstein:606623 CAS:66-22-8 DrugBank:DB03419 Gmelin:2896 HMDB:HMDB0000300 KEGG:C00106 KEGG:D00027 KNApSAcK:C00001513 MetaCyc:URACIL PDBeChem:URA PMID:11279060 PMID:12855717 PMID:15274295 PMID:16834123 PMID:17439666 PMID:18533995 PMID:18815805 PMID:19175333 PMID:22020693 PMID:22074393 PMID:22120518 PMID:22171528 PMID:22237209 PMID:22299724 PMID:22356544 PMID:22447672 PMID:22483865 PMID:22567906 PMID:22685418 PMID:3654008 Reaxys:606623 Wikipedia:Uracil URACIL Uracil pyrimidine-2,4(1H,3H)-dione uracil chebi_ontology 2,4(1H,3H)-pyrimidinedione 2,4-Dioxopyrimidine 2,4-Pyrimidinedione U Ura Urazil CHEBI:17568 uracil Beilstein:606623 Beilstein CAS:66-22-8 ChemIDplus CAS:66-22-8 KEGG COMPOUND CAS:66-22-8 NIST Chemistry WebBook Gmelin:2896 Gmelin PMID:11279060 Europe PMC PMID:12855717 Europe PMC PMID:15274295 Europe PMC PMID:16834123 Europe PMC PMID:17439666 Europe PMC PMID:18533995 Europe PMC PMID:18815805 Europe PMC PMID:19175333 Europe PMC PMID:22020693 Europe PMC PMID:22074393 Europe PMC PMID:22120518 Europe PMC PMID:22171528 Europe PMC PMID:22237209 Europe PMC PMID:22299724 Europe PMC PMID:22356544 Europe PMC PMID:22447672 Europe PMC PMID:22483865 Europe PMC PMID:22567906 Europe PMC PMID:22685418 Europe PMC PMID:3654008 Europe PMC Reaxys:606623 Reaxys URACIL PDBeChem Uracil KEGG_COMPOUND pyrimidine-2,4(1H,3H)-dione IUPAC uracil UniProt 2,4(1H,3H)-pyrimidinedione NIST_Chemistry_WebBook 2,4-Dioxopyrimidine HMDB 2,4-Pyrimidinedione HMDB U ChEBI Ura CBN Urazil ChEBI The simplest member of the class toluenes consisting of a benzene core which bears a single methyl substituent. 0 C7H8 InChI=1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3 YXFVVABEGXRONW-UHFFFAOYSA-N 92.13842 92.06260 Cc1ccccc1 CHEBI:15248 CHEBI:27022 CHEBI:44023 CHEBI:9624 Beilstein:635760 CAS:108-88-3 DrugBank:DB01900 Gmelin:2456 KEGG:C01455 PDBeChem:MBN PMID:11182169 PMID:11314682 PMID:11846266 PMID:11991009 PMID:12062755 PMID:12213539 PMID:12237258 PMID:12784113 PMID:12876426 PMID:14512097 PMID:14559343 PMID:14605898 PMID:15015825 PMID:15019953 PMID:15119846 PMID:15193425 PMID:15542760 PMID:15567510 PMID:15695158 PMID:15796064 PMID:16316648 PMID:16348226 PMID:16601996 PMID:17145141 PMID:17175136 PMID:17497535 PMID:17725881 PMID:18397809 PMID:18832024 PMID:19261054 PMID:19384711 PMID:19429395 PMID:19635754 PMID:19765629 PMID:19825861 PMID:19928203 PMID:19969016 PMID:20347282 PMID:20837561 PMID:21430649 PMID:21655021 PMID:21731073 PMID:21802510 PMID:21840036 Reaxys:635760 UM-BBD_compID:c0114 Wikipedia:Toluene TOLUENE Toluene toluene chebi_ontology Toluen Toluol methylbenzene phenylmethane CHEBI:17578 toluene Beilstein:635760 Beilstein CAS:108-88-3 ChemIDplus CAS:108-88-3 KEGG COMPOUND CAS:108-88-3 NIST Chemistry WebBook Gmelin:2456 Gmelin PMID:11182169 Europe PMC PMID:11314682 Europe PMC PMID:11846266 Europe PMC PMID:11991009 Europe PMC PMID:12062755 Europe PMC PMID:12213539 Europe PMC PMID:12237258 Europe PMC PMID:12784113 Europe PMC PMID:12876426 Europe PMC PMID:14512097 Europe PMC PMID:14559343 Europe PMC PMID:14605898 Europe PMC PMID:15015825 Europe PMC PMID:15019953 Europe PMC PMID:15119846 Europe PMC PMID:15193425 Europe PMC PMID:15542760 Europe PMC PMID:15567510 Europe PMC PMID:15695158 Europe PMC PMID:15796064 Europe PMC PMID:16316648 Europe PMC PMID:16348226 Europe PMC PMID:16601996 Europe PMC PMID:17145141 Europe PMC PMID:17175136 Europe PMC PMID:17497535 Europe PMC PMID:17725881 Europe PMC PMID:18397809 Europe PMC PMID:18832024 Europe PMC PMID:19261054 Europe PMC PMID:19384711 Europe PMC PMID:19429395 Europe PMC PMID:19635754 Europe PMC PMID:19765629 Europe PMC PMID:19825861 Europe PMC PMID:19928203 Europe PMC PMID:19969016 Europe PMC PMID:20347282 Europe PMC PMID:20837561 Europe PMC PMID:21430649 Europe PMC PMID:21655021 Europe PMC PMID:21731073 Europe PMC PMID:21802510 Europe PMC PMID:21840036 Europe PMC Reaxys:635760 Reaxys UM-BBD_compID:c0114 UM-BBD TOLUENE PDBeChem Toluene KEGG_COMPOUND toluene ChEBI toluene IUPAC toluene UniProt Toluen NIST_Chemistry_WebBook Toluol NIST_Chemistry_WebBook methylbenzene PDBeChem phenylmethane ChemIDplus A glycosylglucose disaccharide, found most notably in milk, that consists of D-galactose and D-glucose fragments bonded through a beta-1->4 glycosidic linkage. The glucose fragment can be in either the alpha- or beta-pyranose form, whereas the galactose fragment can only have the beta-pyranose form. lactose http://langual.org 0 C12H22O11 InChI=1S/C12H22O11/c13-1-3-5(15)6(16)9(19)12(22-3)23-10-4(2-14)21-11(20)8(18)7(10)17/h3-20H,1-2H2/t3-,4-,5+,6+,7-,8-,9-,10-,11?,12+/m1/s1 GUBGYTABKSRVRQ-QKKXKWKRSA-N 342.29648 342.11621 OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO)OC(O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@H]1O CHEBI:10296 CHEBI:10380 CHEBI:14497 CHEBI:22460 CHEBI:22760 CHEBI:25005 CHEBI:27755 CHEBI:613009 Beilstein:1292745 CAS:63-42-3 GlyTouCan:G74621DY Gmelin:882872 KEGG:C00243 KEGG:D00046 KEGG:G10504 KNApSAcK:C00001136 PMID:1292745 PMID:17329833 PMID:18300214 PMID:19053747 PMID:19846069 PMID:19913595 PMID:20094999 PMID:20503067 PMID:20699559 PMID:20873837 PMID:20961532 PMID:21403918 PMID:2432147 PMID:2456994 PMID:28690131 PMID:28807538 PMID:6194884 PMID:7574700 Reaxys:1292745 http://www.langual.org/langual_thesaurus.asp?termid=C0209 beta-D-galactopyranosyl-(1->4)-D-glucopyranose lactose chebi_ontology (+)-lactose (Gal)1 (Glc)1 1-beta-D-Galactopyranosyl-4-D-glucopyranose 4-(beta-D-galactosido)-D-glucose 4-O-beta-D-galactopyranosyl-D-glucose D-lactose Galbeta1-4Glc Lac Laktobiose Laktose Milchzucker Milk sugar beta-D-Gal-(1->4)-D-Glc beta-D-Galp-(1->4)-D-Glcp beta-Gal1,4-Glc lactobiose milk sugar CHEBI:17716 LanguaL term definition: Used when lactose or a high lactose sweetener is the major ingredient. lactose Beilstein:1292745 Beilstein CAS:63-42-3 ChemIDplus CAS:63-42-3 KEGG COMPOUND CAS:63-42-3 NIST Chemistry WebBook Gmelin:882872 Gmelin PMID:1292745 Europe PMC PMID:17329833 Europe PMC PMID:18300214 Europe PMC PMID:19053747 ChEMBL PMID:19846069 Europe PMC PMID:19913595 Europe PMC PMID:20094999 Europe PMC PMID:20503067 Europe PMC PMID:20699559 Europe PMC PMID:20873837 Europe PMC PMID:20961532 Europe PMC PMID:21403918 Europe PMC PMID:2432147 Europe PMC PMID:2456994 Europe PMC PMID:28690131 Europe PMC PMID:28807538 Europe PMC PMID:6194884 Europe PMC PMID:7574700 Europe PMC Reaxys:1292745 Reaxys beta-D-galactopyranosyl-(1->4)-D-glucopyranose IUPAC lactose UniProt (+)-lactose NIST_Chemistry_WebBook (Gal)1 (Glc)1 KEGG_GLYCAN 1-beta-D-Galactopyranosyl-4-D-glucopyranose KEGG_COMPOUND 4-(beta-D-galactosido)-D-glucose NIST_Chemistry_WebBook 4-O-beta-D-galactopyranosyl-D-glucose IUPAC D-lactose ChemIDplus Galbeta1-4Glc ChEBI Lac JCBN Laktobiose ChEBI Laktose ChEBI Milchzucker ChEBI Milk sugar KEGG_COMPOUND beta-D-Gal-(1->4)-D-Glc KEGG_COMPOUND beta-D-Galp-(1->4)-D-Glcp IUPAC beta-Gal1,4-Glc ChEBI lactobiose NIST_Chemistry_WebBook milk sugar NIST_Chemistry_WebBook A triol with a structure of propane substituted at positions 1, 2 and 3 by hydroxy groups. 0 C3H8O3 InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2 PEDCQBHIVMGVHV-UHFFFAOYSA-N 92.09382 92.04734 OCC(O)CO CHEBI:131422 CHEBI:14334 CHEBI:24351 CHEBI:42998 CHEBI:5448 Beilstein:635685 CAS:56-81-5 DrugBank:DB04077 Drug_Central:1316 ECMDB:ECMDB00131 Gmelin:26279 HMDB:HMDB0000131 KEGG:C00116 KEGG:D00028 KNApSAcK:C00001163 LINCS:LSM-37180 MetaCyc:GLYCEROL PDB:2AJS PDB:2D03 PDBeChem:GOL PMID:11958517 PMID:12672239 PMID:12689633 PMID:14559393 PMID:14563847 PMID:15342117 PMID:15786693 PMID:16244855 PMID:16258193 PMID:16319039 PMID:16349488 PMID:16651733 PMID:16664750 PMID:16901854 PMID:17336832 PMID:17439666 PMID:17979222 PMID:19184438 PMID:19231894 PMID:19460032 PMID:19548674 PMID:19795216 PMID:19956799 PMID:22705534 PMID:23562176 PMID:23747440 PMID:24643482 PMID:25108762 PMID:7031247 PMID:7392035 PPDB:1317 Reaxys:635685 UM-BBD_compID:c0066 Wikipedia:Glycerol YMDB:YMDB00283 GLYCEROL Glycerol glycerol propane-1,2,3-triol chebi_ontology 1,2,3-Propanetriol 1,2,3-Trihydroxypropane Glycerin Glyceritol Glyzerin Gro Oelsuess Propanetriol Trihydroxypropane glycerine glycerol glycerolum glycyl alcohol CHEBI:17754 glycerol Beilstein:635685 Beilstein CAS:56-81-5 ChemIDplus CAS:56-81-5 KEGG COMPOUND CAS:56-81-5 NIST Chemistry WebBook Drug_Central:1316 DrugCentral Gmelin:26279 Gmelin PMID:11958517 Europe PMC PMID:12672239 ChEMBL PMID:12689633 Europe PMC PMID:14559393 Europe PMC PMID:14563847 Europe PMC PMID:15342117 Europe PMC PMID:15786693 Europe PMC PMID:16244855 Europe PMC PMID:16258193 Europe PMC PMID:16319039 Europe PMC PMID:16349488 Europe PMC PMID:16651733 Europe PMC PMID:16664750 Europe PMC PMID:16901854 Europe PMC PMID:17336832 Europe PMC PMID:17439666 Europe PMC PMID:17979222 Europe PMC PMID:19184438 Europe PMC PMID:19231894 Europe PMC PMID:19460032 Europe PMC PMID:19548674 Europe PMC PMID:19795216 Europe PMC PMID:19956799 Europe PMC PMID:22705534 Europe PMC PMID:23562176 Europe PMC PMID:23747440 Europe PMC PMID:24643482 Europe PMC PMID:25108762 Europe PMC PMID:7031247 ChEMBL PMID:7392035 ChEMBL Reaxys:635685 Reaxys UM-BBD_compID:c0066 UM-BBD GLYCEROL PDBeChem Glycerol KEGG_COMPOUND glycerol ChEBI glycerol UniProt propane-1,2,3-triol IUPAC 1,2,3-Propanetriol KEGG_COMPOUND 1,2,3-Trihydroxypropane KEGG_COMPOUND Glycerin KEGG_COMPOUND Glyceritol HMDB Glyzerin ChEBI Gro JCBN Oelsuess ChEBI Propanetriol HMDB Trihydroxypropane HMDB glycerine ChEBI glycerol ChemIDplus glycerolum ChemIDplus glycyl alcohol NIST_Chemistry_WebBook A compound showing blue fluorescence, formed by a photolysis of riboflavin in acid or neutral solution. 0 C12H10N4O2 InChI=1S/C12H10N4O2/c1-5-3-7-8(4-6(5)2)14-10-9(13-7)11(17)16-12(18)15-10/h3-4H,1-2H3,(H2,14,15,16,17,18) ZJTJUVIJVLLGSP-UHFFFAOYSA-N 242.23356 242.08038 Cc1cc2nc3[nH]c(=O)[nH]c(=O)c3nc2cc1C CHEBI:14534 CHEBI:25080 CHEBI:43772 CHEBI:6561 Beilstein:226631 CAS:1086-80-2 DrugBank:DB04345 KEGG:C01727 KNApSAcK:C00030694 MetaCyc:CPD-605 PDBeChem:LUM PMID:15819908 PMID:21126007 PMID:22953948 PMID:24001807 PMID:24451190 PMID:24643482 Reaxys:226631 7,8-dimethylbenzo[g]pteridine-2,4(1H,3H)-dione LUMICHROME Lumichrome lumichrome chebi_ontology 7,8-Dimethylalloxazine CHEBI:17781 lumichrome Beilstein:226631 Beilstein CAS:1086-80-2 ChemIDplus CAS:1086-80-2 KEGG COMPOUND CAS:1086-80-2 NIST Chemistry WebBook PMID:15819908 Europe PMC PMID:21126007 Europe PMC PMID:22953948 Europe PMC PMID:24001807 Europe PMC PMID:24451190 Europe PMC PMID:24643482 Europe PMC Reaxys:226631 Reaxys 7,8-dimethylbenzo[g]pteridine-2,4(1H,3H)-dione IUPAC LUMICHROME PDBeChem Lumichrome KEGG_COMPOUND lumichrome UniProt 7,8-Dimethylalloxazine KEGG_COMPOUND The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group. 0 CH4O InChI=1S/CH4O/c1-2/h2H,1H3 OKKJLVBELUTLKV-UHFFFAOYSA-N 32.04186 32.02621 CO CHEBI:14588 CHEBI:25227 CHEBI:44080 CHEBI:44553 CHEBI:6816 Beilstein:1098229 CAS:67-56-1 Gmelin:449 HMDB:HMDB0001875 KEGG:C00132 KEGG:D02309 MetaCyc:METOH PDBeChem:MOH PMID:11141607 PMID:11430978 PMID:11489599 PMID:11680737 PMID:11684179 PMID:14012711 PMID:14678513 PMID:14760634 PMID:15172721 PMID:15906011 PMID:16705261 PMID:17451998 PMID:17733096 PMID:19064074 PMID:19850112 PMID:20314698 Reaxys:1098229 UM-BBD_compID:c0132 Wikipedia:Methanol METHANOL Methanol methanol chebi_ontology CH3OH MeOH Methyl alcohol Methylalkohol carbinol spirit of wood wood alcohol wood naphtha wood spirit CHEBI:17790 methanol Beilstein:1098229 Beilstein CAS:67-56-1 ChemIDplus CAS:67-56-1 KEGG COMPOUND CAS:67-56-1 NIST Chemistry WebBook Gmelin:449 Gmelin PMID:11141607 Europe PMC PMID:11430978 Europe PMC PMID:11489599 Europe PMC PMID:11680737 Europe PMC PMID:11684179 Europe PMC PMID:14012711 Europe PMC PMID:14678513 Europe PMC PMID:14760634 Europe PMC PMID:15172721 Europe PMC PMID:15906011 Europe PMC PMID:16705261 Europe PMC PMID:17451998 Europe PMC PMID:17733096 Europe PMC PMID:19064074 Europe PMC PMID:19850112 Europe PMC PMID:20314698 Europe PMC Reaxys:1098229 Reaxys UM-BBD_compID:c0132 UM-BBD METHANOL PDBeChem Methanol KEGG_COMPOUND methanol IUPAC methanol UniProt CH3OH ChEBI MeOH ChEBI Methyl alcohol KEGG_COMPOUND Methylalkohol NIST_Chemistry_WebBook carbinol ChemIDplus spirit of wood HMDB wood alcohol ChemIDplus wood naphtha ChemIDplus wood spirit NIST_Chemistry_WebBook An alpha-amino acid that is alanine substituted at position 3 by a hydroxy group. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7) MTCFGRXMJLQNBG-UHFFFAOYSA-N 105.09262 105.04259 NC(CO)C(O)=O CHEBI:15081 CHEBI:26648 CHEBI:9116 Beilstein:1721402 CAS:302-84-1 Gmelin:26429 KEGG:C00716 KNApSAcK:C00001393 Reaxys:1721402 Wikipedia:Serine Serine serine chebi_ontology 2-Amino-3-hydroxypropionic acid 2-amino-3-hydroxypropanoic acid 3-Hydroxyalanine Serin CHEBI:17822 serine Beilstein:1721402 Beilstein CAS:302-84-1 ChemIDplus CAS:302-84-1 KEGG COMPOUND CAS:302-84-1 NIST Chemistry WebBook Gmelin:26429 Gmelin Reaxys:1721402 Reaxys Serine KEGG_COMPOUND serine IUPAC 2-Amino-3-hydroxypropionic acid KEGG_COMPOUND 2-amino-3-hydroxypropanoic acid IUPAC 3-Hydroxyalanine KEGG_COMPOUND Serin ChEBI Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. 0 C6H5O6R3 173.10030 173.00861 [*]C(=O)OCC(COC([*])=O)OC([*])=O CHEBI:15255 CHEBI:27085 CHEBI:9664 KEGG:C00422 LIPID_MAPS_class:LMGL0301 PMID:2474544 Triglyceride triglycerides chebi_ontology Triacylglycerol Triglycerid Triglyzerid a triacylglycerol triacylglycerols triglycerides CHEBI:17855 triglyceride LIPID_MAPS_class:LMGL0301 LIPID MAPS PMID:2474544 Europe PMC Triglyceride KEGG_COMPOUND triglycerides IUPAC Triacylglycerol KEGG_COMPOUND Triglycerid ChEBI Triglyzerid ChEBI a triacylglycerol UniProt triacylglycerols LIPID_MAPS triglycerides ChEBI A molecular entity that can transfer ("donate") an electron, a pair of electrons, an atom or a group to another molecular entity. CHEBI:14202 CHEBI:4697 KEGG:C01351 Donor chebi_ontology Donator donneur CHEBI:17891 donor Donor KEGG_COMPOUND Donator ChEBI donneur ChEBI A short-chain fatty acid anion that is the conjugate base of butyric acid, obtained by deprotonation of the carboxy group. -1 C4H7O2 InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6)/p-1 FERIUCNNQQJTOY-UHFFFAOYSA-M 87.09718 87.04515 CCCC([O-])=O CHEBI:13924 CHEBI:22946 Beilstein:3601060 CAS:461-55-2 Gmelin:324289 KEGG:C00246 MetaCyc:BUTYRIC_ACID PMID:17190852 PMID:7496326 Reaxys:3601060 UM-BBD_compID:c0035 butanoate butyrate chebi_ontology 1-butanoate 1-butyrate 1-propanecarboxylate CH3-[CH2]2-COO(-) butanate butanoate butanoic acid, ion(1-) n-butanoate n-butyrate propanecarboxylate propylformate CHEBI:17968 butyrate Beilstein:3601060 Beilstein CAS:461-55-2 ChemIDplus Gmelin:324289 Gmelin PMID:17190852 Europe PMC PMID:7496326 Europe PMC Reaxys:3601060 Reaxys UM-BBD_compID:c0035 UM-BBD butanoate IUPAC butyrate IUPAC 1-butanoate ChEBI 1-butyrate ChEBI 1-propanecarboxylate ChEBI CH3-[CH2]2-COO(-) IUPAC butanate ChEBI butanoate ChEBI butanoate UniProt butanoic acid, ion(1-) ChemIDplus n-butanoate ChEBI n-butyrate ChemIDplus propanecarboxylate ChEBI propylformate ChEBI A glycosyl glycoside formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose. 0 C12H22O11 InChI=1S/C12H22O11/c13-1-4-6(16)8(18)9(19)11(21-4)23-12(3-15)10(20)7(17)5(2-14)22-12/h4-11,13-20H,1-3H2/t4-,5-,6-,7-,8+,9-,10+,11-,12+/m1/s1 CZMRCDWAGMRECN-UGDNZRGBSA-N 342.29650 342.11621 OC[C@H]1O[C@H](O[C@]2(CO)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@H](O)[C@@H](O)[C@@H]1O CHEBI:15128 CHEBI:26812 CHEBI:45795 CHEBI:9314 Beilstein:90825 CAS:57-50-1 DrugBank:DB02772 Drug_Central:4610 Gmelin:97695 HMDB:HMDB0000258 KEGG:C00089 KEGG:D00025 KEGG:D06533 KEGG:G00370 KNApSAcK:C00001151 MetaCyc:SUCROSE PDBeChem:SUC PMID:11021636 PMID:11093712 PMID:11111003 PMID:12065720 PMID:12706980 PMID:13508893 PMID:15291457 PMID:15660210 PMID:15792978 PMID:15845855 PMID:16228482 PMID:16304615 PMID:16313996 PMID:16525719 PMID:16660545 PMID:16663947 PMID:16665852 PMID:17233733 PMID:17439666 PMID:17597061 PMID:18625236 PMID:19199566 PMID:19726178 PMID:21703290 PMID:21972845 PMID:22085755 PMID:22311778 PMID:22404833 PMID:22751876 Reaxys:1435311 Reaxys:90825 SUBSET_SIREN:F15176 Wikipedia:Sucrose http://www.langual.org/langual_thesaurus.asp?termid=C0210 http://www.langual.org/langual_thesaurus.asp?termid=H0136 http://www.langual.org/langual_thesaurus.asp?termid=H0158 SUCROSE Sucrose beta-D-fructofuranosyl alpha-D-glucopyranoside sucrose chebi_ontology 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside Cane sugar Saccharose Sacharose White sugar beta-D-Fruf-(2<->1)-alpha-D-Glcp sacarosa table sugar CHEBI:17992 subset_siren LanguaL term definition: Used when sucrose (e.g., cane sugar or beet sugar) is the major ingredient. Note: on a product label or in a recipe, 'sugar' means sucrose. sucrose Beilstein:90825 Beilstein CAS:57-50-1 ChemIDplus CAS:57-50-1 KEGG COMPOUND CAS:57-50-1 NIST Chemistry WebBook Drug_Central:4610 DrugCentral Gmelin:97695 Gmelin PMID:11021636 Europe PMC PMID:11093712 Europe PMC PMID:11111003 Europe PMC PMID:12065720 Europe PMC PMID:12706980 Europe PMC PMID:13508893 Europe PMC PMID:15291457 Europe PMC PMID:15660210 Europe PMC PMID:15792978 Europe PMC PMID:15845855 Europe PMC PMID:16228482 Europe PMC PMID:16304615 Europe PMC PMID:16313996 Europe PMC PMID:16525719 Europe PMC PMID:16660545 Europe PMC PMID:16663947 Europe PMC PMID:16665852 Europe PMC PMID:17233733 Europe PMC PMID:17439666 Europe PMC PMID:17597061 Europe PMC PMID:18625236 Europe PMC PMID:19199566 Europe PMC PMID:19726178 Europe PMC PMID:21703290 Europe PMC PMID:21972845 Europe PMC PMID:22085755 Europe PMC PMID:22311778 Europe PMC PMID:22404833 Europe PMC PMID:22751876 Europe PMC Reaxys:1435311 Reaxys Reaxys:90825 Reaxys SUCROSE PDBeChem Sucrose KEGG_COMPOUND beta-D-fructofuranosyl alpha-D-glucopyranoside IUPAC sucrose UniProt 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside KEGG_COMPOUND Cane sugar KEGG_COMPOUND Saccharose KEGG_COMPOUND Sacharose ChEBI White sugar HMDB beta-D-Fruf-(2<->1)-alpha-D-Glcp JCBN sacarosa ChEBI table sugar ChemIDplus 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. CHEBI:14517 CHEBI:25054 CHEBI:6486 KEGG:C01356 Lipid lipids chebi_ontology CHEBI:18059 lipid Lipid KEGG_COMPOUND lipids IUPAC Any six-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldohexose) or a ketone group at position 2 (ketohexose). CHEBI:14399 CHEBI:24590 CHEBI:5709 GlyTouCan:G70994MS KEGG:C00738 Hexose chebi_ontology WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/ hexoses CHEBI:18133 hexose Hexose KEGG_COMPOUND WURCS=2.0/1,1,0/[axxxxh-1x_1-5_2*NCC/3=O]/1/ GlyTouCan hexoses ChEBI A tertiary amine that is ammonia in which each hydrogen atom is substituted by an methyl group. 0 C3H9N InChI=1S/C3H9N/c1-4(2)3/h1-3H3 GETQZCLCWQTVFV-UHFFFAOYSA-N 59.11030 59.07350 CN(C)C CHEBI:15261 CHEBI:27125 CHEBI:27127 CHEBI:9732 Beilstein:956566 CAS:75-50-3 Gmelin:1309 HMDB:HMDB0000906 KEGG:C00565 KNApSAcK:C00001433 MetaCyc:TRIMETHYLAMINE PDBeChem:KEN PMID:14047118 PMID:15304308 PMID:15752091 PMID:17190852 PMID:1801314 PMID:24591617 PMID:2501587 PMID:5161463 Reaxys:956566 Wikipedia:Trimethylamine N,N-dimethylmethanamine Trimethylamine chebi_ontology (CH3)3N N(CH3)3 N,N,N-trimethylamine N,N-Dimethylmethanamine NMe3 TMA Trimethylamin tridimethylaminomethane CHEBI:18139 trimethylamine Beilstein:956566 Beilstein CAS:75-50-3 ChemIDplus CAS:75-50-3 KEGG COMPOUND CAS:75-50-3 NIST Chemistry WebBook Gmelin:1309 Gmelin PMID:14047118 Europe PMC PMID:15304308 Europe PMC PMID:15752091 Europe PMC PMID:17190852 Europe PMC PMID:1801314 Europe PMC PMID:24591617 Europe PMC PMID:2501587 Europe PMC PMID:5161463 Europe PMC Reaxys:956566 Reaxys N,N-dimethylmethanamine IUPAC Trimethylamine KEGG_COMPOUND (CH3)3N KEGG_COMPOUND N(CH3)3 ChEBI N,N,N-trimethylamine ChEBI N,N-Dimethylmethanamine KEGG_COMPOUND NMe3 ChEBI TMA NIST_Chemistry_WebBook Trimethylamin ChEBI tridimethylaminomethane ChEBI 0 HX 1.008 1.00783 [F,Cl,Br,I] CHEBI:13368 CHEBI:37140 CHEBI:5599 hydrogen halide hydrogen halides chebi_ontology HX hydrogen halides CHEBI:18140 hydrogen halide hydrogen halide IUPAC hydrogen halides IUPAC HX UniProt hydrogen halides ChEBI An alpha-amino acid that is phenylalanine bearing a hydroxy substituent at position 4 on the phenyl ring. 0 C9H11NO3 InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13) OUYCCCASQSFEME-UHFFFAOYSA-N 181.18858 181.07389 NC(Cc1ccc(O)cc1)C(O)=O CHEBI:15277 CHEBI:27176 CHEBI:9800 Beilstein:515881 CAS:55520-40-6 CAS:556-03-6 Gmelin:27744 KEGG:C01536 KNApSAcK:C00001397 PMID:17190852 Reaxys:515881 Tyrosine tyrosine chebi_ontology 2-Amino-3-(p-hydroxyphenyl)propionic acid 2-amino-3-(4-hydroxyphenyl)propanoic acid 3-(p-Hydroxyphenyl)alanine Tyr Tyrosin Y tirosina CHEBI:18186 tyrosine Beilstein:515881 Beilstein CAS:55520-40-6 ChemIDplus CAS:556-03-6 KEGG COMPOUND Gmelin:27744 Gmelin PMID:17190852 Europe PMC Reaxys:515881 Reaxys Tyrosine KEGG_COMPOUND tyrosine IUPAC 2-Amino-3-(p-hydroxyphenyl)propionic acid KEGG_COMPOUND 2-amino-3-(4-hydroxyphenyl)propanoic acid IUPAC 3-(p-Hydroxyphenyl)alanine KEGG_COMPOUND Tyr ChEBI Tyrosin ChEBI Y ChEBI tirosina ChEBI The parent compound of the citrulline class consisting of ornithine having a carbamoyl group at the N(5)-position. 0 C6H13N3O3 InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12) RHGKLRLOHDJJDR-UHFFFAOYSA-N 175.18584 175.09569 NC(CCCNC(N)=O)C(O)=O CHEBI:14002 CHEBI:3730 Beilstein:1725417 Beilstein:2328251 CAS:627-77-0 PMID:11094453 PMID:11113071 PMID:11696417 PMID:1378088 PMID:16082501 PMID:16708633 PMID:17005970 PMID:17513438 PMID:17558653 PMID:17693747 PMID:18437289 PMID:18440672 PMID:18989563 PMID:19144577 PMID:21129371 PMID:21482070 Reaxys:1725417 Wikipedia:Citrulline 2-amino-5-(carbamoylamino)pentanoic acid Citrulline N(5)-carbamoylornithine citrulline chebi_ontology 2-Amino-5-uredovaleric acid Cit Citrullin DL-2-amino-5-ureidovaleric acid N(5)-(aminocarbonyl)-DL-ornithine N(5)-(aminocarbonyl)ornithine N(5)-carbamoyl-DL-ornithine citrulina dl-citrulline CHEBI:18211 citrulline Beilstein:1725417 Beilstein Beilstein:2328251 Beilstein CAS:627-77-0 ChemIDplus CAS:627-77-0 NIST Chemistry WebBook PMID:11094453 Europe PMC PMID:11113071 Europe PMC PMID:11696417 Europe PMC PMID:1378088 Europe PMC PMID:16082501 Europe PMC PMID:16708633 Europe PMC PMID:17005970 Europe PMC PMID:17513438 Europe PMC PMID:17558653 Europe PMC PMID:17693747 Europe PMC PMID:18437289 Europe PMC PMID:18440672 Europe PMC PMID:18989563 Europe PMC PMID:19144577 Europe PMC PMID:21129371 Europe PMC PMID:21482070 Europe PMC Reaxys:1725417 Reaxys 2-amino-5-(carbamoylamino)pentanoic acid IUPAC Citrulline KEGG_COMPOUND N(5)-carbamoylornithine IUPAC citrulline IUPAC 2-Amino-5-uredovaleric acid KEGG_COMPOUND Cit IUPAC Citrullin ChEBI DL-2-amino-5-ureidovaleric acid ChemIDplus N(5)-(aminocarbonyl)-DL-ornithine NIST_Chemistry_WebBook N(5)-(aminocarbonyl)ornithine ChEBI N(5)-carbamoyl-DL-ornithine NIST_Chemistry_WebBook citrulina ChEBI dl-citrulline NIST_Chemistry_WebBook An alpha-amino acid that is glutaric acid bearing a single amino substituent at position 2. 0 C5H9NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10) WHUUTDBJXJRKMK-UHFFFAOYSA-N 147.12930 147.05316 NC(CCC(O)=O)C(O)=O CHEBI:24314 CHEBI:5431 Beilstein:1723799 CAS:617-65-2 Gmelin:101971 KEGG:C00302 KEGG:D04341 KNApSAcK:C00001358 KNApSAcK:C00019577 PMID:15739367 PMID:17190852 PMID:24616376 PMID:24984001 Reaxys:1723799 Wikipedia:Glutamic_acid 2-aminopentanedioic acid Glutamic acid glutamic acid chebi_ontology 2-Aminoglutaric acid DL-Glutamic acid DL-Glutaminic acid E Glu Glutamate Glutaminic acid Glutaminsaeure CHEBI:18237 glutamic acid Beilstein:1723799 Beilstein CAS:617-65-2 ChemIDplus CAS:617-65-2 KEGG COMPOUND CAS:617-65-2 NIST Chemistry WebBook Gmelin:101971 Gmelin PMID:15739367 Europe PMC PMID:17190852 Europe PMC PMID:24616376 Europe PMC PMID:24984001 Europe PMC Reaxys:1723799 Reaxys 2-aminopentanedioic acid IUPAC Glutamic acid KEGG_COMPOUND glutamic acid IUPAC 2-Aminoglutaric acid KEGG_COMPOUND DL-Glutamic acid KEGG_DRUG DL-Glutaminic acid KEGG_COMPOUND E ChEBI Glu ChEBI Glutamate KEGG_COMPOUND Glutaminic acid KEGG_COMPOUND Glutaminsaeure ChEBI An iron group element atom that has atomic number 26. 0 Fe InChI=1S/Fe XEEYBQQBJWHFJM-UHFFFAOYSA-N 55.84500 55.93494 [Fe] CHEBI:13322 CHEBI:24872 CHEBI:5974 CAS:7439-89-6 DrugBank:DB01592 HMDB:HMDB0015531 KEGG:C00023 Reaxys:4122945 WebElements:Fe iron chebi_ontology 26Fe Eisen Fe Iron fer ferrum hierro iron CHEBI:18248 iron atom CAS:7439-89-6 ChemIDplus CAS:7439-89-6 KEGG COMPOUND CAS:7439-89-6 NIST Chemistry WebBook Reaxys:4122945 Reaxys iron IUPAC 26Fe IUPAC Eisen ChEBI Fe IUPAC Iron KEGG_COMPOUND fer ChEBI ferrum IUPAC hierro ChEBI iron ChEBI Any nucleoside where the sugar component is D-ribose. 0 C5H9O4R 133.123 133.05008 OC[C@H]1O[C@@H]([*])[C@H](O)[C@@H]1O CHEBI:13014 CHEBI:13015 CHEBI:13685 CHEBI:21085 CHEBI:26560 CHEBI:4240 CHEBI:8844 KEGG:C00911 Ribonucleoside chebi_ontology a ribonucleoside ribonucleosides CHEBI:18254 ribonucleoside Ribonucleoside KEGG_COMPOUND a ribonucleoside UniProt ribonucleosides ChEBI An alpha-amino acid that is pentanoic acid bearing two amino substituents at positions 2 and 5. 0 C5H12N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9) AHLPHDHHMVZTML-UHFFFAOYSA-N 132.16106 132.08988 NCCCC(N)C(O)=O CHEBI:7784 Beilstein:1722296 CAS:616-07-9 Gmelin:847696 KEGG:C01602 KNApSAcK:C00001384 PMID:15449570 PMID:17190852 PMID:22264337 Reaxys:1722296 2,5-diaminopentanoic acid Ornithine ornithine chebi_ontology 2,5-Diaminopentanoic acid 2,5-Diaminovaleric acid DL-Ornithine Orn CHEBI:18257 ornithine Beilstein:1722296 Beilstein CAS:616-07-9 ChemIDplus Gmelin:847696 Gmelin PMID:15449570 Europe PMC PMID:17190852 Europe PMC PMID:22264337 Europe PMC Reaxys:1722296 Reaxys 2,5-diaminopentanoic acid IUPAC Ornithine KEGG_COMPOUND ornithine IUPAC 2,5-Diaminopentanoic acid KEGG_COMPOUND 2,5-Diaminovaleric acid KEGG_COMPOUND DL-Ornithine ChemIDplus Orn IUPAC That part of DNA or RNA that may be involved in pairing. CHEBI:13873 CHEBI:25598 CHEBI:2995 KEGG:C00701 Wikipedia:Nucleobase chebi_ontology Base nucleobases CHEBI:18282 nucleobase Base KEGG_COMPOUND nucleobases ChEBI An acyclic branched or unbranched hydrocarbon having the general formula CnH2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms. 0 CH3R 15.035 15.02348 C[*] CHEBI:13435 CHEBI:22317 CHEBI:2576 KEGG:C01371 Alkane alkane alkanes chebi_ontology Alkan RH alcane alcanes alcano alcanos an alkane CHEBI:18310 alkane Alkane KEGG_COMPOUND alkane IUPAC alkanes IUPAC Alkan ChEBI RH KEGG_COMPOUND alcane IUPAC alcanes IUPAC alcano IUPAC alcanos IUPAC an alkane UniProt A phosphate ion that is the conjugate base of hydrogenphosphate. -3 O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3 NBIIXXVUZAFLBC-UHFFFAOYSA-K 94.97136 94.95507 [O-]P([O-])([O-])=O CHEBI:14791 CHEBI:45024 CHEBI:7793 Beilstein:3903772 CAS:14265-44-2 Gmelin:1997 KEGG:C00009 PDBeChem:PO4 Reaxys:3903772 phosphate tetraoxidophosphate(3-) tetraoxophosphate(3-) tetraoxophosphate(V) chebi_ontology Orthophosphate PHOSPHATE ION PO4(3-) Phosphate [PO4](3-) CHEBI:18367 phosphate(3-) Beilstein:3903772 Beilstein CAS:14265-44-2 ChemIDplus CAS:14265-44-2 KEGG COMPOUND Gmelin:1997 Gmelin PDBeChem:PO4 ChEBI Reaxys:3903772 Reaxys phosphate IUPAC tetraoxidophosphate(3-) IUPAC tetraoxophosphate(3-) IUPAC tetraoxophosphate(V) IUPAC Orthophosphate KEGG_COMPOUND PHOSPHATE ION PDBeChem PO4(3-) IUPAC Phosphate KEGG_COMPOUND [PO4](3-) IUPAC 0 C24H42 InChI=1S/C24H42/c1-5-8-17(2)20-12-13-21-19-11-10-18-9-6-7-15-23(18,3)22(19)14-16-24(20,21)4/h17-22H,5-16H2,1-4H3/t17-,18+,19+,20-,21+,22+,23+,24-/m1/s1 QSHQKIURKJITMZ-OBUPQJQESA-N 330.59028 330.32865 [H][C@@]12CCCC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])CC2)[C@H](C)CCC Beilstein:2048472 5beta-cholane chebi_ontology CHEBI:20664 5beta-cholane Beilstein:2048472 Beilstein 5beta-cholane IUPAC vitamin C role vitamin C An N-acetyl-amino acid having D-configuration. CHEBI:7109 KEGG:C03135 chebi_ontology N-Acetyl-D-amino-acid N-acetyl-D-amino acids CHEBI:21501 N-acetyl-D-amino acid N-Acetyl-D-amino-acid KEGG_COMPOUND N-acetyl-D-amino acids ChEBI An L-amino acid having an N-acetyl substituent. chebi_ontology CHEBI:21545 N-acetyl-L-amino acid An N-acyl-amino acid that has acetyl as the acyl group. CHEBI:7105 KEGG:C02847 chebi_ontology N-Acetyl amino acid N-acetyl-amino acids CHEBI:21575 N-acetyl-amino acid N-Acetyl amino acid KEGG_COMPOUND N-acetyl-amino acids ChEBI Any N-acylamino acid having L-configuration. chebi_ontology CHEBI:21644 N-acyl-L-amino acid A glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond. glycosylamine chebi_ontology N-glycoside N-glycosides N-glycosyl compounds glycosylamines CHEBI:21731 N-glycosyl compound glycosylamine IUPAC N-glycoside ChEBI N-glycosides ChEBI N-glycosyl compounds ChEBI glycosylamines IUPAC Compounds with the general formula RNHC(=O)CH3. chebi_ontology CHEBI:22160 acetamides Any amino acid derivative that is the N-acetyl or O-acetyl derivative of an amino acid. chebi_ontology acetyl-amino acids CHEBI:22195 acetyl-amino acid acetyl-amino acids ChEBI chebi_ontology CHEBI:22198 acetylcysteine An organic group formed by removing one or more hydroxy groups from an oxoacid that has the general structure RkE(=O)l(OH)m (l =/= 0). Although the term is almost always applied to organic compounds, with carboxylic acid as the oxoacid, acyl groups can in principle be derived from other types of acids such as sulfonic acids or phosphonic acids. acyl group alkanoyl chebi_ontology acyl groups alkanoyl group groupe acyle CHEBI:22221 acyl group acyl group IUPAC alkanoyl IUPAC acyl groups ChEBI alkanoyl group ChEBI groupe acyle IUPAC alkaline earth metals chebi_ontology Erdalkalimetall Erdalkalimetalle alkaline earth metal alkaline-earth metal alkaline-earth metals metal alcalino-terreux metal alcalinoterreo metales alcalinoterreos metaux alcalino-terreux CHEBI:22313 alkaline earth metal atom alkaline earth metals IUPAC Erdalkalimetall ChEBI Erdalkalimetalle ChEBI alkaline earth metal ChEBI alkaline-earth metal ChEBI alkaline-earth metals ChEBI metal alcalino-terreux ChEBI metal alcalinoterreo ChEBI metales alcalinoterreos ChEBI metaux alcalino-terreux ChEBI alkali metals chebi_ontology Alkalimetall Alkalimetalle alkali metal metal alcalin metal alcalino metales alcalinos metaux alcalins CHEBI:22314 alkali metal atom alkali metals IUPAC Alkalimetall ChEBI Alkalimetalle ChEBI alkali metal ChEBI metal alcalin ChEBI metal alcalino ChEBI metales alcalinos ChEBI metaux alcalins ChEBI Any of the naturally occurring, basic nitrogen compounds (mostly heterocyclic) occurring mostly in the plant kingdom, but also found in bacteria, fungi, and animals. By extension, certain neutral compounds biogenetically related to basic alkaloids are also classed as alkaloids. Amino acids, peptides, proteins, nucleotides, nucleic acids, amino sugars and antibiotics are not normally regarded as alkaloids. Compounds in which the nitrogen is exocyclic (dopamine, mescaline, serotonin, etc.) are usually classed as amines rather than alkaloids. Wikipedia:Alkaloid Alkaloid alkaloids chebi_ontology Alkaloide alcaloide alcaloides CHEBI:22315 alkaloid Alkaloid ChEBI alkaloids IUPAC Alkaloide ChEBI alcaloide ChEBI alcaloides ChEBI A univalent group -CnH2n+1 derived from an alkane by removal of a hydrogen atom from any carbon atom. alkyl group alkyl groups chebi_ontology groupe alkyle grupo alquilo grupos alquilo CHEBI:22323 alkyl group alkyl group IUPAC alkyl groups IUPAC groupe alkyle IUPAC grupo alquilo IUPAC grupos alquilo IUPAC Any amine formally derived from ammonia by replacing one, two or three hydrogen atoms by alkyl groups. chebi_ontology CHEBI:22331 alkylamines Highly reactive chemical that introduces alkyl radicals into biologically active molecules and thereby prevents their proper functioning. It could be used as an antineoplastic agent, but it might be very toxic, with carcinogenic, mutagenic, teratogenic, and immunosuppressant actions. It could also be used as a component of poison gases. chebi_ontology CHEBI:22333 alkylating agent chebi_ontology aminobenzoates CHEBI:22494 aminobenzoate aminobenzoates ChEBI A monoatomic or polyatomic species having one or more elementary charges of the electron. Anion anion chebi_ontology Anionen aniones anions CHEBI:22563 anion Anion ChEBI anion ChEBI anion IUPAC Anionen ChEBI aniones ChEBI anions IUPAC A substance that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. chebi_ontology antioxidants antioxydant antoxidant CHEBI:22586 antioxidant antioxidants ChEBI antioxydant ChEBI antoxidant ChEBI A substance that destroys or inhibits replication of viruses. chebi_ontology anti-viral agent anti-viral agents antiviral antiviral agents antivirals CHEBI:22587 antiviral agent anti-viral agent ChEBI anti-viral agents ChEBI antiviral ChEBI antiviral agents ChEBI antivirals ChEBI A ketoaldonate that is the conjugate base of ascorbic acid. chebi_ontology CHEBI:22651 ascorbate ascorbic acid http://langual.org Codex::300 Europe::300 http://www.langual.org/langual_thesaurus.asp?termid=B3005 vitamin c chebi_ontology ascorbic acid, l- l-ascorbic acid CHEBI:22652 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): acidity regulator, antioxidant, flour treatment agent. ascorbic acid An L-alpha-amino acid which is L-aspartic acid or any of the essential amino acids biosynthesised from it (asparagine, lysine, methionine, threonine and isoleucine). A closed class. PMID:4386082 PMID:4394351 PMID:4721772 PMID:5016260 PMID:5074276 chebi_ontology aspartate family amino acids aspartic acid family amino acid aspartic acid family amino acids oxaloacetate family amino acid oxaloacetate family amino acids oxaloacetate/aspartate family amino acid oxaloacetate/aspartate family amino acids CHEBI:22658 aspartate family amino acid PMID:4386082 Europe PMC PMID:4394351 Europe PMC PMID:4721772 Europe PMC PMID:5016260 Europe PMC PMID:5074276 Europe PMC aspartate family amino acids ChEBI aspartic acid family amino acid ChEBI aspartic acid family amino acids ChEBI oxaloacetate family amino acid ChEBI oxaloacetate family amino acids ChEBI oxaloacetate/aspartate family amino acid ChEBI oxaloacetate/aspartate family amino acids ChEBI A molecular entity having an available pair of electrons capable of forming a covalent bond with a hydron (Bronsted base) or with the vacant orbital of some other molecular entity (Lewis base). KEGG:C00701 Base base chebi_ontology Base1 Base2 Basen Nucleobase bases CHEBI:22695 base Base ChEBI base ChEBI base IUPAC Base1 KEGG_COMPOUND Base2 KEGG_COMPOUND Basen ChEBI Nucleobase KEGG_COMPOUND bases ChEBI Any benzenoid aromatic compound consisting of the benzene skeleton and its substituted derivatives. chebi_ontology CHEBI:22712 benzenes A monocarboxylic acid anion obtained by deprotonation of the carboxy group of any benzoic acid. chebi_ontology benzoate anion CHEBI:22718 benzoates benzoate anion ChEBI Any quinone resulting from the formal oxidation of catechol, hydroquinone, or their C-substituted derivatives. chebi_ontology CHEBI:22729 benzoquinones 0 C7H7 91.13048 91.05478 C1=C(C=CC=C1)C* benzyl chebi_ontology Bn C6H5-CH2- phenylalanine side-chain phenylmethyl CHEBI:22744 benzyl group benzyl IUPAC Bn ChEBI C6H5-CH2- IUPAC phenylalanine side-chain ChEBI phenylmethyl IUPAC Any amino acid-derived zwitterion - such as glycine betaine (N,N,N-trimethylammonioacetate) - in which the ammonium nitrogen carries three methyl substituents. chebi_ontology amino acid betaines amino-acid betaines betaines CHEBI:22860 amino-acid betaine amino acid betaines ChEBI amino-acid betaines ChEBI betaines ChEBI Any amino acid in which the parent hydrocarbon chain has one or more alkyl substituents chebi_ontology branched chain amino acids CHEBI:22918 branched-chain amino acid branched chain amino acids ChEBI 0 Ca InChI=1S/Ca OYPRJOBELJOOCE-UHFFFAOYSA-N 40.07800 39.96259 [Ca] CAS:7440-70-2 DrugBank:DB01373 KEGG:C00076 WebElements:Ca calcium chebi_ontology 20Ca Ca Calcium Kalzium calcio calcium CHEBI:22984 calcium atom CAS:7440-70-2 ChemIDplus calcium IUPAC 20Ca IUPAC Ca IUPAC Calcium KEGG_COMPOUND Kalzium ChEBI calcio ChEBI calcium ChEBI calcium molecular entity chebi_ontology calcium compounds calcium molecular entities CHEBI:22985 calcium molecular entity calcium molecular entity ChEBI calcium compounds ChEBI calcium molecular entities ChEBI The univalent carboacyl group formed by loss of -OH from the carboxy group of carbamic acid. 0 CH2NO 44.03272 44.01364 *C(N)=O PMID:24168430 carbamoyl chebi_ontology -C(O)NH2 -CONH2 aminocarbonyl carbamyl carbamyl group carboxamide CHEBI:23004 carbamoyl group PMID:24168430 Europe PMC carbamoyl IUPAC -C(O)NH2 ChEBI -CONH2 IUPAC aminocarbonyl IUPAC carbamyl ChEBI carbamyl group ChEBI carboxamide IUPAC Organooxygen compounds that are salts or esters of carbonic acid, H2CO3. chebi_ontology CHEBI:23016 carbonates 0 CO 28.01010 27.99491 O=C(*)* carbonyl carbonyl group chebi_ontology >C=O CHEBI:23019 carbonyl group carbonyl IUPAC carbonyl group ChEBI carbonyl group UniProt >C=O IUPAC Hydrocarbon carotenoids. carotene carotenes chebi_ontology carotenes CHEBI:23042 carotene carotene ChEBI carotenes IUPAC carotenes ChEBI One of a class of tetraterpenoids (C40), formally derived from the acyclic parent, psi,psi-carotene by hydrogenation, dehydrogenation, cyclization, oxidation, or combination of these processes. This class includes carotenes, xanthophylls and certain compounds that arise from rearrangement of the skeleton of psi,psi-carotene or by loss of part of this structure. Retinoids are excluded. CAS:36-88-4 carotenoid chebi_ontology carotenes and carotenoids carotenoids CHEBI:23044 carotenoid CAS:36-88-4 ChemIDplus carotenoid IUPAC carotenes and carotenoids ChemIDplus carotenoids ChEBI chebi_ontology carotenols hydroxycarotenoids CHEBI:23045 carotenol carotenols ChEBI hydroxycarotenoids ChEBI A class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. 0 C7H5NO3SR2 183.18500 182.99901 [H][C@]12SCC([*])=C(N1C(=O)[C@H]2[*])C(O)=O CHEBI:3538 KEGG:C00875 PMID:10069359 PMID:11936371 PMID:12833570 PMID:24269048 PMID:3320614 PMID:6762896 PMID:8426246 Wikipedia:Cephalosporin Cephalosporin chebi_ontology cephalosphorin cephalosphorins cephalosporins CHEBI:23066 cephalosporin PMID:10069359 Europe PMC PMID:11936371 Europe PMC PMID:12833570 Europe PMC PMID:24269048 Europe PMC PMID:3320614 Europe PMC PMID:6762896 Europe PMC PMID:8426246 Europe PMC Cephalosporin KEGG_COMPOUND cephalosphorin ChEBI cephalosphorins ChEBI cephalosporins ChEBI A quaternary ammonium ion based on the choline ion and its substituted derivatives thereof. chebi_ontology CHEBI:23217 cholines chebi_ontology CHEBI:23324 citrullines chebi_ontology CHEBI:23333 cob(III)alamins chebi_ontology CHEBI:23334 cobalamins chebi_ontology CHEBI:23341 cobamides A low-molecular-weight, non-protein organic compound participating in enzymatic reactions as dissociable acceptor or donor of chemical groups or electrons. coenzyme chebi_ontology coenzymes CHEBI:23354 coenzyme coenzyme IUPAC coenzymes ChEBI An organic molecule or ion (usually a metal ion) that is required by an enzyme for its activity. It may be attached either loosely (coenzyme) or tightly (prosthetic group). Wikipedia:Cofactor_(biochemistry) cofactor cofactors chebi_ontology CHEBI:23357 cofactor cofactor IUPAC cofactors IUPAC molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. fake:2 molecular entity IUPAC entidad molecular IUPAC entidades moleculares IUPAC entite moleculaire IUPAC molecular entities IUPAC molekulare Entitaet ChEBI chebi_ontology CHEBI:23390 cobalt-corrinoid hexaamide CHEBI:3990 cyclic amide chebi_ontology cyclic amides CHEBI:23443 cyclic amide cyclic amide ChEBI cyclic amides ChEBI An amino acid derivative resulting from reaction of cysteine at the amino group, carboxy group, or thiol group, or from the replacement of any hydrogen of cysteine by a heteroatom. The definition normally excludes peptides containing cysteine residues. cysteine derivative chebi_ontology CHEBI:23509 cysteine derivative cysteine derivative ChEBI A hydroxy-5beta-cholanic acid carrying two hydroxy groups at unspecified positions. 0 C24H40O4 392.573 392.29266 chebi_ontology dihydroxy-5beta-cholanic acids CHEBI:23775 dihydroxy-5beta-cholanic acid dihydroxy-5beta-cholanic acids ChEBI Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. chebi_ontology drugs medicine CHEBI:23888 drug drugs ChEBI medicine ChEBI chebi_ontology monoatomic anions CHEBI:23905 monoatomic anion monoatomic anions ChEBI chebi_ontology monoatomic cations CHEBI:23906 monoatomic cation monoatomic cations ChEBI A compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. enzyme inhibitor chebi_ontology enzyme inhibitors inhibidor enzimatico inhibidores enzimaticos inhibiteur enzymatique inhibiteurs enzymatiques CHEBI:23924 enzyme inhibitor enzyme inhibitor IUPAC enzyme inhibitors ChEBI inhibidor enzimatico ChEBI inhibidores enzimaticos ChEBI inhibiteur enzymatique ChEBI inhibiteurs enzymatiques ChEBI Vitamins like A, D, E and K that dissolve in fats and are stored in body tissues. Unlike the water-soluble vitamins, these are stored in the body for long periods of time and generally pose a greater risk for toxicity when consumed in excess. chebi_ontology fat-soluble vitamins fettloesliche Vitamine CHEBI:24020 fat-soluble vitamin fat-soluble vitamins ChEBI fettloesliche Vitamine ChEBI Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. chebi_ontology glucocorticoids CHEBI:24261 glucocorticoid glucocorticoids ChEBI An amino acid derivative resulting from reaction of glutamic acid at the amino group or either of the carboxy groups, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing glutamic acid residues. chebi_ontology CHEBI:24315 glutamic acid derivative An L-alpha-amino acid which is L-glutamic acid or any of the essential amino acids biosynthesised from it (glutamine, proline and arginine). A closed class. PMID:20716061 chebi_ontology glutamine family amino acids CHEBI:24318 glutamine family amino acid PMID:20716061 Europe PMC glutamine family amino acids ChEBI An EC 6.3.* (C-N bond-forming ligase) inhibitor that interferes with the action of glutamate--ammonia ligase (EC 6.3.1.2). Wikipedia:Glutamine_synthetase chebi_ontology EC 6.3.1.2 (glutamate--ammonia ligase) inhibitors EC 6.3.1.2 inhibitor EC 6.3.1.2 inhibitors L-glutamate:ammonia ligase (ADP-forming) inhibitor L-glutamate:ammonia ligase (ADP-forming) inhibitors L-glutamine synthetase inhibitor L-glutamine synthetase inhibitors glutamate--ammonia ligase (EC 6.3.1.2) inhibitor glutamate--ammonia ligase (EC 6.3.1.2) inhibitors glutamate--ammonia ligase inhibitor glutamate--ammonia ligase inhibitors glutamine synthetase inhibitor glutamine synthetase inhibitors glutamylhydroxamic synthetase inhibitor glutamylhydroxamic synthetase inhibitors CHEBI:24319 EC 6.3.1.2 (glutamate--ammonia ligase) inhibitor EC 6.3.1.2 (glutamate--ammonia ligase) inhibitors ChEBI EC 6.3.1.2 inhibitor ChEBI EC 6.3.1.2 inhibitors ChEBI L-glutamate:ammonia ligase (ADP-forming) inhibitor ChEBI L-glutamate:ammonia ligase (ADP-forming) inhibitors ChEBI L-glutamine synthetase inhibitor ChEBI L-glutamine synthetase inhibitors ChEBI glutamate--ammonia ligase (EC 6.3.1.2) inhibitor ChEBI glutamate--ammonia ligase (EC 6.3.1.2) inhibitors ChEBI glutamate--ammonia ligase inhibitor ChEBI glutamate--ammonia ligase inhibitors ChEBI glutamine synthetase inhibitor ChEBI glutamine synthetase inhibitors ChEBI glutamylhydroxamic synthetase inhibitor ChEBI glutamylhydroxamic synthetase inhibitors ChEBI A proteinogenic amino acid derivative resulting from reaction of glycine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. chebi_ontology CHEBI:24373 glycine derivative chebi_ontology glycosylglucoses CHEBI:24405 glycosylglucose glycosylglucoses ChEBI Any disaccharide in which the two monosaccharide components are connected by a glycosidic linkage between their anomeric centres. glycosyl glycoside chebi_ontology glycosyl glycosides CHEBI:24407 glycosyl glycoside glycosyl glycoside ChEBI glycosyl glycosides ChEBI A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity chemical entity UniProt A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function CHEBI:24432 biological role biological function ChEBI A defined linked collection of atoms or a single atom within a molecular entity. group chebi_ontology Gruppe Rest groupe grupo grupos CHEBI:24433 group group IUPAC Gruppe ChEBI Rest ChEBI groupe IUPAC grupo IUPAC grupos IUPAC Any organonitrogen compound containing a carbamimidamido (guanidino) group. Guanidines have the general structure (R(1)R(2)N)(R(3)R(4)N)C=N-R(5) and are related structurally to amidines and ureas. chebi_ontology CHEBI:24436 guanidines chebi_ontology CHEBI:24531 heterocyclic antibiotic A cyclic compound having as ring members atoms of carbon and at least of one other element. chebi_ontology organic heterocycle organic heterocyclic compounds CHEBI:24532 organic heterocyclic compound organic heterocycle ChEBI organic heterocyclic compounds ChEBI Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. chebi_ontology endocrine hormones CHEBI:24621 hormone endocrine ChEBI hormones ChEBI A compound consisting of carbon and hydrogen only. hydrocarbon hydrocarbons chebi_ontology Kohlenwasserstoff Kohlenwasserstoffe hidrocarburo hidrocarburos hydrocarbure CHEBI:24632 hydrocarbon hydrocarbon IUPAC hydrocarbons IUPAC Kohlenwasserstoff ChEBI Kohlenwasserstoffe ChEBI hidrocarburo IUPAC hidrocarburos IUPAC hydrocarbure IUPAC Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)). chebi_ontology CHEBI:24651 hydroxides Any member of the class of 5beta-cholanic acids carrying at least one hydroxy group at unspecified position. chebi_ontology hydroxy-5beta-cholanic acids CHEBI:24663 hydroxy-5beta-cholanic acid hydroxy-5beta-cholanic acids ChEBI Any carboxylic acid with at least one hydroxy group. chebi_ontology hydroxy carboxylic acids hydroxycarboxylic acid hydroxycarboxylic acids CHEBI:24669 hydroxy carboxylic acid hydroxy carboxylic acids ChEBI hydroxycarboxylic acid ChEBI hydroxycarboxylic acids ChEBI 0 CH3O 31.03392 31.01839 C(*)O hydroxymethyl chebi_ontology -CH3-OH serine side-chain CHEBI:24712 hydroxymethyl group hydroxymethyl IUPAC -CH3-OH IUPAC serine side-chain ChEBI Any member of the class of pyridines with at least one hydroxy substituent. chebi_ontology hydroxypyridines CHEBI:24745 hydroxypyridine hydroxypyridines ChEBI A compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). oxoacid oxoacids chebi_ontology oxacids oxiacids oxo acid oxy-acids oxyacids CHEBI:24833 oxoacid oxoacid IUPAC oxoacids IUPAC oxacids ChEBI oxiacids ChEBI oxo acid ChEBI oxy-acids ChEBI oxyacids ChEBI chebi_ontology inorganic anions CHEBI:24834 inorganic anion inorganic anions ChEBI A molecular entity that contains no carbon. chebi_ontology anorganische Verbindungen inorganic compounds inorganic entity inorganic molecular entities inorganics CHEBI:24835 inorganic molecular entity anorganische Verbindungen ChEBI inorganic compounds ChEBI inorganic entity ChEBI inorganic molecular entities ChEBI inorganics ChEBI chebi_ontology inorganic oxides CHEBI:24836 inorganic oxide inorganic oxides ChEBI A salt is an assembly of cations and anions. salt chebi_ontology Salz Salze ionic compound ionic compounds sal sales salts sel sels CHEBI:24866 salt salt IUPAC Salz ChEBI Salze ChEBI ionic compound ChEBI ionic compounds ChEBI sal ChEBI sales ChEBI salts ChEBI sel ChEBI sels ChEBI chebi_ontology monoatomic ions CHEBI:24867 monoatomic ion monoatomic ions ChEBI chebi_ontology organic salts organisches Salz CHEBI:24868 organic salt organic salts ChEBI organisches Salz ChEBI A molecular entity having a net electric charge. Ion ion chebi_ontology Ionen iones ions CHEBI:24870 ion Ion ChEBI ion ChEBI ion IUPAC Ionen ChEBI iones ChEBI ions ChEBI iron molecular entity chebi_ontology iron compounds iron molecular entities CHEBI:24873 iron molecular entity iron molecular entity ChEBI iron compounds ChEBI iron molecular entities ChEBI Fe 55.845 55.93494 iron cation chebi_ontology Fe cation iron cations CHEBI:24875 iron cation iron cation IUPAC Fe cation UniProt iron cations ChEBI A 2-amino-3-methylpentanoic acid having either (2R,3R)- or (2S,3S)-configuration. Beilstein:1721790 CAS:443-79-8 PMID:17190852 Reaxys:1721790 isoleucine chebi_ontology Hile rel-(2R,3R)-2-amino-3-methylpentanoic acid CHEBI:24898 isoleucine Beilstein:1721790 Beilstein CAS:443-79-8 ChemIDplus CAS:443-79-8 NIST Chemistry WebBook PMID:17190852 Europe PMC Reaxys:1721790 Reaxys isoleucine IUPAC Hile IUPAC rel-(2R,3R)-2-amino-3-methylpentanoic acid IUPAC Any lipid formally derived from isoprene (2-methylbuta-1,3-diene), the skeleton of which can generally be discerned in repeated occurrence in the molecule. The skeleton of isoprenoids may differ from strict additivity of isoprene units by loss or shift of a fragment, commonly a methyl group. The class includes both hydrocarbons and oxygenated derivatives. LIPID_MAPS_class:LMPR01 PMID:12769708 PMID:19219049 isoprenoid isoprenoids chebi_ontology isoprenoids CHEBI:24913 isoprenoid LIPID_MAPS_class:LMPR01 LIPID MAPS PMID:12769708 Europe PMC PMID:19219049 Europe PMC isoprenoid ChEBI isoprenoids IUPAC isoprenoids ChEBI ketoaldonate chebi_ontology ketoaldonates CHEBI:24961 ketoaldonate ketoaldonate ChEBI ketoaldonates ChEBI Oxo carboxylic acids formally derived from aldonic acids by replacement of a secondary CHOH group by a carbonyl group. ketoaldonic acid chebi_ontology ketoaldonic acids CHEBI:24963 ketoaldonic acid ketoaldonic acid ChEBI ketoaldonic acids ChEBI Any hexose containing a single ketone group. ketohexose chebi_ontology ketohexoses CHEBI:24973 ketohexose ketohexose ChEBI ketohexoses ChEBI Ketonic parent sugars (polyhydroxy ketones H[CH(OH)]nC(=O)[CH(OH)]mH) and their intramolecular hemiketals. CHEBI:6131 ketose chebi_ontology ketoses CHEBI:24978 ketose ketose ChEBI ketoses ChEBI Cyclic amides of amino carboxylic acids, having a 1-azacycloalkan-2-one structure, or analogues having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. lactam lactams chebi_ontology Laktam Laktame lactams CHEBI:24995 lactam lactam IUPAC lactams IUPAC Laktam ChEBI Laktame ChEBI lactams ChEBI Any cyclic carboxylic ester containing a 1-oxacycloalkan-2-one structure, or an analogue having unsaturation or heteroatoms replacing one or more carbon atoms of the ring. lactone lactones chebi_ontology Lacton Lakton Laktone lactona lactonas CHEBI:25000 lactone lactone IUPAC lactones IUPAC Lacton ChEBI Lakton ChEBI Laktone ChEBI lactona IUPAC lactonas IUPAC A branched-chain amino acid that consists of glycine in which one of the hydrogens attached to the alpha-carbon is substituted by an isobutyl group. 0 C6H13NO2 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9) ROHFNLRQFUQHCH-UHFFFAOYSA-N 131.17296 131.09463 CC(C)CC(N)C(O)=O Beilstein:636005 CAS:328-39-2 Gmelin:50203 KEGG:C16439 LIPID_MAPS_instance:LMFA01100048 PMID:17439666 Reaxys:636005 Wikipedia:Leucine leucine chebi_ontology (+-)-Leucine (RS)-Leucine 2-amino-4-methylpentanoic acid DL-Leucine Hleu L Leu Leucin Leuzin CHEBI:25017 leucine Beilstein:636005 Beilstein CAS:328-39-2 ChemIDplus CAS:328-39-2 NIST Chemistry WebBook Gmelin:50203 Gmelin LIPID_MAPS_instance:LMFA01100048 LIPID MAPS PMID:17439666 Europe PMC Reaxys:636005 Reaxys leucine IUPAC (+-)-Leucine ChemIDplus (RS)-Leucine ChemIDplus 2-amino-4-methylpentanoic acid IUPAC DL-Leucine ChemIDplus Hleu IUPAC L ChEBI Leu ChEBI Leucin ChEBI Leuzin ChEBI A diamino acid that is caproic (hexanoic) acid bearing two amino substituents at positions 2 and 6. 0 C6H14N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10) KDXKERNSBIXSRK-UHFFFAOYSA-N 146.18764 146.10553 NCCCCC(N)C(O)=O Beilstein:1616991 CAS:70-54-2 Gmelin:279284 KEGG:C16440 PMID:17439666 PMID:22264337 Reaxys:1616991 Wikipedia:Lysine 2,6-diaminohexanoic acid lysine chebi_ontology K LYS Lysin alpha,epsilon-diaminocaproic acid CHEBI:25094 lysine Beilstein:1616991 Beilstein CAS:70-54-2 ChemIDplus CAS:70-54-2 NIST Chemistry WebBook Gmelin:279284 Gmelin PMID:17439666 Europe PMC PMID:22264337 Europe PMC Reaxys:1616991 Reaxys 2,6-diaminohexanoic acid IUPAC lysine IUPAC K ChEBI LYS ChEBI Lysin ChEBI alpha,epsilon-diaminocaproic acid ChEBI A macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity. chebi_ontology Makrolidantibiotika macrolide antibiotics CHEBI:25105 macrolide antibiotic Makrolidantibiotika ChEBI macrolide antibiotics ChEBI A macrocyclic lactone with a ring of twelve or more members derived from a polyketide. Wikipedia:Macrolide macrolide macrolides chebi_ontology Makrolid macrolides CHEBI:25106 macrolide macrolide ChEBI macrolides IUPAC Makrolid ChEBI macrolides ChEBI 0 Mg InChI=1S/Mg FYYHWMGAXLPEAU-UHFFFAOYSA-N 24.30500 23.98504 [Mg] CAS:7439-95-4 DrugBank:DB01378 Gmelin:16207 KEGG:C00305 WebElements:Mg magnesium chebi_ontology 12Mg Magnesium Mg magnesio magnesium CHEBI:25107 magnesium atom CAS:7439-95-4 ChemIDplus Gmelin:16207 Gmelin magnesium IUPAC 12Mg IUPAC Magnesium ChEBI Mg IUPAC magnesio ChEBI magnesium ChEBI Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. CHEBI:26619 CHEBI:35220 metabolite chebi_ontology metabolites primary metabolites secondary metabolites CHEBI:25212 metabolite metabolite IUPAC metabolites ChEBI primary metabolites ChEBI secondary metabolites ChEBI chebi_ontology a metal cation metal cations CHEBI:25213 metal cation a metal cation UniProt metal cations ChEBI chebi_ontology methylated amines CHEBI:25274 methylamines methylated amines ChEBI Any member of the class of pyridines that carries at least one methyl substituent. chebi_ontology CHEBI:25340 methylpyridines Any polyatomic entity that is an electrically neutral entity consisting of more than one atom. molecule chebi_ontology Molekuel molecula molecules neutral molecular compounds CHEBI:25367 molecule molecule IUPAC Molekuel ChEBI molecula IUPAC molecules IUPAC neutral molecular compounds IUPAC An oxoacid containing a single carboxy group. chebi_ontology monocarboxylic acids CHEBI:25384 monocarboxylic acid monocarboxylic acids ChEBI +1 0.00000 [*+] chebi_ontology monoatomic monocations monovalent inorganic cations CHEBI:25414 monoatomic monocation monoatomic monocations ChEBI monovalent inorganic cations ChEBI An agent that increases the frequency of mutations above the normal background level, usually by interacting directly with DNA and causing it damage, including base substitution. Wikipedia:Mutagen chebi_ontology mutagene mutagenes mutagenic agent mutageno mutagenos mutagens CHEBI:25435 mutagen mutagene ChEBI mutagenes ChEBI mutagenic agent ChEBI mutageno ChEBI mutagenos ChEBI mutagens ChEBI An endogenous compound that is used to transmit information across the synapse between a neuron and another cell. Wikipedia:Neurotransmitter chebi_ontology neurotransmitters CHEBI:25512 neurotransmitter neurotransmitters ChEBI 0 N 14.007 14.00307 WebElements:N nitrogen chebi_ontology 7N N Stickstoff azote nitrogen nitrogeno CHEBI:25555 nitrogen atom nitrogen IUPAC 7N IUPAC N IUPAC Stickstoff ChEBI azote IUPAC nitrogen ChEBI nitrogeno ChEBI chebi_ontology organonitrogen heterocyclic antibiotics CHEBI:25558 organonitrogen heterocyclic antibiotic organonitrogen heterocyclic antibiotics ChEBI nonmetal chebi_ontology Nichtmetall Nichtmetalle no metal no metales non-metal non-metaux nonmetal nonmetals CHEBI:25585 nonmetal atom nonmetal IUPAC Nichtmetall ChEBI Nichtmetalle ChEBI no metal ChEBI no metales ChEBI non-metal ChEBI non-metaux ChEBI nonmetal ChEBI nonmetals ChEBI A family of polyunsaturated fatty acids that have in common a final carbon-carbon double bond in the omega-3 position, i.e., the third bond from the methyl end of the fatty acid. PMID:15129302 PMID:15253883 PMID:15555528 PMID:16741195 PMID:19154523 PMID:19439966 PMID:21975796 PMID:23643471 PMID:24012777 PMID:24122252 PMID:24128563 PMID:24172034 PMID:24211484 PMID:24240437 PMID:24246761 PMID:24281905 PMID:24397938 PMID:24401220 PMID:24418228 Wikipedia:Omega-3_fatty_acid omega-3 fatty acid chebi_ontology n-3 fatty acid n-3 fatty acids omega-3 fatty acids CHEBI:25681 omega-3 fatty acid PMID:15129302 Europe PMC PMID:15253883 Europe PMC PMID:15555528 Europe PMC PMID:16741195 Europe PMC PMID:19154523 Europe PMC PMID:19439966 Europe PMC PMID:21975796 Europe PMC PMID:23643471 Europe PMC PMID:24012777 Europe PMC PMID:24122252 Europe PMC PMID:24128563 Europe PMC PMID:24172034 Europe PMC PMID:24211484 Europe PMC PMID:24240437 Europe PMC PMID:24246761 Europe PMC PMID:24281905 Europe PMC PMID:24397938 Europe PMC PMID:24401220 Europe PMC PMID:24418228 Europe PMC omega-3 fatty acid ChEBI n-3 fatty acid ChEBI n-3 fatty acids ChEBI omega-3 fatty acids ChEBI chebi_ontology organic heteromonocyclic compounds CHEBI:25693 organic heteromonocyclic compound organic heteromonocyclic compounds ChEBI Any organic ion with a net negative charge. chebi_ontology organic anions CHEBI:25696 organic anion organic anions ChEBI Any organic ion with a net positive charge. chebi_ontology organic cations CHEBI:25697 organic cation organic cations ChEBI chebi_ontology organic ions CHEBI:25699 organic ion organic ions ChEBI An alcohol derived from an aliphatic compound. 0 HOR 17.007 17.00274 O* KEGG:C02525 Aliphatic alcohol chebi_ontology aliphatic alcohols an aliphatic alcohol CHEBI:2571 aliphatic alcohol Aliphatic alcohol KEGG_COMPOUND aliphatic alcohols ChEBI an aliphatic alcohol UniProt A solute used by a cell under water stress to maintain cell volume. chebi_ontology osmolytes CHEBI:25728 osmolyte osmolytes ChEBI An oxide is a chemical compound of oxygen with other chemical elements. oxide chebi_ontology oxides CHEBI:25741 oxide oxide ChEBI oxides ChEBI Any compound that has an aldehydic or ketonic group as well as a carboxylic acid group in the same molecule. oxo carboxylic acids chebi_ontology oxo acids oxo carboxylic acids CHEBI:25754 oxo carboxylic acid oxo carboxylic acids IUPAC oxo acids IUPAC oxo carboxylic acids ChEBI Any fatty acid anion containing at least one C-C unsaturated bond; formed by deprotonation of the carboxylic acid moiety. chebi_ontology CHEBI:2580 unsaturated fatty acid anion 0 O InChI=1S/O QVGXLLKOCUKJST-UHFFFAOYSA-N 15.99940 15.99491 [O] KEGG:C00007 WebElements:O oxygen chebi_ontology 8O O Sauerstoff oxigeno oxygen oxygene CHEBI:25805 oxygen atom oxygen IUPAC 8O IUPAC O IUPAC Sauerstoff ChEBI oxigeno ChEBI oxygen ChEBI oxygene ChEBI oxygen molecular entity chebi_ontology oxygen molecular entities CHEBI:25806 oxygen molecular entity oxygen molecular entity ChEBI oxygen molecular entities ChEBI A quinone in which the two oxo groups of the quinone are located para to each other on the 6-membered quinonoid ring. chebi_ontology p-quinone para-quinones CHEBI:25830 p-quinones p-quinone ChEBI para-quinones ChEBI chebi_ontology CHEBI:25865 penicillanic acids A five-carbon monosaccharide which in its linear form contains either an aldehyde group at position 1 (aldopentose) or a ketone group at position 2 (ketopentose). pentose chebi_ontology pentoses CHEBI:25901 pentose pentose ChEBI pentoses ChEBI Salts and esters of phosphoric and oligophosphoric acids and their chalcogen analogues. In inorganic chemistry, the term is also used to describe anionic coordination entities with phosphorus as central atom. phosphates chebi_ontology phosphates CHEBI:26020 phosphate phosphates IUPAC phosphates ChEBI A phosphorus oxoacid that consists of one oxo and three hydroxy groups joined covalently to a central phosphorus atom. 0 H3O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N 97.99520 97.97690 [H]OP(=O)(O[H])O[H] Beilstein:1921286 CAS:7664-38-2 Drug_Central:4478 Gmelin:2000 HMDB:HMDB0002142 KEGG:C00009 KEGG:D05467 KNApSAcK:C00007408 PMID:11455380 PMID:15630224 PMID:17439666 PMID:17518491 PMID:22282755 PMID:22333268 PMID:22381614 PMID:22401268 Reaxys:1921286 Wikipedia:Phosphoric_Acid Phosphoric acid phosphoric acid tetraoxophosphoric acid trihydrogen tetraoxophosphate(3-) trihydroxidooxidophosphorus chebi_ontology H3PO4 Orthophosphoric acid Phosphate Phosphorsaeure Phosphorsaeureloesungen [PO(OH)3] acide phosphorique acidum phosphoricum orthophosphoric acid CHEBI:26078 phosphoric acid Beilstein:1921286 Beilstein CAS:7664-38-2 ChemIDplus CAS:7664-38-2 KEGG COMPOUND CAS:7664-38-2 NIST Chemistry WebBook Drug_Central:4478 DrugCentral Gmelin:2000 Gmelin PMID:11455380 Europe PMC PMID:15630224 Europe PMC PMID:17439666 Europe PMC PMID:17518491 Europe PMC PMID:22282755 Europe PMC PMID:22333268 Europe PMC PMID:22381614 Europe PMC PMID:22401268 Europe PMC Reaxys:1921286 Reaxys Phosphoric acid KEGG_COMPOUND phosphoric acid IUPAC tetraoxophosphoric acid IUPAC trihydrogen tetraoxophosphate(3-) IUPAC trihydroxidooxidophosphorus IUPAC H3PO4 IUPAC Orthophosphoric acid KEGG_COMPOUND Phosphate KEGG_COMPOUND Phosphorsaeure ChEBI Phosphorsaeureloesungen ChEBI [PO(OH)3] IUPAC acide phosphorique ChEBI acidum phosphoricum ChEBI orthophosphoric acid NIST_Chemistry_WebBook chebi_ontology CHEBI:26079 phosphoric acid derivative chebi_ontology phosphorus molecular entities CHEBI:26082 phosphorus molecular entity phosphorus molecular entities ChEBI Any amino acid whose side chain is capable of forming one or more hydrogen bonds. 0 C2H4NO2R 74.059 74.02420 OC(C(*)N)=O CHEBI:8283 MetaCyc:Polar-amino-acids PMID:12016058 polar amino acid chebi_ontology polar amino acids polar amino-acid polar amino-acids CHEBI:26167 polar amino acid PMID:12016058 Europe PMC polar amino acid ChEBI polar amino acids ChEBI polar amino-acid ChEBI polar amino-acids ChEBI Natural and synthetic compounds containing alternating carbonyl and methylene groups ('beta-polyketones'), biogenetically derived from repeated condensation of acetyl coenzyme A (via malonyl coenzyme A), and usually the compounds derived from them by further condensations, etc. Considered by many to be synonymous with the less frequently used terms acetogenins and ketides. polyketide chebi_ontology polyketides CHEBI:26188 polyketide polyketide ChEBI polyketides ChEBI A compound that contains two or more hydroxy groups. chebi_ontology polyols CHEBI:26191 polyol polyols ChEBI Any fatty acid containing more than one double bond. Acids in this group are reported to have cardioprotective effects; and levels are lowered in chronic fatigue syndrome. PMID:14977874 PMID:16380690 PMID:17891522 chebi_ontology PUFA PUFAs polyunsaturated fatty acids CHEBI:26208 polyunsaturated fatty acid PMID:14977874 Europe PMC PMID:16380690 Europe PMC PMID:17891522 Europe PMC PUFA ChEBI PUFAs ChEBI polyunsaturated fatty acids ChEBI 0 K InChI=1S/K ZLMJMSJWJFRBEC-UHFFFAOYSA-N 39.09830 38.96371 [K] CAS:7440-09-7 DrugBank:DB01345 KEGG:C00238 WebElements:K potassium chebi_ontology 19K K Kalium kalium potasio potassium CHEBI:26216 potassium atom CAS:7440-09-7 ChemIDplus potassium IUPAC 19K IUPAC K IUPAC Kalium ChemIDplus kalium IUPAC potasio ChEBI potassium ChEBI potassium molecular entity chebi_ontology potassium molecular entities CHEBI:26217 potassium molecular entity potassium molecular entity ChEBI potassium molecular entities ChEBI A quinone substituted by a polyprenyl-derived side-chain. Prenylquinones occur in all living cells. Due to their amphiphilic character, they are mainly located in biological membranes where they function as electron and proton carriers in the photosynthetic and respiratory electron transport chains. Some prenylquinones also perform more specialised roles sucy as antioxidants and enzyme cofactors. Prenylquinones are classified according to ring structure: the main classes are menaquinones, phylloquinones, ubiquinones and plastoquinones. CHEBI:72751 PMID:19928587 PMID:21777468 PMID:21844348 PMID:22371323 PMID:3985624 chebi_ontology polyprenylquinone polyprenylquinones prenylquinones CHEBI:26255 prenylquinone PMID:19928587 Europe PMC PMID:21777468 Europe PMC PMID:21844348 Europe PMC PMID:22371323 Europe PMC PMID:3985624 Europe PMC polyprenylquinone ChEBI polyprenylquinones ChEBI prenylquinones ChEBI A tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity. prosthetic group chebi_ontology groupe prosthetique prosthetic groups CHEBI:26348 prosthetic group prosthetic group IUPAC groupe prosthetique IUPAC prosthetic groups ChEBI chebi_ontology CHEBI:26373 pteridines chebi_ontology CHEBI:26375 pterins A class of imidazopyrimidines that consists of purine and its substituted derivatives. 0 C5N4R7 116.080 116.01230 CHEBI:13678 chebi_ontology CHEBI:26401 purines chebi_ontology pyridine alkaloids CHEBI:26416 pyridine alkaloid pyridine alkaloids ChEBI A monocarboxylic acid in which the carboxy group is attached to a pyridine (or substituted pyridine) ring. chebi_ontology pyridinemonocarboxylic acids CHEBI:26420 pyridinemonocarboxylic acid pyridinemonocarboxylic acids ChEBI Any organonitrogen heterocyclic compound based on a pyridine skeleton and its substituted derivatives. chebi_ontology CHEBI:26421 pyridines A nucleobase whose skeleton is derived from pyrimidine. 0 C4HN2R4 77.064 77.01397 N1C(=C(C(=NC1=*)*)*)* pyrimidine nucleobase chebi_ontology a pyrimidine nucleobase pyrimidine bases pyrimidine nucleobases CHEBI:26432 pyrimidine nucleobase pyrimidine nucleobase ChEBI a pyrimidine nucleobase UniProt pyrimidine bases ChEBI pyrimidine nucleobases ChEBI KEGG:C03169 chebi_ontology N-D-Ribosylpyrimidine pyrimidine nucleosides CHEBI:26440 pyrimidine nucleoside N-D-Ribosylpyrimidine KEGG_COMPOUND pyrimidine nucleosides ChEBI A nitrogen molecular entity that is electronically neutral but which contains a quaternary nitrogen. chebi_ontology CHEBI:26469 quaternary nitrogen compound Any fatty acid containing no carbon to carbon multiple bonds. Known to produce adverse biological effects when ingested to excess. PMID:16492686 PMID:19763019 PMID:20237329 saturated fatty acid chebi_ontology SFA SFAs saturated fatty acids CHEBI:26607 saturated fatty acid PMID:16492686 Europe PMC PMID:19763019 Europe PMC PMID:20237329 Europe PMC saturated fatty acid ChEBI SFA ChEBI SFAs ChEBI saturated fatty acids ChEBI An L-alpha-amino acid which is biosynthesised from 3-phosphoglycerate (i.e. serine, glycine, cysteine and homocysteine). A closed class. PMID:20709681 chebi_ontology 3-phosphoglycerate family amino acid 3-phosphoglycerate family amino acids serine family amino acids CHEBI:26650 serine family amino acid PMID:20709681 Europe PMC 3-phosphoglycerate family amino acid ChEBI 3-phosphoglycerate family amino acids ChEBI serine family amino acids ChEBI An aliphatic monocarboxylic acid with a chain length of less than C6. If any non-hydrocarbon substituent is present, the compound is not normally regarded as a short-chain fatty acid. 0 CH2OR 45.017 44.99765 OC([*])=O PMID:16633129 PMID:16870803 PMID:18203540 PMID:20148677 chebi_ontology SCFA SCFAs short-chain fatty acids CHEBI:26666 short-chain fatty acid PMID:16633129 Europe PMC PMID:16870803 Europe PMC PMID:18203540 Europe PMC PMID:20148677 Europe PMC SCFA ChEBI SCFAs ChEBI short-chain fatty acids ChEBI 0 Na InChI=1S/Na KEAYESYHFKHZAL-UHFFFAOYSA-N 22.98977 22.98977 [Na] CAS:7440-23-5 Gmelin:16221 KEGG:C01330 WebElements:Na sodium chebi_ontology 11Na Na Natrium natrium sodio sodium CHEBI:26708 sodium atom CAS:7440-23-5 ChemIDplus Gmelin:16221 Gmelin sodium IUPAC 11Na IUPAC Na IUPAC Natrium ChemIDplus natrium IUPAC sodio ChemIDplus sodium ChEBI chebi_ontology sodium compounds sodium molecular entities CHEBI:26712 sodium molecular entity sodium compounds ChEBI sodium molecular entities ChEBI Any alkali metal salt having sodium(1+) as the cation. chebi_ontology Natriumsalz Natriumsalze sodium salts CHEBI:26714 sodium salt Natriumsalz ChEBI Natriumsalze ChEBI sodium salts ChEBI Any steroid that acts as hormone. chebi_ontology Steroidhormon Steroidhormone hormona esteroide hormonas esteroideas hormone steroide hormones steroides steroid hormones CHEBI:26764 steroid hormone Steroidhormon ChEBI Steroidhormone ChEBI hormona esteroide ChEBI hormonas esteroideas ChEBI hormone steroide ChEBI hormones steroides ChEBI steroid hormones ChEBI chebi_ontology CHEBI:26830 sulfonium compound 0 S InChI=1S/S NINIDFKCEFEMDL-UHFFFAOYSA-N 32.06600 31.97207 [S] CAS:7704-34-9 KEGG:C00087 KEGG:D06527 PPDB:605 WebElements:S sulfur chebi_ontology 16S Elemental sulfur S Schwefel azufre soufre sulfur sulphur theion CHEBI:26833 sulfur atom CAS:7704-34-9 ChemIDplus CAS:7704-34-9 NIST Chemistry WebBook sulfur IUPAC 16S IUPAC Elemental sulfur KEGG_COMPOUND S IUPAC S KEGG_COMPOUND Schwefel ChEBI azufre ChEBI soufre ChEBI sulfur ChEBI sulfur UniProt sulphur ChEBI theion IUPAC chebi_ontology sulfur-containing amino acids CHEBI:26834 sulfur-containing amino acid sulfur-containing amino acids ChEBI sulfur molecular entity chebi_ontology sulfur molecular entities CHEBI:26835 sulfur molecular entity sulfur molecular entity ChEBI sulfur molecular entities ChEBI Any isoprenoid that is a natural product or related compound formally derived from isoprene units. Terpenoids may contain oxygen in various functional groups. This class is subdivided according to the number of carbon atoms in the parent terpene. The skeleton of terpenoids may differ from strict additivity of isoprene units by the loss or shift of a fragment, generally a methyl group. Wikipedia:Terpenoid Terpenoid terpenoids chebi_ontology terpenoide terpenoides CHEBI:26873 terpenoid Terpenoid ChEBI terpenoids IUPAC terpenoide IUPAC terpenoides IUPAC A tertiary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has three other carbon atoms attached to it. 0 C4H7OR3 71.09780 71.04969 OC(C[*])(C[*])C[*] tertiary alcohol chebi_ontology tertiary alcohols CHEBI:26878 tertiary alcohol tertiary alcohol ChEBI tertiary alcohols ChEBI A subclass of polyketides having an octahydrotetracene-2-carboxamide skeleton, substituted with many hydroxy and other groups. chebi_ontology CHEBI:26895 tetracyclines Any oxacycle having an oxolane (tetrahydrofuran) skeleton. chebi_ontology CHEBI:26912 oxolanes A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. tetrapyrrole tetrapyrroles chebi_ontology a tetrapyrrole CHEBI:26932 tetrapyrrole tetrapyrrole IUPAC tetrapyrroles IUPAC a tetrapyrrole UniProt Any terpenoid derived from a tetraterpene. The term includes compounds in which the C40 skeleton of the parent tetraterpene has been rearranged or modified by the removal of one or more skeletal atoms (generally methyl groups). LIPID_MAPS_class:LMPR0107 tetraterpenoids chebi_ontology C40 isoprenoids tetraterpenoides CHEBI:26935 tetraterpenoid LIPID_MAPS_class:LMPR0107 LIPID MAPS tetraterpenoids IUPAC C40 isoprenoids LIPID_MAPS tetraterpenoides ChEBI http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3755 vitamin b1 chebi_ontology thiamines CHEBI:26948 thiamine thiamines ChEBI An organic tricyclic compound in which at least one of the rings of the tricyclic skeleton contains one or more heteroatoms. chebi_ontology heterotricyclic compounds organic heterotricyclic compounds CHEBI:26979 organic heterotricyclic compound heterotricyclic compounds ChEBI organic heterotricyclic compounds ChEBI Any member of the class of benzenes that is a substituted benzene in which the substituents include one (and only one) methyl group. chebi_ontology CHEBI:27024 toluenes micronutrient role Any nutrient required in small quantities by organisms throughout their life in order to orchestrate a range of physiological functions. Wikipedia:Micronutrient chebi_ontology micronutrients trace elements CHEBI:27027 micronutrient micronutrients ChEBI trace elements ChEBI An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell. transition element chebi_ontology Uebergangselement Uebergangsmetalle metal de transicion metal de transition metales de transicion metaux de transition transition element transition elements transition metal transition metals CHEBI:27081 transition element atom transition element IUPAC Uebergangselement ChEBI Uebergangsmetalle ChEBI metal de transicion ChEBI metal de transition ChEBI metales de transicion ChEBI metaux de transition ChEBI transition element ChEBI transition elements ChEBI transition metal ChEBI transition metals ChEBI A chemical compound containing three hydroxy groups. chebi_ontology triols CHEBI:27136 triol triols ChEBI chebi_ontology heterobicyclic compounds organic heterobicyclic compounds CHEBI:27171 organic heterobicyclic compound heterobicyclic compounds ChEBI organic heterobicyclic compounds ChEBI A univalent carboacyl group is a group formed by loss of OH from the carboxy group of a carboxylic acid. chebi_ontology univalent acyl group univalent carboacyl groups univalent carboxylic acyl groups CHEBI:27207 univalent carboacyl group univalent acyl group ChEBI univalent carboacyl groups ChEBI univalent carboxylic acyl groups ChEBI Any fatty acid containing at least one C=C or C#C bond. LIPID_MAPS_class:LMFA0103 PMID:5322381 chebi_ontology alkene acid olefinic acid unsaturated fatty acids CHEBI:27208 unsaturated fatty acid LIPID_MAPS_class:LMFA0103 LIPID MAPS PMID:5322381 Europe PMC alkene acid ChEBI olefinic acid ChEBI unsaturated fatty acids ChEBI unsaturated fatty acids LIPID_MAPS chebi_ontology CHEBI:27242 uridines A branched-chain amino acid that consists of glycine in which one of the hydrogens attached to the alpha-carbon is substituted by an isopropyl group. 0 C5H11NO2 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8) KZSNJWFQEVHDMF-UHFFFAOYSA-N 117.14638 117.07898 CC(C)C(N)C(O)=O Beilstein:506689 CAS:516-06-3 Gmelin:49877 KEGG:C16436 PMID:17190852 PMID:22770225 Reaxys:506689 Wikipedia:Valine valine chebi_ontology 2-amino-3-methylbutanoic acid DL-valine Hval Valin valina CHEBI:27266 valine Beilstein:506689 Beilstein CAS:516-06-3 ChemIDplus CAS:516-06-3 KEGG COMPOUND CAS:516-06-3 NIST Chemistry WebBook Gmelin:49877 Gmelin PMID:17190852 Europe PMC PMID:22770225 Europe PMC Reaxys:506689 Reaxys valine IUPAC 2-amino-3-methylbutanoic acid IUPAC DL-valine ChEBI Hval IUPAC Valin ChEBI valina ChEBI Vitamin D is a group of fat-soluble prohormones, which can be obtained from sun exposure, food and supplements. Vitamin D is biologically inactive and converted into the biologically active calcitriol via double hydroxylation in the body. vitamin d http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3752 chebi_ontology D vitamins CHEBI:27300 vitamin D D vitamins ChEBI vitamin b6 http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3759 Vitamin B6 chebi_ontology vitamin B-6 vitamina B6 vitamine B6 CHEBI:27306 vitamin B6 Vitamin B6 ChEBI vitamin B-6 JCBN vitamina B6 ChEBI vitamine B6 ChEBI water-soluble vitamin role chebi_ontology wasserloesliche Vitamine water-soluble vitamins CHEBI:27314 water-soluble vitamin wasserloesliche Vitamine ChEBI water-soluble vitamins ChEBI A subclass of carotenoids consisting of the oxygenated carotenes. DrugBank:DB00137 xanthophylls chebi_ontology xanthophylls CHEBI:27325 xanthophyll xanthophylls IUPAC xanthophylls ChEBI 0 Zn InChI=1S/Zn HCHKCACWOHOZIP-UHFFFAOYSA-N 65.39000 63.92914 [Zn] CAS:7440-66-6 Gmelin:16321 KEGG:C00038 PDBeChem:ZN WebElements:Zn zinc chebi_ontology 30Zn Zink Zn Zn(II) Zn2+ cinc zinc zincum CHEBI:27363 zinc atom CAS:7440-66-6 ChemIDplus CAS:7440-66-6 KEGG COMPOUND Gmelin:16321 Gmelin zinc IUPAC 30Zn IUPAC Zink ChEBI Zn IUPAC Zn(II) KEGG_COMPOUND Zn2+ KEGG_COMPOUND cinc ChEBI zinc ChEBI zincum ChEBI chebi_ontology zinc compounds zinc molecular entities CHEBI:27364 zinc molecular entity zinc compounds ChEBI zinc molecular entities ChEBI A neutral compound having formal unit electrical charges of opposite sign on non-adjacent atoms. Sometimes referred to as inner salts, dipolar ions (a misnomer). zwitterion zwitterions chebi_ontology compose zwitterionique compuestos zwitterionicos zwitteriones zwitterionic compounds CHEBI:27369 zwitterion zwitterion IUPAC zwitterions IUPAC compose zwitterionique IUPAC compuestos zwitterionicos IUPAC zwitteriones IUPAC zwitterionic compounds IUPAC An N-acyl-amino acid that is a form of the water-soluble vitamin B9. Its biologically active forms (tetrahydrofolate and others) are essential for nucleotide biosynthesis and homocysteine remethylation. folic acid http://langual.org 0 C19H19N7O6 InChI=1S/C19H19N7O6/c20-19-25-15-14(17(30)26-19)23-11(8-22-15)7-21-10-3-1-9(2-4-10)16(29)24-12(18(31)32)5-6-13(27)28/h1-4,8,12,21H,5-7H2,(H,24,29)(H,27,28)(H,31,32)(H3,20,22,25,26,30)/t12-/m0/s1 OVBPIULPVIDEAO-LBPRGKRZSA-N 441.39750 441.13968 Nc1nc2ncc(CNc3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O)nc2c(=O)[nH]1 CHEBI:24075 CHEBI:42610 CHEBI:5140 CHEBI:569217 Beilstein:100781 CAS:59-30-3 DrugBank:DB00158 Drug_Central:1231 KEGG:C00504 KEGG:D00070 KNApSAcK:C00001539 LINCS:LSM-5355 MetaCyc:CPD-12826 PDBeChem:FOL PMID:11261364 PMID:11451208 PMID:14387833 PMID:15754725 PMID:17784727 PMID:18788725 PMID:19355913 PMID:24650098 PMID:9040515 Reaxys:100781 Wikipedia:Folic_Acid http://www.langual.org/langual_thesaurus.asp?termid=B3760 FOLIC ACID Folic acid N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid chebi_ontology Folate Folsaeure N-[(4-{[(2-amino-4-oxo-1,4-dihydropteridin-6-yl)methyl]amino}phenyl)carbonyl]-L-glutamic acid N-pteroyl-L-glutamic acid PGA PteGlu Pteroylglutamic acid pteroyl-L-glutamic acid pteroyl-L-monoglutamic acid vitamin Bc vitamin M CHEBI:27470 LanguaL curation note: Used when folic acid is added at any level. Always use this term for enriched flour or rice, enriched bakery products, and enriched macaroni or noodle products. (21 CFR 137. 610(a), 21 CFR 136.115(a)(1), and others). folic acid Beilstein:100781 Beilstein CAS:59-30-3 ChemIDplus CAS:59-30-3 KEGG COMPOUND CAS:59-30-3 NIST Chemistry WebBook Drug_Central:1231 DrugCentral PMID:11261364 Europe PMC PMID:11451208 Europe PMC PMID:14387833 Europe PMC PMID:15754725 Europe PMC PMID:17784727 Europe PMC PMID:18788725 ChEMBL PMID:19355913 Europe PMC PMID:24650098 Europe PMC PMID:9040515 Europe PMC Reaxys:100781 Reaxys FOLIC ACID PDBeChem Folic acid KEGG_COMPOUND N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamic acid IUPAC Folate KEGG_COMPOUND Folsaeure ChEBI N-[(4-{[(2-amino-4-oxo-1,4-dihydropteridin-6-yl)methyl]amino}phenyl)carbonyl]-L-glutamic acid PDBeChem N-pteroyl-L-glutamic acid ChEBI PGA NIST_Chemistry_WebBook PteGlu NIST_Chemistry_WebBook Pteroylglutamic acid KEGG_COMPOUND pteroyl-L-glutamic acid ChemIDplus pteroyl-L-monoglutamic acid ChemIDplus vitamin Bc ChemIDplus vitamin M ChemIDplus 0 C InChI=1S/C OKTJSMMVPCPJKN-UHFFFAOYSA-N 12.01070 12.00000 [C] CHEBI:23009 CHEBI:3399 CAS:7440-44-0 KEGG:C06265 WebElements:C carbon chebi_ontology 6C C Carbon Kohlenstoff carbon carbone carbonium carbono CHEBI:27594 carbon atom CAS:7440-44-0 ChemIDplus CAS:7440-44-0 KEGG COMPOUND carbon IUPAC 6C IUPAC C IUPAC C KEGG_COMPOUND Carbon KEGG_COMPOUND Kohlenstoff ChEBI carbon ChEBI carbone ChEBI carbonium ChEBI carbono ChEBI A cobalt group element atom that has atomic number 27. 0 Co InChI=1S/Co GUTLYIVDDKVIGB-UHFFFAOYSA-N 58.93320 58.93319 [Co] CHEBI:23335 CHEBI:3788 CAS:7440-48-4 KEGG:C00175 KEGG:C19171 PDBeChem:3CO WebElements:Co cobalt chebi_ontology 27Co Co Cobalt Kobalt cobalt cobalto cobaltum CHEBI:27638 cobalt atom CAS:7440-48-4 ChemIDplus CAS:7440-48-4 KEGG COMPOUND CAS:7440-48-4 NIST Chemistry WebBook cobalt IUPAC 27Co IUPAC Co IUPAC Cobalt KEGG_COMPOUND Kobalt NIST_Chemistry_WebBook cobalt ChEBI cobalto ChEBI cobaltum ChEBI A surfactant (or a mixture containing one or more surfactants) having cleaning properties in dilute solutions. CHEBI:23648 CHEBI:4456 KEGG:C01689 detergent chebi_ontology Detergents CHEBI:27780 detergent detergent IUPAC Detergents KEGG_COMPOUND hydroxocobalamin http://langual.org 0 C62H89CoN13O15P InChI=1S/C62H90N13O14P.Co.H2O/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);;1H2/q;+3;/p-3/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 YOZNUFWCRFCGIH-WZHZPDAFSA-K 1346.35510 1345.56706 [H]O[Co-3]1234N5C6=C(C)C7=[N+]1C(=CC1=[N+]2C(=C(C)C2=[N+]3[C@@](C)([C@@]5([H])[C@H](CC(N)=O)[C@@]6(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@H]3[C@@H](O)[C@H](O[C@@H]3CO)n3c[n+]4c4cc(C)c(C)cc34)[C@@](C)(CC(N)=O)[C@@H]2CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]1CCC(N)=O)C(C)(C)[C@@H]7CCC(N)=O CHEBI:24652 CHEBI:5795 CHEBI:5803 CAS:13422-51-0 DrugBank:DB00200 Gmelin:5723 KEGG:C08230 KEGG:D01027 http://www.langual.org/langual_thesaurus.asp?termid=B3780 Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-hydroxocobamide Hydroxocobalamin hydroxocobalamin chebi_ontology Hydroxycobalamin OH-Cbl vitamin B-12b CHEBI:27786 hydroxocobalamin CAS:13422-51-0 ChemIDplus CAS:13422-51-0 KEGG COMPOUND Gmelin:5723 Gmelin Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-hydroxocobamide IUPAC Hydroxocobalamin KEGG_COMPOUND hydroxocobalamin CBN Hydroxycobalamin KEGG_COMPOUND OH-Cbl CBN vitamin B-12b CBN A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. 0 C22H24N2O8 InChI=1S/C22H24N2O8/c1-21(31)8-5-4-6-11(25)12(8)16(26)13-9(21)7-10-15(24(2)3)17(27)14(20(23)30)19(29)22(10,32)18(13)28/h4-6,9-10,15,25,27-28,31-32H,7H2,1-3H3,(H2,23,30)/t9-,10-,15-,21+,22-/m0/s1 OFVLGDICTFRJMM-WESIUVDSSA-N 444.43460 444.15327 [H][C@@]12C[C@@]3([H])C(C(=O)c4c(O)cccc4[C@@]3(C)O)=C(O)[C@]1(O)C(=O)C(C(N)=O)=C(O)[C@H]2N(C)C CHEBI:26894 CHEBI:45729 CHEBI:9474 Beilstein:2230417 CAS:60-54-8 DrugBank:DB00759 Drug_Central:2611 Gmelin:1103368 KEGG:C06570 KEGG:D00201 MetaCyc:CPD0-1414 PDBeChem:TAC PMID:11061623 PMID:11550419 PMID:11744940 PMID:12934399 PMID:14585720 PMID:15825421 PMID:15913752 PMID:16443056 PMID:1650428 PMID:16749547 PMID:17251127 PMID:17260506 PMID:18326855 PMID:18406588 PMID:19032078 PMID:19112759 PMID:19136803 PMID:25286144 PMID:26876942 Patent:US2699054 Patent:US2712517 Patent:US2886595 Patent:US3005023 Patent:US3019173 Patent:US3301899 Reaxys:2230417 VSDB:1739 Wikipedia:Tetracycline (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide TETRACYCLINE Tetracycline tetracycline chebi_ontology (4S,4aS,5aS,12aS)-4-(Dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamide Abramycin Achromycin Anhydrotetracycline Deschlorobiomycin Liquamycin Tetracyclin Tetrazyklin Tsiklomitsin tetracycline tetracyclinum CHEBI:27902 tetracycline Beilstein:2230417 Beilstein CAS:60-54-8 ChemIDplus CAS:60-54-8 KEGG COMPOUND Drug_Central:2611 DrugCentral Gmelin:1103368 Gmelin PMID:11061623 Europe PMC PMID:11550419 Europe PMC PMID:11744940 Europe PMC PMID:12934399 Europe PMC PMID:14585720 Europe PMC PMID:15825421 Europe PMC PMID:15913752 Europe PMC PMID:16443056 Europe PMC PMID:1650428 Europe PMC PMID:16749547 Europe PMC PMID:17251127 Europe PMC PMID:17260506 Europe PMC PMID:18326855 Europe PMC PMID:18406588 Europe PMC PMID:19032078 Europe PMC PMID:19112759 Europe PMC PMID:19136803 Europe PMC PMID:25286144 Europe PMC PMID:26876942 Europe PMC Reaxys:2230417 Reaxys (4S,4aS,5aS,6S,12aS)-4-(dimethylamino)-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide IUPAC TETRACYCLINE PDBeChem Tetracycline KEGG_COMPOUND tetracycline ChEBI (4S,4aS,5aS,12aS)-4-(Dimethylamino)-1,4,4a,5,5a,6,11,12a-octahydro-3,6,10,12,12a-pentahydroxy-6-methyl-1,11-dioxo-2-naphthacenecarboxamide ChemIDplus Abramycin ChemIDplus Achromycin ChEBI Anhydrotetracycline DrugBank Deschlorobiomycin ChemIDplus Liquamycin ChemIDplus Tetracyclin ChEBI Tetrazyklin ChEBI Tsiklomitsin ChemIDplus tetracycline ChemIDplus tetracyclinum ChemIDplus An organonitrogen heterocyclic antibiotic that contains a beta-lactam ring. CHEBI:10427 CHEBI:22844 KEGG:C03438 PMID:19254642 PMID:22594007 Wikipedia:Beta-lactam_antibiotic chebi_ontology beta-Lactam antibiotics beta-lactam antibiotics CHEBI:27933 beta-lactam antibiotic PMID:19254642 Europe PMC PMID:22594007 Europe PMC beta-Lactam antibiotics KEGG_COMPOUND beta-lactam antibiotics ChEBI An aromatic amino acid that is alanine in which one of the methyl hydrogens is substituted by a phenyl group. 0 C9H11NO2 InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12) COLNVLDHVKWLRT-UHFFFAOYSA-N 165.18918 165.07898 NC(Cc1ccccc1)C(O)=O CHEBI:25984 CHEBI:8089 Beilstein:1910407 CAS:150-30-1 Gmelin:50836 KEGG:C02057 PMID:17439666 PMID:22264337 Reaxys:1910407 Wikipedia:Phenylalanine 2-amino-3-phenylpropanoic acid Phenylalanine phenylalanine chebi_ontology DL-Phenylalanine F PHE Phenylalanin alpha-Amino-beta-phenylpropionic acid fenilalanina CHEBI:28044 phenylalanine Beilstein:1910407 Beilstein CAS:150-30-1 ChemIDplus CAS:150-30-1 NIST Chemistry WebBook Gmelin:50836 Gmelin PMID:17439666 Europe PMC PMID:22264337 Europe PMC Reaxys:1910407 Reaxys 2-amino-3-phenylpropanoic acid IUPAC Phenylalanine KEGG_COMPOUND phenylalanine ChEBI phenylalanine IUPAC DL-Phenylalanine KEGG_COMPOUND F ChEBI PHE ChEBI Phenylalanin ChEBI alpha-Amino-beta-phenylpropionic acid KEGG_COMPOUND fenilalanina ChEBI 0 C63H91CoN13O14P InChI=1S/C62H90N13O14P.CH3.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);1H3;/q;;+2/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;;/m1../s1 JEWJRMKHSMTXPP-WZHZPDAFSA-L 1344.38230 1343.58780 [H][C@]12[C@H](CC(N)=O)[C@@]3(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@H]4[C@@H](O)[C@H](O[C@@H]4CO)n4c[n+](c5cc(C)c(C)cc45)[Co-3]456(C)N1C3=C(C)C1=[N+]4C(=CC3=[N+]5C(=C(C)C4=[N+]6[C@]2(C)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O CHEBI:25291 CHEBI:48831 CHEBI:6869 CAS:13422-55-4 COMe:MOL000085 DrugBank:DB03614 Gmelin:124528 KEGG:C06453 KEGG:D03246 PDBeChem:COB Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-methylcobamide Methylcobalamin methylcobalamin chebi_ontology CO-METHYLCOBALAMIN MeCbl mecobalamin methylcob(III)alamin CHEBI:28115 methylcobalamin CAS:13422-55-4 ChemIDplus CAS:13422-55-4 KEGG COMPOUND Gmelin:124528 Gmelin Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-Cobeta-methylcobamide IUPAC Methylcobalamin KEGG_COMPOUND methylcobalamin CBN CO-METHYLCOBALAMIN PDBeChem MeCbl CBN mecobalamin ChEBI methylcob(III)alamin UniProt An aldohexose that is the C-4 epimer of glucose. galactose http://langual.org 0 C6H12O6 180.156 180.06339 CHEBI:24162 CHEBI:33933 CHEBI:5256 CAS:26566-61-0 KEGG:C01582 Wikipedia:Galactose http://www.langual.org/langual_thesaurus.asp?termid=C0254 Galactose galacto-hexose galactose chebi_ontology Gal Galaktose galactose, d- CHEBI:28260 galactose CAS:26566-61-0 ChemIDplus CAS:26566-61-0 NIST Chemistry WebBook Galactose KEGG_COMPOUND galacto-hexose IUPAC galactose IUPAC Gal JCBN Galaktose ChEBI CHEBI:10197 CHEBI:13780 CHEBI:22361 KEGG:C04025 alpha,omega-Dicarboxylic acid chebi_ontology alpha(omega)-Dicarboxylic acid alpha,omega-dicarboxylic acids CHEBI:28383 alpha,omega-dicarboxylic acid alpha,omega-Dicarboxylic acid KEGG_COMPOUND alpha(omega)-Dicarboxylic acid KEGG_COMPOUND alpha,omega-dicarboxylic acids ChEBI A cyclic carotene with a beta- and an epsilon-ring at opposite ends respectively. 0 C40H56 InChI=1S/C40H56/c1-31(19-13-21-33(3)25-27-37-35(5)23-15-29-39(37,7)8)17-11-12-18-32(2)20-14-22-34(4)26-28-38-36(6)24-16-30-40(38,9)10/h11-14,17-23,25-28,37H,15-16,24,29-30H2,1-10H3/b12-11+,19-13+,20-14+,27-25+,28-26+,31-17+,32-18+,33-21+,34-22+ ANVAOWXLWRTKGA-JLTXGRSLSA-N 536.87264 536.43820 CC(\C=C\C=C(C)\C=C\C1C(C)=CCCC1(C)C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C CHEBI:10215 CHEBI:22447 Beilstein:2067408 Beilstein:3227599 CAS:432-70-2 HMDB:HMDB0003993 KEGG:C05433 KNApSAcK:C00003765 LIPID_MAPS_instance:LMPR01070258 PMID:23620017 PMID:24169341 PMID:9408998 Reaxys:2682045 alpha-Carotene alpha-carotene beta,epsilon-carotene chebi_ontology all-trans-alpha-carotene CHEBI:28425 alpha-carotene Beilstein:2067408 Beilstein Beilstein:3227599 Beilstein CAS:432-70-2 ChemIDplus LIPID_MAPS_instance:LMPR01070258 LIPID MAPS PMID:23620017 Europe PMC PMID:24169341 Europe PMC PMID:9408998 Europe PMC Reaxys:2682045 Reaxys alpha-Carotene KEGG_COMPOUND alpha-carotene UniProt beta,epsilon-carotene IUPAC all-trans-alpha-carotene ChemIDplus A one-carbon compound that is ammonia in which one of the hydrogens is replaced by a carboxy group. Although carbamic acid derivatives are common, carbamic acid itself has never been synthesised. 0 CH3NO2 InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4) KXDHJXZQYSOELW-UHFFFAOYSA-N 61.04006 61.01638 NC(O)=O CHEBI:22504 CHEBI:23002 CHEBI:3386 CHEBI:44573 Beilstein:1734754 CAS:463-77-4 DrugBank:DB04261 Gmelin:130345 KEGG:C01563 PDBeChem:OUT Wikipedia:Carbamic_acid CARBAMIC ACID Carbamic acid carbamic acid chebi_ontology Aminoameisensaeure Aminoformic acid Carbamate Carbamidsaeure CHEBI:28616 carbamic acid Beilstein:1734754 Beilstein CAS:463-77-4 ChemIDplus CAS:463-77-4 KEGG COMPOUND Gmelin:130345 Gmelin CARBAMIC ACID PDBeChem Carbamic acid KEGG_COMPOUND carbamic acid IUPAC Aminoameisensaeure ChEBI Aminoformic acid KEGG_COMPOUND Carbamate KEGG_COMPOUND Carbamidsaeure ChEBI 0 P InChI=1S/P OAICVXFJPJFONN-UHFFFAOYSA-N 30.97376 30.97376 [P] CHEBI:26080 CHEBI:8168 CAS:7723-14-0 Gmelin:16235 KEGG:C06262 WebElements:P phosphorus chebi_ontology 15P P Phosphor Phosphorus fosforo phosphore phosphorus CHEBI:28659 phosphorus atom CAS:7723-14-0 ChemIDplus CAS:7723-14-0 KEGG COMPOUND Gmelin:16235 Gmelin phosphorus IUPAC 15P IUPAC P IUPAC P KEGG_COMPOUND Phosphor ChEBI Phosphorus KEGG_COMPOUND fosforo ChEBI phosphore ChEBI phosphorus ChEBI A ketohexose that is an isomer of glucose. fructose http://langual.org CHEBI:24104 CHEBI:24110 CHEBI:5172 CAS:30237-26-4 DrugBank:DB04173 KEGG:C01496 Wikipedia:Fructose http://www.langual.org/langual_thesaurus.asp?termid=C0223 Fructose arabino-hex-2-ulose fructose chebi_ontology Fru Fruchtzucker Fruktose arabino-Hexulose levulose CHEBI:28757 LanguaL curation note: Used when pure fructose is the major ingredient. If *HIGH FRUCTOSE SYRUP* is the major ingredient, use that term for indexing. fructose CAS:30237-26-4 ChemIDplus Fructose KEGG_COMPOUND arabino-hex-2-ulose IUPAC fructose IUPAC Fru JCBN Fruchtzucker ChEBI Fruktose ChEBI arabino-Hexulose KEGG_COMPOUND lutein http://langual.org 0 C40H56O2 InChI=1S/C40H56O2/c1-29(17-13-19-31(3)21-23-37-33(5)25-35(41)27-39(37,7)8)15-11-12-16-30(2)18-14-20-32(4)22-24-38-34(6)26-36(42)28-40(38,9)10/h11-25,35-37,41-42H,26-28H2,1-10H3/b12-11+,17-13+,18-14+,23-21+,24-22+,29-15+,30-16+,31-19+,32-20+/t35-,36+,37-/m0/s1 KBPHJBAIARWVSC-RGZFRNHPSA-N 568.87144 568.42803 CC(\C=C\C=C(C)\C=C\[C@H]1C(C)=C[C@H](O)CC1(C)C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)C[C@@H](O)CC1(C)C CHEBI:27324 CHEBI:43817 CHEBI:6576 Beilstein:2068550 CAS:127-40-2 Codex::161b DrugBank:DB00137 Drug_Central:4145 Europe::161b HMDB:HMDB0003233 KEGG:C08601 KNApSAcK:C00003776 LIPID_MAPS_instance:LMPR01070274 MetaCyc:CPD1F-119 PDBeChem:LUT PMID:10714278 PMID:14670087 PMID:23543147 PMID:24451312 Reaxys:2068550 Wikipedia:Lutein http://www.langual.org/langual_thesaurus.asp?termid=B3133 (3R,3'R,6'R)-beta,epsilon-carotene-3,3'-diol Lutein lutein chebi_ontology (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL Bo-Xan E 161b Xanthophyll luteins CHEBI:28838 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive. lutein Beilstein:2068550 Beilstein CAS:127-40-2 ChemIDplus CAS:127-40-2 KEGG COMPOUND Drug_Central:4145 DrugCentral LIPID_MAPS_instance:LMPR01070274 LIPID MAPS PMID:10714278 Europe PMC PMID:14670087 Europe PMC PMID:23543147 Europe PMC PMID:24451312 Europe PMC Reaxys:2068550 Reaxys (3R,3'R,6'R)-beta,epsilon-carotene-3,3'-diol IUPAC Lutein KEGG_COMPOUND lutein UniProt (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL PDBeChem Bo-Xan ChemIDplus E 161b ChEBI Xanthophyll KEGG_COMPOUND The conjugate base of a fatty acid, arising from deprotonation of the carboxylic acid group of the corresponding fatty acid. -1 CO2R 44.00950 43.98983 [O-]C([*])=O CHEBI:13634 CHEBI:24022 CHEBI:4985 KEGG:C02403 PMID:18628202 Fatty acid anion chebi_ontology Alkanate Fettsaeureanion Fettsaeureanionen a fatty acid acido graso anionico acidos grasos anionicos anion de l'acide gras fatty acid anions CHEBI:28868 fatty acid anion PMID:18628202 Europe PMC Fatty acid anion KEGG_COMPOUND Alkanate KEGG_COMPOUND Fettsaeureanion ChEBI Fettsaeureanionen ChEBI a fatty acid UniProt acido graso anionico ChEBI acidos grasos anionicos ChEBI anion de l'acide gras ChEBI fatty acid anions ChEBI An onium cation obtained by protonation of ammonia. +1 H4N InChI=1S/H3N/h1H3/p+1 QGZKDVFQNNGYKY-UHFFFAOYSA-O 18.03850 18.03383 [H][N+]([H])([H])[H] CHEBI:22534 CHEBI:49783 CHEBI:7435 CAS:14798-03-9 Gmelin:84 KEGG:C01342 MetaCyc:AMMONIUM MolBase:929 PDBeChem:NH4 PMID:11319011 PMID:11341317 PMID:12096804 PMID:14512268 PMID:14879753 PMID:16345391 PMID:16903292 PMID:17392693 PMID:18515490 PMID:19199063 PMID:19596600 PMID:19682559 PMID:19716251 PMID:21993530 PMID:22265469 PMID:22524020 PMID:22562341 PMID:22631217 Reaxys:16093784 Wikipedia:Ammonium ammonium azanium chebi_ontology Ammonium(1+) NH4(+) NH4+ [NH4](+) ammonium cation ammonium ion CHEBI:28938 ammonium CAS:14798-03-9 ChemIDplus CAS:14798-03-9 NIST Chemistry WebBook Gmelin:84 Gmelin PMID:11319011 Europe PMC PMID:11341317 Europe PMC PMID:12096804 Europe PMC PMID:14512268 Europe PMC PMID:14879753 Europe PMC PMID:16345391 Europe PMC PMID:16903292 Europe PMC PMID:17392693 Europe PMC PMID:18515490 Europe PMC PMID:19199063 Europe PMC PMID:19596600 Europe PMC PMID:19682559 Europe PMC PMID:19716251 Europe PMC PMID:21993530 Europe PMC PMID:22265469 Europe PMC PMID:22524020 Europe PMC PMID:22562341 Europe PMC PMID:22631217 Europe PMC Reaxys:16093784 Reaxys ammonium ChEBI ammonium IUPAC azanium IUPAC Ammonium(1+) ChemIDplus NH4(+) IUPAC NH4(+) UniProt NH4+ KEGG_COMPOUND [NH4](+) MolBase ammonium cation ChemIDplus ammonium ion PDBeChem An N-acetyl-L-amino acid that is the N-acetylated derivative of the natural amino acid L-cysteine. 0 C5H9NO3S InChI=1S/C5H9NO3S/c1-3(7)6-4(2-10)5(8)9/h4,10H,2H2,1H3,(H,6,7)(H,8,9)/t4-/m0/s1 PWKSKIMOESPYIA-BYPYZUCNSA-N 163.19590 163.03031 CC(=O)N[C@@H](CS)C(O)=O CHEBI:21548 CHEBI:2418 CHEBI:45481 Beilstein:1724426 CAS:616-91-1 DrugBank:DB06151 Drug_Central:66 Gmelin:142554 HMDB:HMDB0001890 KEGG:C06809 KEGG:D00221 LINCS:LSM-4672 MetaCyc:CPD-9175 PDBeChem:SC2 PMID:10651166 PMID:17174578 PMID:2026726 PMID:24119926 PMID:25553484 Reaxys:1724426 Wikipedia:Acetylcysteine N-ACETYL-L-CYSTEINE N-acetyl-L-cysteine chebi_ontology (2R)-2-acetylamino-3-sulfanylpropanoic acid (R)-2-acetylamino-3-mercaptopropanoic acid (R)-mercapturic acid Acetylcysteine L-acetylcysteine L-alpha-acetamido-beta-mercaptopropionic acid N-acetyl-L-(+)-cysteine N-acetylcysteine NAC acetilcisteina acetylcysteinum mercapturic acid CHEBI:28939 N-acetyl-L-cysteine Beilstein:1724426 Beilstein CAS:616-91-1 ChemIDplus CAS:616-91-1 KEGG COMPOUND CAS:616-91-1 NIST Chemistry WebBook Drug_Central:66 DrugCentral Gmelin:142554 Gmelin PMID:10651166 Europe PMC PMID:17174578 Europe PMC PMID:2026726 Europe PMC PMID:24119926 Europe PMC PMID:25553484 Europe PMC Reaxys:1724426 Reaxys N-ACETYL-L-CYSTEINE PDBeChem N-acetyl-L-cysteine IUPAC (2R)-2-acetylamino-3-sulfanylpropanoic acid IUPAC (R)-2-acetylamino-3-mercaptopropanoic acid ChEBI (R)-mercapturic acid ChemIDplus Acetylcysteine KEGG_COMPOUND L-acetylcysteine ChemIDplus L-alpha-acetamido-beta-mercaptopropionic acid NIST_Chemistry_WebBook N-acetyl-L-(+)-cysteine NIST_Chemistry_WebBook N-acetylcysteine ChemIDplus NAC ChEBI acetilcisteina ChemIDplus acetylcysteinum ChemIDplus mercapturic acid ChemIDplus A carboxylic acid dianion obtained by deprotonation of both carboxy groups of any dicarboxylic acid. -2 C2O4R 88.019 87.97966 [O-]C(=O)[*]C([O-])=O CHEBI:13632 CHEBI:23688 CHEBI:23689 CHEBI:38711 dicarboxylic acid dianion chebi_ontology a dicarboxylate dicarboxylate dicarboxylates dicarboxylic acid dianions CHEBI:28965 dicarboxylic acid dianion dicarboxylic acid dianion ChEBI a dicarboxylate UniProt dicarboxylate ChEBI dicarboxylates ChEBI dicarboxylic acid dianions ChEBI 0 CH2O3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4) BVKZGUZCCUSVTD-UHFFFAOYSA-N 62.02478 62.00039 OC(O)=O CHEBI:13351 CHEBI:23017 CHEBI:23744 CHEBI:3401 CAS:463-79-6 Gmelin:25554 KEGG:C01353 PDBeChem:CO3 Carbonic acid carbonic acid dihydroxidooxidocarbon chebi_ontology Dihydrogen carbonate H2CO3 Koehlensaeure [CO(OH)2] CHEBI:28976 carbonic acid CAS:463-79-6 ChemIDplus CAS:463-79-6 KEGG COMPOUND Gmelin:25554 Gmelin Carbonic acid KEGG_COMPOUND carbonic acid IUPAC dihydroxidooxidocarbon IUPAC Dihydrogen carbonate KEGG_COMPOUND H2CO3 IUPAC H2CO3 KEGG_COMPOUND Koehlensaeure ChEBI [CO(OH)2] IUPAC An alpha-amino acid that is glycine in which the alpha-is substituted by a 3-guanidinopropyl group. 0 C6H14N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10) ODKSFYDXXFIFQN-UHFFFAOYSA-N 174.20112 174.11168 NC(CCCNC(N)=N)C(O)=O CHEBI:22616 CHEBI:2643 Beilstein:1725411 CAS:7200-25-1 KEGG:C02385 PMID:10848923 Reaxys:1725411 Wikipedia:L-Arginine Arginine arginine chebi_ontology 2-Amino-5-guanidinovaleric acid 2-amino-5-(carbamimidamido)pentanoic acid 2-amino-5-guanidinopentanoic acid Arginin Harg CHEBI:29016 arginine Beilstein:1725411 Beilstein CAS:7200-25-1 ChemIDplus PMID:10848923 Europe PMC Reaxys:1725411 Reaxys Arginine KEGG_COMPOUND arginine IUPAC 2-Amino-5-guanidinovaleric acid KEGG_COMPOUND 2-amino-5-(carbamimidamido)pentanoic acid IUPAC 2-amino-5-guanidinopentanoic acid JCBN Arginin ChEBI Harg IUPAC The conjugate base formed when the carboxy group of a carboxylic acid is deprotonated. -1 CO2R 44.00950 43.98983 [O-]C([*])=O CHEBI:13626 CHEBI:13945 CHEBI:23026 CHEBI:58657 chebi_ontology a carboxylate carboxylic acid anions carboxylic anions CHEBI:29067 carboxylic acid anion a carboxylate UniProt carboxylic acid anions ChEBI carboxylic anions ChEBI A monoatomic monocation obtained from sodium. +1 Na InChI=1S/Na/q+1 FKNQFGJONOIPTF-UHFFFAOYSA-N 22.98977 22.98922 [Na+] CHEBI:26717 CHEBI:49766 CHEBI:9175 CAS:17341-25-2 Gmelin:15196 KEGG:C01330 PDBeChem:NA sodium cation sodium(1+) sodium(1+) ion sodium(I) cation chebi_ontology Na(+) Na+ SODIUM ION CHEBI:29101 sodium(1+) CAS:17341-25-2 ChemIDplus CAS:17341-25-2 NIST Chemistry WebBook Gmelin:15196 Gmelin sodium cation IUPAC sodium(1+) IUPAC sodium(1+) ion IUPAC sodium(I) cation IUPAC Na(+) IUPAC Na(+) UniProt Na+ KEGG_COMPOUND SODIUM ION PDBeChem A monoatomic monocation obtained from potassium. +1 K InChI=1S/K/q+1 NPYPAHLBTDXSSS-UHFFFAOYSA-N 39.09830 38.96316 [K+] CHEBI:26219 CHEBI:49685 CHEBI:8345 CAS:24203-36-9 Gmelin:15203 KEGG:C00238 KEGG:D08403 PDBeChem:K potassium cation potassium(1+) potassium(1+) ion potassium(I) cation chebi_ontology K(+) K+ POTASSIUM ION CHEBI:29103 potassium(1+) CAS:24203-36-9 NIST Chemistry WebBook Gmelin:15203 Gmelin potassium cation IUPAC potassium(1+) IUPAC potassium(1+) ion IUPAC potassium(I) cation IUPAC K(+) IUPAC K(+) UniProt K+ KEGG_COMPOUND POTASSIUM ION PDBeChem +2 Ca InChI=1S/Ca/q+2 BHPQYMZQTOCNFJ-UHFFFAOYSA-N 40.07800 39.96149 [Ca++] CHEBI:22988 CHEBI:3308 CHEBI:48760 CAS:14127-61-8 Gmelin:6850 KEGG:C00076 PDBeChem:CA calcium(2+) calcium(2+) ion calcium(II) cation chebi_ontology CALCIUM ION Ca(2+) Ca2+ calcium, doubly charged positive ion CHEBI:29108 calcium(2+) CAS:14127-61-8 ChemIDplus CAS:14127-61-8 NIST Chemistry WebBook Gmelin:6850 Gmelin calcium(2+) IUPAC calcium(2+) ion IUPAC calcium(II) cation IUPAC CALCIUM ION PDBeChem Ca(2+) IUPAC Ca(2+) UniProt Ca2+ KEGG_COMPOUND calcium, doubly charged positive ion NIST_Chemistry_WebBook 0 H2O3S InChI=1S/H2O3S/c1-4(2)3/h4H,(H,1,2,3) BDHFUVZGWQCTTF-UHFFFAOYSA-N 82.08008 81.97247 [H]S(O)(=O)=O Gmelin:1404640 hydridohydroxidodioxidosulfur sulfonic acid chebi_ontology HSHO3 Sulfonsaeure [SHO2(OH)] acide sulfonique sulphonic acid CHEBI:29214 sulfonic acid Gmelin:1404640 Gmelin hydridohydroxidodioxidosulfur IUPAC sulfonic acid IUPAC HSHO3 IUPAC Sulfonsaeure ChEBI [SHO2(OH)] IUPAC acide sulfonique ChEBI sulphonic acid ChEBI A diatomic molecule containing covalently bonded hydrogen and fluorine atoms. 0 FH InChI=1S/FH/h1H KRHYYFGTRYWZRS-UHFFFAOYSA-N 20.00634 20.00623 F[H] CAS:7664-39-3 Drug_Central:4499 Gmelin:166 KEGG:C16487 Hydrogen fluoride fluorane fluoridohydrogen hydrogen fluoride chebi_ontology Fluoride Fluorwasserstoff HF Hydrogenfluorid [HF] fluorure d'hydrogene hydrofluoric acid CHEBI:29228 hydrogen fluoride CAS:7664-39-3 ChemIDplus CAS:7664-39-3 KEGG COMPOUND CAS:7664-39-3 NIST Chemistry WebBook Drug_Central:4499 DrugCentral Gmelin:166 Gmelin Hydrogen fluoride KEGG_COMPOUND fluorane IUPAC fluoridohydrogen IUPAC hydrogen fluoride IUPAC Fluoride KEGG_COMPOUND Fluorwasserstoff ChEBI HF IUPAC Hydrogenfluorid ChEBI [HF] IUPAC fluorure d'hydrogene ChEBI hydrofluoric acid ChemIDplus -1 H2N InChI=1S/H2N/h1H2/q-1 HYGWNUKOUCZBND-UHFFFAOYSA-N 16.02262 16.01927 [H][N-][H] amide azanide dihydridonitrate(1-) chebi_ontology NH2(-) CHEBI:29337 azanide amide IUPAC azanide IUPAC dihydridonitrate(1-) IUPAC NH2(-) IUPAC A divalent inorganic anion resulting from the removal of two protons from ammonia. -2 HN InChI=1S/HN/h1H/q-2 DZQYTNGKSBCIOE-UHFFFAOYSA-N 15.01468 15.01200 [N--][H] azanediide hydridonitrate(2-) chebi_ontology NH(2-) imide CHEBI:29340 hydridonitrate(2-) azanediide IUPAC hydridonitrate(2-) IUPAC NH(2-) IUPAC imide IUPAC A carboxamide derived from a monocarboxylic acid. 0 CNOR3 42.01680 41.99799 [*]N([*])C([*])=O CHEBI:13211 CHEBI:22207 CHEBI:25383 CHEBI:6977 chebi_ontology monocarboxylic acid amides CHEBI:29347 monocarboxylic acid amide monocarboxylic acid amides ChEBI An alpha-amino-acid anion that is the conjugate base of L-glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m0/s1 WHUUTDBJXJRKMK-VKHMYHEASA-M 146.12136 146.04588 [NH3+][C@@H](CCC([O-])=O)C([O-])=O CHEBI:13107 CHEBI:21301 CAS:11070-68-1 Gmelin:936654 MetaCyc:GLT L-glutamate(1-) hydrogen L-glutamate chebi_ontology (2S)-2-ammoniopentanedioate L-glutamate L-glutamic acid monoanion L-glutamic acid, ion(1-) CHEBI:29985 L-glutamate(1-) CAS:11070-68-1 ChemIDplus Gmelin:936654 Gmelin L-glutamate(1-) JCBN hydrogen L-glutamate IUPAC (2S)-2-ammoniopentanedioate IUPAC L-glutamate ChEBI L-glutamate UniProt L-glutamic acid monoanion JCBN L-glutamic acid, ion(1-) ChemIDplus An alpha-amino-acid anion that is the conjugate base of D-glutamic acid, having anionic carboxy groups and a cationic amino group -1 C5H8NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-1/t3-/m1/s1 WHUUTDBJXJRKMK-GSVOUGTGSA-M 146.12136 146.04588 [NH3+][C@H](CCC([O-])=O)C([O-])=O CHEBI:12979 CHEBI:21022 Beilstein:8319427 MetaCyc:D-GLT D-glutamate(1-) hydrogen D-glutamate chebi_ontology (2R)-2-ammoniopentanedioate D-glutamate D-glutamic acid monoanion CHEBI:29986 D-glutamate(1-) Beilstein:8319427 Beilstein D-glutamate(1-) JCBN hydrogen D-glutamate IUPAC (2R)-2-ammoniopentanedioate IUPAC D-glutamate UniProt D-glutamic acid monoanion JCBN A dicarboxylic acid dianion that is the conjugate base of glutamate(1-). -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2 WHUUTDBJXJRKMK-UHFFFAOYSA-L 145.11342 145.03860 NC(CCC([O-])=O)C([O-])=O Beilstein:4134100 Gmelin:327903 Reaxys:4134100 2-aminopentanedioate glutamate glutamate(2-) chebi_ontology glutamic acid dianion CHEBI:29987 glutamate(2-) Beilstein:4134100 Beilstein Gmelin:327903 Gmelin Reaxys:4134100 Reaxys 2-aminopentanedioate IUPAC glutamate IUPAC glutamate(2-) JCBN glutamic acid dianion JCBN An L-alpha-amino acid anion that is the dianion obtained by the deprotonation of the both the carboxy groups of L-glutamic acid. -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2/t3-/m0/s1 WHUUTDBJXJRKMK-VKHMYHEASA-L 145.11342 145.03860 N[C@@H](CCC([O-])=O)C([O-])=O Gmelin:327905 (2S)-2-aminopentanedioate L-glutamate L-glutamate(2-) chebi_ontology L-glutamic acid dianion CHEBI:29988 L-glutamate(2-) Gmelin:327905 Gmelin (2S)-2-aminopentanedioate IUPAC L-glutamate IUPAC L-glutamate(2-) JCBN L-glutamic acid dianion JCBN -2 C5H7NO4 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/p-2/t3-/m1/s1 WHUUTDBJXJRKMK-GSVOUGTGSA-L 145.11342 145.03860 N[C@H](CCC([O-])=O)C([O-])=O Beilstein:8143000 Gmelin:327904 (2R)-2-aminopentanedioate D-glutamate D-glutamate(2-) chebi_ontology D-glutamic acid dianion CHEBI:29989 D-glutamate(2-) Beilstein:8143000 Beilstein Gmelin:327904 Gmelin (2R)-2-aminopentanedioate IUPAC D-glutamate IUPAC D-glutamate(2-) JCBN D-glutamic acid dianion JCBN A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of acetic acid. -1 C2H3O2 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1 QTBSBXVTEAMEQO-UHFFFAOYSA-M 59.04402 59.01385 CC([O-])=O CHEBI:13704 CHEBI:22165 CHEBI:40480 Beilstein:1901470 CAS:71-50-1 DrugBank:DB03166 Gmelin:1379 KEGG:C00033 MetaCyc:ACET PDBeChem:ACT PMID:17190852 PMID:22211106 PMID:22371380 Reaxys:1901470 UM-BBD_compID:c0050 Wikipedia:Acetate acetate chebi_ontology ACETATE ION Azetat CH3-COO(-) Ethanoat MeCO2 anion acetic acid, ion(1-) ethanoate CHEBI:30089 acetate Beilstein:1901470 Beilstein CAS:71-50-1 ChemIDplus CAS:71-50-1 NIST Chemistry WebBook Gmelin:1379 Gmelin PMID:17190852 Europe PMC PMID:22211106 Europe PMC PMID:22371380 Europe PMC Reaxys:1901470 Reaxys UM-BBD_compID:c0050 UM-BBD acetate IUPAC acetate UniProt ACETATE ION PDBeChem Azetat ChEBI CH3-COO(-) IUPAC Ethanoat ChEBI MeCO2 anion NIST_Chemistry_WebBook acetic acid, ion(1-) ChemIDplus ethanoate ChEBI 0 C3H7 43.08768 43.05478 CC(*)C isopropyl propan-2-yl chebi_ontology (CH3)2CH- -CH(CH3)2 1-methylethyl iPr valine side-chain CHEBI:30353 isopropyl group isopropyl IUPAC propan-2-yl IUPAC (CH3)2CH- IUPAC -CH(CH3)2 ChEBI 1-methylethyl IUPAC iPr CBN valine side-chain ChEBI 0 C4H9 57.11426 57.07043 CC(C)C* 2-methylpropan-1-ido 2-methylpropyl isobutyl chebi_ontology (CH3)2CH-CH2- -CH2-CH(CH3)2 iBu leucine side-chain CHEBI:30356 isobutyl group 2-methylpropan-1-ido IUPAC 2-methylpropyl IUPAC isobutyl IUPAC (CH3)2CH-CH2- IUPAC -CH2-CH(CH3)2 ChEBI iBu CBN leucine side-chain ChEBI An alkane that is propane substituted by a methyl group at position 2. 0 C4H10 InChI=1S/C4H10/c1-4(2)3/h4H,1-3H3 NNPPMTNAJDCUHE-UHFFFAOYSA-N 58.12220 58.07825 CC(C)C Beilstein:1730720 CAS:75-28-5 Gmelin:1301 KEGG:D04623 PMID:24179026 PMID:24464945 Reaxys:1730720 Wikipedia:Isobutane 2-methylpropane isobutane chebi_ontology (CH3)2CH-CH3 E943b R-600a CHEBI:30363 isobutane Beilstein:1730720 Beilstein CAS:75-28-5 ChemIDplus CAS:75-28-5 NIST Chemistry WebBook Gmelin:1301 Gmelin PMID:24179026 Europe PMC PMID:24464945 Europe PMC Reaxys:1730720 Reaxys 2-methylpropane IUPAC isobutane IUPAC (CH3)2CH-CH3 IUPAC E943b ChEBI R-600a ChEBI A cobalt-corrinoid hexaamide that is cobalamin with the oxidation state of the central cobalt atom unspecified. COMe:MOL000036 PDBeChem:B12 PMID:11371572 PMID:15181872 COBALAMIN Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-cobamide cobalamin chebi_ontology CHEBI:30411 cobalamin PMID:11371572 Europe PMC PMID:15181872 Europe PMC COBALAMIN PDBeChem Coalpha-[alpha-(5,6-dimethylbenzimidazolyl)]-cobamide IUPAC cobalamin IUPAC +2 0.00000 [*++] CHEBI:23856 CHEBI:4665 KEGG:C00572 chebi_ontology Divalent cation divalent inorganic cations monoatomic dications CHEBI:30412 monoatomic dication Divalent cation KEGG_COMPOUND divalent inorganic cations ChEBI monoatomic dications ChEBI A derivative of the dimethylisoalloxazine (7,8-dimethylbenzo[g]pteridine-2,4(3H,10H)-dione) skeleton, with a substituent on the 10 position. 0 C12H9N4O2R 241.22550 241.07255 Cc1cc2nc3c(nc(=O)[nH]c3=O)n([*])c2cc1C CHEBI:24042 CHEBI:5073 KEGG:C00176 Flavin flavins chebi_ontology CHEBI:30527 flavin Flavin KEGG_COMPOUND flavins IUPAC A dicarboxylic acid dianion obtained by deprotonation of both carboxy groups of oxalic acid. -2 C2O4 InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)/p-2 MUBZPKHOEPUJKR-UHFFFAOYSA-L 88.01900 87.98076 [O-]C(=O)C([O-])=O CHEBI:14702 CHEBI:25729 CHEBI:44820 Beilstein:1905970 CAS:338-70-5 Gmelin:2207 KEGG:C00209 PDBeChem:OXL Reaxys:1905970 UM-BBD_compID:c0017 ethanedioate chebi_ontology OXALATE ION ethanedioic acid, ion(2-) ox oxalate CHEBI:30623 oxalate(2-) Beilstein:1905970 Beilstein CAS:338-70-5 ChemIDplus Gmelin:2207 Gmelin Reaxys:1905970 Reaxys UM-BBD_compID:c0017 UM-BBD ethanedioate IUPAC OXALATE ION PDBeChem ethanedioic acid, ion(2-) ChemIDplus ox IUPAC oxalate UniProt A short-chain saturated fatty acid comprising ethane attached to the carbon of a carboxy group. 0 C3H6O2 InChI=1S/C3H6O2/c1-2-3(4)5/h2H2,1H3,(H,4,5) XBDQKXXYIPTUBI-UHFFFAOYSA-N 74.07850 74.03678 CCC(O)=O CHEBI:26304 CHEBI:45227 CHEBI:8476 Beilstein:506071 CAS:79-09-4 DrugBank:DB03766 Gmelin:1821 KEGG:C00163 KEGG:D02310 LIPID_MAPS_instance:LMFA01010003 PDBeChem:PPI PMID:15868474 PMID:1628870 PMID:16763906 PPDB:1341 Propionic acid propanoic acid propionic acid chebi_ontology CH3-CH2-COOH PA PROPANOIC ACID Propanoic acid Propionsaeure acide propanoique acide propionique carboxyethane ethanecarboxylic acid ethylformic acid metacetonic acid methylacetic acid propioic acid propoic acid pseudoacetic acid CHEBI:30768 propionic acid Beilstein:506071 Beilstein CAS:79-09-4 ChemIDplus CAS:79-09-4 KEGG COMPOUND CAS:79-09-4 NIST Chemistry WebBook Gmelin:1821 Gmelin LIPID_MAPS_instance:LMFA01010003 LIPID MAPS PMID:15868474 Europe PMC PMID:1628870 Europe PMC PMID:16763906 Europe PMC Propionic acid KEGG_COMPOUND propanoic acid IUPAC propionic acid IUPAC CH3-CH2-COOH IUPAC PA ChEBI PROPANOIC ACID PDBeChem Propanoic acid KEGG_COMPOUND Propionsaeure ChEBI acide propanoique ChEBI acide propionique NIST_Chemistry_WebBook carboxyethane ChemIDplus ethanecarboxylic acid ChemIDplus ethylformic acid ChemIDplus metacetonic acid ChemIDplus methylacetic acid ChemIDplus propioic acid LIPID_MAPS propoic acid ChEBI pseudoacetic acid ChemIDplus A straight-chain saturated fatty acid that is butane in which one of the terminal methyl groups has been oxidised to a carboxy group. 0 C4H8O2 InChI=1S/C4H8O2/c1-2-3-4(5)6/h2-3H2,1H3,(H,5,6) FERIUCNNQQJTOY-UHFFFAOYSA-N 88.10510 88.05243 CCCC(O)=O CHEBI:113450 CHEBI:22948 CHEBI:3234 CHEBI:41208 Beilstein:906770 CAS:107-92-6 DrugBank:DB03568 Gmelin:26242 HMDB:HMDB0000039 KEGG:C00246 KNApSAcK:C00001180 LIPID_MAPS_instance:LMFA01010004 MetaCyc:BUTYRIC_ACID PDBeChem:BUA PMID:10736622 PMID:10956204 PMID:11201044 PMID:11208715 PMID:11238216 PMID:11305323 PMID:12068484 PMID:13678314 PMID:14962641 PMID:1542095 PMID:15809727 PMID:15810631 PMID:15938880 PMID:19318247 PMID:19366864 PMID:19703412 PMID:21699495 PMID:22038864 PMID:22194341 PMID:22322557 PMID:22339023 PMID:22466881 Reaxys:906770 Wikipedia:Butyric_acid Butyric acid butanoic acid butyric acid chebi_ontology 1-butanoic acid 1-butyric acid 1-propanecarboxylic acid 4:0 BUTANOIC ACID Butanoate Butanoic acid Buttersaeure C4:0 CH3-[CH2]2-COOH acide butanoique acide butyrique butanic acid butoic acid ethylacetic acid n-butanoic acid n-butyric acid propanecarboxylic acid propylformic acid CHEBI:30772 butyric acid Beilstein:906770 Beilstein CAS:107-92-6 ChemIDplus CAS:107-92-6 KEGG COMPOUND CAS:107-92-6 NIST Chemistry WebBook Gmelin:26242 Gmelin LIPID_MAPS_instance:LMFA01010004 LIPID MAPS PMID:10736622 Europe PMC PMID:10956204 ChEMBL PMID:11201044 Europe PMC PMID:11208715 Europe PMC PMID:11238216 Europe PMC PMID:11305323 Europe PMC PMID:12068484 Europe PMC PMID:13678314 Europe PMC PMID:14962641 Europe PMC PMID:1542095 ChEMBL PMID:15809727 Europe PMC PMID:15810631 Europe PMC PMID:15938880 Europe PMC PMID:19318247 Europe PMC PMID:19366864 Europe PMC PMID:19703412 Europe PMC PMID:21699495 Europe PMC PMID:22038864 Europe PMC PMID:22194341 Europe PMC PMID:22322557 Europe PMC PMID:22339023 Europe PMC PMID:22466881 Europe PMC Reaxys:906770 Reaxys Butyric acid KEGG_COMPOUND butanoic acid IUPAC butyric acid IUPAC 1-butanoic acid HMDB 1-butyric acid HMDB 1-propanecarboxylic acid MetaCyc 4:0 ChEBI BUTANOIC ACID PDBeChem Butanoate KEGG_COMPOUND Butanoic acid KEGG_COMPOUND Buttersaeure ChEBI C4:0 ChEBI CH3-[CH2]2-COOH IUPAC acide butanoique IUPAC acide butyrique ChEBI butanic acid ChEBI butoic acid ChEBI ethylacetic acid NIST_Chemistry_WebBook n-butanoic acid NIST_Chemistry_WebBook n-butyric acid NIST_Chemistry_WebBook propanecarboxylic acid HMDB propylformic acid MetaCyc A C6, straight-chain saturated fatty acid. 0 C6H12O2 InChI=1S/C6H12O2/c1-2-3-4-5-6(7)8/h2-5H2,1H3,(H,7,8) FUZZWVXGSFPDMH-UHFFFAOYSA-N 116.15830 116.08373 CCCCCC(O)=O CHEBI:24571 CHEBI:40213 CHEBI:5702 Beilstein:773837 CAS:142-62-1 ECMDB:ECMDB21229 Gmelin:185066 HMDB:HMDB0000535 KEGG:C01585 KNApSAcK:C00001218 LIPID_MAPS_instance:LMFA01010006 MetaCyc:HEXANOATE PDBeChem:6NA PMID:10685018 PMID:1556177 PMID:24357269 PMID:24924750 Reaxys:773837 Wikipedia:Hexanoic_acid YMDB:YMDB01424 HEXANOIC ACID Hexanoic acid hexanoic acid chebi_ontology 1-hexanoic acid 1-pentanecarboxylic acid 6:0 C6:0 CH3-[CH2]4-COOH Hexanoate Hexylic acid Pentanecarboxylic acid butylacetic acid caproic acid capronic acid hexoic acid n-Caproic acid n-hexanoic acid n-hexoic acid n-hexylic acid pentiformic acid pentylformic acid CHEBI:30776 hexanoic acid Beilstein:773837 Beilstein CAS:142-62-1 ChemIDplus CAS:142-62-1 KEGG COMPOUND CAS:142-62-1 NIST Chemistry WebBook Gmelin:185066 Gmelin LIPID_MAPS_instance:LMFA01010006 LIPID MAPS PMID:10685018 Europe PMC PMID:1556177 Europe PMC PMID:24357269 Europe PMC PMID:24924750 Europe PMC Reaxys:773837 Reaxys HEXANOIC ACID PDBeChem Hexanoic acid KEGG_COMPOUND hexanoic acid IUPAC 1-hexanoic acid ChemIDplus 1-pentanecarboxylic acid ChemIDplus 6:0 ChEBI C6:0 ChEBI CH3-[CH2]4-COOH IUPAC Hexanoate KEGG_COMPOUND Hexylic acid KEGG_COMPOUND Pentanecarboxylic acid ChemIDplus butylacetic acid ChemIDplus caproic acid ChEBI capronic acid NIST_Chemistry_WebBook hexoic acid NIST_Chemistry_WebBook n-Caproic acid KEGG_COMPOUND n-hexanoic acid NIST_Chemistry_WebBook n-hexoic acid ChemIDplus n-hexylic acid ChemIDplus pentiformic acid ChemIDplus pentylformic acid ChemIDplus A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. 0 HOR 17.007 17.00274 O[*] CHEBI:13804 CHEBI:22288 CHEBI:2553 KEGG:C00069 Alcohol alcohols chebi_ontology an alcohol CHEBI:30879 alcohol Alcohol KEGG_COMPOUND alcohols IUPAC an alcohol UniProt -1 C8H11N2O3S InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/p-1/t3-,4+,6-/m1/s1 NGHVIOIJCVXTGV-ALEPSDHESA-M 215.25062 215.04959 [H][C@@]1(N)C(=O)N2[C@]1([H])SC(C)(C)[C@]2([H])C([O-])=O CHEBI:12207 CHEBI:20704 Gmelin:604420 KEGG:C02954 (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate chebi_ontology CHEBI:30938 6-aminopenicillanate Gmelin:604420 Gmelin (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate IUPAC Any member of a group of hydroxy-5beta-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5beta-configuration. KEGG:C01558 Bile acid chebi_ontology 5beta-bile acid 5beta-bile acids Bile salt Gallensaeure Gallensaeuren bile acids CHEBI:3098 bile acid Bile acid KEGG_COMPOUND 5beta-bile acid ChEBI 5beta-bile acids ChEBI Bile salt KEGG_COMPOUND Gallensaeure ChEBI Gallensaeuren ChEBI bile acids ChEBI A short-chain fatty acid anion that is the conjugate base of valeric acid; present in ester form as component of many steroid-based pharmaceuticals. -1 C5H9O2 InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7)/p-1 NQPDZGIKBAWPEJ-UHFFFAOYSA-M 101.12376 101.06080 CCCCC([O-])=O CHEBI:14751 CHEBI:25890 Beilstein:3903735 CAS:10023-74-2 Gmelin:325619 PMID:17314444 PMID:18783570 Reaxys:3903735 pentanoate chebi_ontology CH3-[CH2]3-COO(-) n-propylacetate pentanoate pentanoic acid, ion(1-) CHEBI:31011 valerate Beilstein:3903735 Beilstein CAS:10023-74-2 ChemIDplus Gmelin:325619 Gmelin PMID:17314444 Europe PMC PMID:18783570 Europe PMC Reaxys:3903735 Reaxys pentanoate IUPAC CH3-[CH2]3-COO(-) IUPAC n-propylacetate ChEBI pentanoate UniProt pentanoic acid, ion(1-) ChemIDplus The L-enantiomer of cysteinate(1-). -1 C3H6NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-1/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-M 120.15128 120.01247 N[C@@H](CS)C([O-])=O Beilstein:4128886 Gmelin:325857 Reaxys:4128886 L-cysteinate(1-) hydrogen L-cysteinate chebi_ontology (2R)-2-amino-3-mercaptopropanoate (2R)-2-amino-3-sulfanylpropanoate L-cysteine anion L-cysteine monoanion CHEBI:32442 L-cysteinate(1-) Beilstein:4128886 Beilstein Gmelin:325857 Gmelin Reaxys:4128886 Reaxys L-cysteinate(1-) JCBN hydrogen L-cysteinate IUPAC (2R)-2-amino-3-mercaptopropanoate ChEBI (2R)-2-amino-3-sulfanylpropanoate IUPAC L-cysteine anion NIST_Chemistry_WebBook L-cysteine monoanion JCBN The L-enantiomer of cysteinate(2-). -2 C3H5NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-2/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-L 119.14334 119.00520 N[C@@H](C[S-])C([O-])=O Beilstein:5921923 Gmelin:325856 Reaxys:5921923 L-cysteinate L-cysteinate(2-) chebi_ontology (2R)-2-amino-3-sulfidopropanoate L-cysteine dianion CHEBI:32443 L-cysteinate(2-) Beilstein:5921923 Beilstein Gmelin:325856 Gmelin Reaxys:5921923 Reaxys L-cysteinate IUPAC L-cysteinate(2-) JCBN (2R)-2-amino-3-sulfidopropanoate IUPAC L-cysteine dianion JCBN The L-enantiomer of cysteinium. +1 C3H8NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p+1/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-O 122.16716 122.02703 [NH3+][C@@H](CS)C(O)=O Gmelin:325860 L-cysteinium chebi_ontology (1R)-1-carboxy-2-mercaptoethanaminium (1R)-1-carboxy-2-sulfanylethanaminium L-cysteine cation L-cysteinium(1+) CHEBI:32445 L-cysteinium Gmelin:325860 Gmelin L-cysteinium IUPAC (1R)-1-carboxy-2-mercaptoethanaminium ChEBI (1R)-1-carboxy-2-sulfanylethanaminium IUPAC L-cysteine cation JCBN L-cysteinium(1+) ChEBI The D-enantiomer of cysteinate(1-). -1 C3H6NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-1/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-M 120.15128 120.01247 N[C@H](CS)C([O-])=O Gmelin:1006156 D-cysteinate(1-) hydrogen D-cysteinate chebi_ontology (2S)-2-amino-3-mercaptopropanoate (2S)-2-amino-3-sulfanylpropanoate D-cysteine monoanion CHEBI:32449 D-cysteinate(1-) Gmelin:1006156 Gmelin D-cysteinate(1-) JCBN hydrogen D-cysteinate IUPAC (2S)-2-amino-3-mercaptopropanoate ChEBI (2S)-2-amino-3-sulfanylpropanoate IUPAC D-cysteine monoanion JCBN The D-enantiomer of cysteinate(2-). -2 C3H5NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-2/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-L 119.14334 119.00520 N[C@H](C[S-])C([O-])=O Gmelin:1342792 D-cysteinate D-cysteinate(2-) chebi_ontology (2S)-2-amino-3-sulfidopropanoate D-cysteine dianion CHEBI:32450 D-cysteinate(2-) Gmelin:1342792 Gmelin D-cysteinate IUPAC D-cysteinate(2-) JCBN (2S)-2-amino-3-sulfidopropanoate IUPAC D-cysteine dianion JCBN The D-enantiomer of cysteinium. +1 C3H8NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p+1/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-O 122.16716 122.02703 [NH3+][C@H](CS)C(O)=O Gmelin:363237 D-cysteinium chebi_ontology (1S)-1-carboxy-2-mercaptoethanaminium (1S)-1-carboxy-2-sulfanylethanaminium D-cysteine cation CHEBI:32451 D-cysteinium Gmelin:363237 Gmelin D-cysteinium IUPAC (1S)-1-carboxy-2-mercaptoethanaminium ChEBI (1S)-1-carboxy-2-sulfanylethanaminium IUPAC D-cysteine cation JCBN A sulfur-containing amino-acid anion that is the conjugate base of cysteine, obtained by deprotonation of the carboxy group. -1 C3H6NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-1 XUJNEKJLAYXESH-UHFFFAOYSA-M 120.15128 120.01247 NC(CS)C([O-])=O Beilstein:4128885 Gmelin:363235 Reaxys:4128885 cysteinate(1-) hydrogen cysteinate chebi_ontology 2-amino-3-mercaptopropanoate 2-amino-3-sulfanylpropanoate cys(-) cysteine monoanion CHEBI:32456 cysteinate(1-) Beilstein:4128885 Beilstein Gmelin:363235 Gmelin Reaxys:4128885 Reaxys cysteinate(1-) JCBN hydrogen cysteinate IUPAC 2-amino-3-mercaptopropanoate ChEBI 2-amino-3-sulfanylpropanoate IUPAC cys(-) IUPAC cysteine monoanion JCBN -2 C3H5NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p-2 XUJNEKJLAYXESH-UHFFFAOYSA-L 119.14334 119.00520 NC(C[S-])C([O-])=O Gmelin:49990 cysteinate cysteinate(2-) chebi_ontology 2-amino-3-sulfidopropanoate cysteine dianion CHEBI:32457 cysteinate(2-) Gmelin:49990 Gmelin cysteinate IUPAC cysteinate(2-) JCBN 2-amino-3-sulfidopropanoate IUPAC cysteine dianion JCBN +1 C3H8NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/p+1 XUJNEKJLAYXESH-UHFFFAOYSA-O 122.16716 122.02703 [NH3+]C(CS)C(O)=O Gmelin:325859 1-carboxy-2-sulfanylethanaminium cysteinium chebi_ontology 1-carboxy-2-mercaptoethanaminium H2cys(+) cysteine cation CHEBI:32458 cysteinium Gmelin:325859 Gmelin 1-carboxy-2-sulfanylethanaminium IUPAC cysteinium JCBN 1-carboxy-2-mercaptoethanaminium ChEBI H2cys(+) IUPAC cysteine cation JCBN An aromatic amino-acid anion that is the conjugate base of phenylalanine, arising from deprotonation of the carboxy group. -1 C9H10NO2 InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/p-1 COLNVLDHVKWLRT-UHFFFAOYSA-M 164.18120 164.07170 NC(Cc1ccccc1)C([O-])=O Gmelin:329083 phenylalaninate chebi_ontology 2-amino-3-phenylpropanoate phenylalanine anion CHEBI:32504 phenylalaninate Gmelin:329083 Gmelin phenylalaninate IUPAC 2-amino-3-phenylpropanoate IUPAC phenylalanine anion JCBN An alpha-amino-acid cation that is the conjugate acid of phenylalanine, arising from protonation of the amino group. +1 C9H12NO2 InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/p+1 COLNVLDHVKWLRT-UHFFFAOYSA-O 166.19710 166.08626 [NH3+]C(Cc1ccccc1)C(O)=O phenylalaninium chebi_ontology 1-carboxy-2-phenylethanaminium phenylalanine cation CHEBI:32505 phenylalaninium phenylalaninium IUPAC 1-carboxy-2-phenylethanaminium IUPAC phenylalanine cation JCBN An alpha-amino-acid cation that is the conjugate acid of glycine, arising from protonation of the amino. +1 C2H6NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/p+1 DHMQDGOQFOQNFH-UHFFFAOYSA-O 76.07458 76.03930 [NH3+]CC(O)=O Gmelin:323509 glycinium chebi_ontology H2gly(+) NH3(+)-CH2-COOH carboxymethanaminium glycine cation CHEBI:32507 glycinium Gmelin:323509 Gmelin glycinium IUPAC H2gly(+) IUPAC NH3(+)-CH2-COOH IUPAC carboxymethanaminium IUPAC glycine cation JCBN An alpha-amino-acid anion that is the conjugate base of glycine, arising from deprotonation of the carboxy group. -1 C2H4NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)/p-1 DHMQDGOQFOQNFH-UHFFFAOYSA-M 74.05870 74.02475 NCC([O-])=O Beilstein:1852023 Gmelin:81890 Reaxys:1852023 UM-BBD_compID:c0559 glycinate chebi_ontology H2N-CH2-COO(-) aminoacetate gly(-) glycine anion CHEBI:32508 glycinate Beilstein:1852023 Beilstein Gmelin:81890 Gmelin Reaxys:1852023 Reaxys UM-BBD_compID:c0559 UM-BBD glycinate IUPAC H2N-CH2-COO(-) IUPAC aminoacetate IUPAC gly(-) IUPAC glycine anion JCBN A pyridinemonocarboxylate that is the conjugate base of nicotinic acid, arising from deprotonation of the carboxy group; major species at pH 7.3. -1 C6H4NO2 InChI=1S/C6H5NO2/c8-6(9)5-2-1-3-7-4-5/h1-4H,(H,8,9)/p-1 PVNIIMVLHYAWGP-UHFFFAOYSA-M 122.10150 122.02475 [O-]C(=O)c1cccnc1 CHEBI:14650 CHEBI:22851 CHEBI:25530 Beilstein:3539722 Gmelin:327384 MetaCyc:NIACINE PMID:17190852 PMID:21742010 PMID:21953179 Reaxys:3539722 nicotinate pyridine-3-carboxylate chebi_ontology 3-pyridinecarboxylate CHEBI:32544 nicotinate Beilstein:3539722 Beilstein Gmelin:327384 Gmelin PMID:17190852 Europe PMC PMID:21742010 Europe PMC PMID:21953179 Europe PMC Reaxys:3539722 Reaxys nicotinate UniProt pyridine-3-carboxylate IUPAC 3-pyridinecarboxylate ChEBI An alpha-amino-acid anion that is the conjugate base of lysine, arising from deprotonation of the carboxy group. -1 C6H13N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p-1 KDXKERNSBIXSRK-UHFFFAOYSA-M 145.17970 145.09825 NCCCCC(N)C([O-])=O Gmelin:815095 lysinate chebi_ontology 2,6-diaminohexanoate lys(-) lysinate(1-) lysine anion CHEBI:32563 lysinate Gmelin:815095 Gmelin lysinate IUPAC 2,6-diaminohexanoate IUPAC lys(-) IUPAC lysinate(1-) ChEBI lysine anion JCBN An alpha-amino-acid cation that is the conjugate acid of lysine, having two cationic amino groups and an anionic carboxy group. +1 C6H15N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1 KDXKERNSBIXSRK-UHFFFAOYSA-O 147.19558 147.11280 [NH3+]CCCCC([NH3+])C([O-])=O lysinium lysinium(1+) chebi_ontology 2,6-diammoniohexanoate lysine monocation CHEBI:32564 lysinium(1+) lysinium IUPAC lysinium(1+) JCBN 2,6-diammoniohexanoate IUPAC lysine monocation JCBN An alpha-amino-acid cation obtained by protonation of both amino groups of lysine. +2 C6H16N2O2 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+2 KDXKERNSBIXSRK-UHFFFAOYSA-P 148.20352 148.12008 [NH3+]CCCCC([NH3+])C(O)=O lysinediium lysinium(2+) chebi_ontology 1-carboxypentane-1,5-diaminium lysine dication CHEBI:32565 lysinium(2+) lysinediium IUPAC lysinium(2+) JCBN 1-carboxypentane-1,5-diaminium IUPAC lysine dication JCBN An acene that consists of four ortho-fused benzene rings in a rectilinear arrangement. 0 C18H12 InChI=1S/C18H12/c1-2-6-14-10-18-12-16-8-4-3-7-15(16)11-17(18)9-13(14)5-1/h1-12H IFLREYGFSNHWGE-UHFFFAOYSA-N 228.28788 228.09390 c1ccc2cc3cc4ccccc4cc3cc2c1 Beilstein:1909299 CAS:92-24-0 Gmelin:306993 PMID:11493061 PMID:24655187 Reaxys:1909299 Wikipedia:Tetracene tetracene chebi_ontology 2,3-benzanthracene benz[b]anthracene naphthacene CHEBI:32600 tetracene Beilstein:1909299 Beilstein CAS:92-24-0 ChemIDplus CAS:92-24-0 NIST Chemistry WebBook Gmelin:306993 Gmelin PMID:11493061 Europe PMC PMID:24655187 Europe PMC Reaxys:1909299 Reaxys tetracene IUPAC 2,3-benzanthracene NIST_Chemistry_WebBook benz[b]anthracene NIST_Chemistry_WebBook naphthacene IUPAC Gmelin:101585 isoleucinate chebi_ontology ile(-) isoleucine anion rel-(2R,3R)-2-amino-3-methylpentanoate CHEBI:32612 isoleucinate Gmelin:101585 Gmelin isoleucinate IUPAC ile(-) IUPAC isoleucine anion JCBN rel-(2R,3R)-2-amino-3-methylpentanoate IUPAC Gmelin:1651827 isoleucinium chebi_ontology H2ile(+) isoleucine cation rel-(1R,2R)-1-carboxy-2-methylbutan-1-aminium CHEBI:32613 isoleucinium Gmelin:1651827 Gmelin isoleucinium IUPAC H2ile(+) IUPAC isoleucine cation JCBN rel-(1R,2R)-1-carboxy-2-methylbutan-1-aminium IUPAC An alpha-amino-acid anion that is the conjugate base of leucine, arising from deprotonation of the carboxy group. -1 C6H12NO2 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/p-1 ROHFNLRQFUQHCH-UHFFFAOYSA-M 130.16502 130.08735 CC(C)CC(N)C([O-])=O Reaxys:5245805 leucinate chebi_ontology 2-amino-4-methylpentanoate leu(-) leucine anion CHEBI:32627 leucinate Reaxys:5245805 Reaxys leucinate IUPAC 2-amino-4-methylpentanoate IUPAC leu(-) IUPAC leucine anion JCBN An alpha-amino-acid cation that is the conjugate acid of leucine, arising from protonation of the amino group. +1 C6H14NO2 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/p+1 ROHFNLRQFUQHCH-UHFFFAOYSA-O 132.18090 132.10191 CC(C)CC([NH3+])C(O)=O Gmelin:1651836 leucinium chebi_ontology 1-carboxy-3-methylbutan-1-aminium H2leu(+) leucine cation CHEBI:32628 leucinium Gmelin:1651836 Gmelin leucinium IUPAC 1-carboxy-3-methylbutan-1-aminium IUPAC H2leu(+) IUPAC leucine cation JCBN The L-enantiomer of methioninate. -1 C5H10NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p-1/t4-/m0/s1 FFEARJCKVFRZRR-BYPYZUCNSA-M 148.20444 148.04377 CSCC[C@H](N)C([O-])=O Beilstein:4740675 Gmelin:326566 Reaxys:4740675 L-methioninate chebi_ontology (2S)-2-amino-4-(methylsulfanyl)butanoate L-methionine anion CHEBI:32631 L-methioninate Beilstein:4740675 Beilstein Gmelin:326566 Gmelin Reaxys:4740675 Reaxys L-methioninate IUPAC (2S)-2-amino-4-(methylsulfanyl)butanoate IUPAC L-methionine anion JCBN The L-enantiomer of methioninium. +1 C5H12NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p+1/t4-/m0/s1 FFEARJCKVFRZRR-BYPYZUCNSA-O 150.22032 150.05833 CSCC[C@H]([NH3+])C(O)=O Gmelin:1568767 L-methioninium chebi_ontology (1S)-1-carboxy-3-(methylsulfanyl)propan-1-aminium L-methionine cation CHEBI:32632 L-methioninium Gmelin:1568767 Gmelin L-methioninium IUPAC (1S)-1-carboxy-3-(methylsulfanyl)propan-1-aminium IUPAC L-methionine cation JCBN The D-enantiomer of methioninate. -1 C5H10NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p-1/t4-/m1/s1 FFEARJCKVFRZRR-SCSAIBSYSA-M 148.20444 148.04377 CSCC[C@@H](N)C([O-])=O Gmelin:720123 D-methioninate chebi_ontology (2R)-2-amino-4-(methylsulfanyl)butanoate D-methionine anion CHEBI:32637 D-methioninate Gmelin:720123 Gmelin D-methioninate IUPAC (2R)-2-amino-4-(methylsulfanyl)butanoate IUPAC D-methionine anion JCBN The D-enantiomer of methioninium. +1 C5H12NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p+1/t4-/m1/s1 FFEARJCKVFRZRR-SCSAIBSYSA-O 150.22032 150.05833 CSCC[C@@H]([NH3+])C(O)=O D-methioninium chebi_ontology (1R)-1-carboxy-3-(methylsulfanyl)propan-1-aminium D-methionine cation CHEBI:32638 D-methioninium D-methioninium IUPAC (1R)-1-carboxy-3-(methylsulfanyl)propan-1-aminium IUPAC D-methionine cation JCBN A sulfur-containing amino-acid anion that is the conjugate base of methionine, arising from deprotonation of the carboxy group. -1 C5H10NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p-1 FFEARJCKVFRZRR-UHFFFAOYSA-M 148.20444 148.04377 CSCCC(N)C([O-])=O Beilstein:3937270 Gmelin:326565 Reaxys:3937270 methioninate chebi_ontology 2-amino-4-(methylsulfanyl)butanoate met(-) methionine anion CHEBI:32644 methioninate Beilstein:3937270 Beilstein Gmelin:326565 Gmelin Reaxys:3937270 Reaxys methioninate IUPAC 2-amino-4-(methylsulfanyl)butanoate IUPAC met(-) IUPAC methionine anion JCBN A sulfur-containing amino-acid anion that is the conjugate acid of methionine, arising from protonation of the amino group. +1 C5H12NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/p+1 FFEARJCKVFRZRR-UHFFFAOYSA-O 150.22032 150.05833 CSCCC([NH3+])C(O)=O Gmelin:326567 methioninium chebi_ontology 1-carboxy-3-(methylsulfanyl)propan-1-aminium H2met(+) methionine cation CHEBI:32646 methioninium Gmelin:326567 Gmelin methioninium IUPAC 1-carboxy-3-(methylsulfanyl)propan-1-aminium IUPAC H2met(+) IUPAC methionine cation JCBN -1 C6H13N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p-1 ODKSFYDXXFIFQN-UHFFFAOYSA-M 173.19318 173.10440 NC(CCCNC(N)=N)C([O-])=O Gmelin:603497 argininate chebi_ontology 2-amino-5-(carbamimidamido)pentanoate 2-amino-5-guanidinopentanoate arg(-) arginine anion CHEBI:32695 argininate Gmelin:603497 Gmelin argininate IUPAC 2-amino-5-(carbamimidamido)pentanoate IUPAC 2-amino-5-guanidinopentanoate JCBN arg(-) IUPAC arginine anion JCBN +1 C6H15N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1 ODKSFYDXXFIFQN-UHFFFAOYSA-O 175.20906 175.11895 NC(=[NH2+])NCCCC([NH3+])C([O-])=O Gmelin:1345599 argininium argininium(1+) chebi_ontology 2-ammonio-5-guanidiniopentanoate H2arg(+) arginine arginine monocation CHEBI:32696 argininium(1+) Gmelin:1345599 Gmelin argininium IUPAC argininium(1+) JCBN 2-ammonio-5-guanidiniopentanoate JCBN H2arg(+) IUPAC arginine UniProt arginine monocation JCBN +2 C6H16N4O2 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+2 ODKSFYDXXFIFQN-UHFFFAOYSA-P 176.21700 176.12623 NC(=[NH2+])NCCCC([NH3+])C(O)=O argininediium argininium(2+) chebi_ontology (1-carboxy-4-guanidiniobutyl)ammonium H3arg(2+) arginine dication CHEBI:32697 argininium(2+) argininediium IUPAC argininium(2+) JCBN (1-carboxy-4-guanidiniobutyl)ammonium ChEBI H3arg(2+) IUPAC arginine dication JCBN An alpha-amino-acid anion that is the conjugate base of tyrosine, arising from deprotonation of the carboxy group. -1 C9H10NO3 InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/p-1 OUYCCCASQSFEME-UHFFFAOYSA-M 180.18064 180.06662 NC(Cc1ccc(O)cc1)C([O-])=O Beilstein:3548387 Beilstein:4139515 Gmelin:329372 hydrogen tyrosinate tyrosinate(1-) chebi_ontology 2-amino-3-(4-hydroxyphenyl)propanoate tyrosine anion CHEBI:32784 tyrosinate(1-) Beilstein:3548387 Beilstein Beilstein:4139515 Beilstein Gmelin:329372 Gmelin hydrogen tyrosinate IUPAC tyrosinate(1-) JCBN 2-amino-3-(4-hydroxyphenyl)propanoate IUPAC tyrosine anion JCBN -2 C9H9NO3 InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/p-2 OUYCCCASQSFEME-UHFFFAOYSA-L 179.17270 179.05934 NC(Cc1ccc([O-])cc1)C([O-])=O tyrosinate tyrosinate(2-) chebi_ontology 2-amino-3-(4-oxidophenyl)propanoate tyrosine dianion CHEBI:32785 tyrosinate(2-) tyrosinate IUPAC tyrosinate(2-) JCBN 2-amino-3-(4-oxidophenyl)propanoate IUPAC tyrosine dianion JCBN An alpha-amino-acid cation that is the conjugate acid of tyrosine, arising from protonation of the amino group. +1 C9H12NO3 InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/p+1 OUYCCCASQSFEME-UHFFFAOYSA-O 182.19652 182.08117 [NH3+]C(Cc1ccc(O)cc1)C(O)=O tyrosinium chebi_ontology 1-carboxy-2-(4-hydroxyphenyl)ethanaminium tyrosine cation CHEBI:32786 tyrosinium tyrosinium IUPAC 1-carboxy-2-(4-hydroxyphenyl)ethanaminium IUPAC tyrosine cation JCBN A 2-oxo monocarboxylic acid that is the 2-keto derivative of propionic acid. It is a metabolite obtained during glycolysis. 0 C3H4O3 InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6) LCTONWCANYUPML-UHFFFAOYSA-N 88.06206 88.01604 CC(=O)C(O)=O CHEBI:26466 CHEBI:45253 CHEBI:8685 Beilstein:506211 CAS:127-17-3 DrugBank:DB00119 ECMDB:ECMDB00243 Gmelin:101087 HMDB:HMDB0000243 KEGG:C00022 KNApSAcK:C00001200 LIPID_MAPS_instance:LMFA01060077 MetaCyc:PYRUVATE PDBeChem:PYR PMID:11762589 PMID:19260671 PMID:22150460 PMID:22233273 PMID:22735334 PMID:22770225 Reaxys:506211 Wikipedia:Pyruvic_acid YMDB:YMDB00175 2-oxopropanoic acid PYRUVIC ACID Pyruvic acid pyruvic acid chebi_ontology 2-Oxopropanoic acid 2-Oxopropansaeure 2-Oxopropionsaeure 2-ketopropionic acid 2-oxopropanoic acid Acetylformic acid BTS Brenztraubensaeure CH3COCOOH Pyroracemic acid acetylformic acid acide pyruvique alpha-Oxopropionsaeure alpha-ketopropionic acid CHEBI:32816 pyruvic acid Beilstein:506211 Beilstein CAS:127-17-3 ChemIDplus CAS:127-17-3 NIST Chemistry WebBook Gmelin:101087 Gmelin LIPID_MAPS_instance:LMFA01060077 LIPID MAPS PMID:11762589 Europe PMC PMID:19260671 Europe PMC PMID:22150460 Europe PMC PMID:22233273 Europe PMC PMID:22735334 Europe PMC PMID:22770225 Europe PMC Reaxys:506211 Reaxys 2-oxopropanoic acid IUPAC PYRUVIC ACID PDBeChem Pyruvic acid KEGG_COMPOUND pyruvic acid ChEBI 2-Oxopropanoic acid KEGG_COMPOUND 2-Oxopropansaeure ChemIDplus 2-Oxopropionsaeure ChemIDplus 2-ketopropionic acid ChemIDplus 2-oxopropanoic acid ChEBI Acetylformic acid HMDB BTS ChemIDplus Brenztraubensaeure ChEBI CH3COCOOH NIST_Chemistry_WebBook Pyroracemic acid KEGG_COMPOUND acetylformic acid NIST_Chemistry_WebBook acide pyruvique ChEBI alpha-Oxopropionsaeure ChemIDplus alpha-ketopropionic acid NIST_Chemistry_WebBook A serinate that is the conjugate base of L-serine, obtained by deprotonation of the carboxy group. -1 C3H6NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p-1/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-M 104.08468 104.03532 N[C@@H](CO)C([O-])=O Beilstein:4372751 Gmelin:324693 L-serinate chebi_ontology (2S)-2-amino-3-hydroxypropanoate L-serine anion CHEBI:32836 L-serinate Beilstein:4372751 Beilstein Gmelin:324693 Gmelin L-serinate IUPAC (2S)-2-amino-3-hydroxypropanoate IUPAC L-serine anion JCBN A serinium that is the conjugate acid of L-serine, obtained by protonation of the amino group. +1 C3H8NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p+1/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-O 106.10056 106.04987 [NH3+][C@@H](CO)C(O)=O L-serinium chebi_ontology (1S)-1-carboxy-2-hydroxyethanaminium L-serine cation CHEBI:32837 L-serinium L-serinium IUPAC (1S)-1-carboxy-2-hydroxyethanaminium IUPAC L-serine cation JCBN The D-enantiomer of serinate. -1 C3H6NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p-1/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-M 104.08468 104.03532 N[C@H](CO)C([O-])=O Gmelin:745975 D-serinate chebi_ontology (2R)-2-amino-3-hydroxypropanoate D-serine anion CHEBI:32840 D-serinate Gmelin:745975 Gmelin D-serinate IUPAC (2R)-2-amino-3-hydroxypropanoate IUPAC D-serine anion JCBN The D-enantiomer of serinium. +1 C3H8NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p+1/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-O 106.10056 106.04987 [NH3+][C@H](CO)C(O)=O D-serinium chebi_ontology (1R)-1-carboxy-2-hydroxyethanaminium D-serine cation CHEBI:32841 D-serinium D-serinium IUPAC (1R)-1-carboxy-2-hydroxyethanaminium IUPAC D-serine cation JCBN An alpha-amino-acid anion that is the conjugate base of serine. -1 C3H6NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p-1 MTCFGRXMJLQNBG-UHFFFAOYSA-M 104.08468 104.03532 NC(CO)C([O-])=O Gmelin:324692 serinate chebi_ontology 2-amino-3-hydroxypropanoate serine anion CHEBI:32845 serinate Gmelin:324692 Gmelin serinate IUPAC 2-amino-3-hydroxypropanoate IUPAC serine anion JCBN An alpha-amino-acid cation that is the conjugate acid of serine. +1 C3H8NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/p+1 MTCFGRXMJLQNBG-UHFFFAOYSA-O 106.10056 106.04987 [NH3+]C(CO)C(O)=O Gmelin:1925675 serinium chebi_ontology 1-carboxy-2-hydroxyethanaminium serine cation CHEBI:32846 serinium Gmelin:1925675 Gmelin serinium IUPAC 1-carboxy-2-hydroxyethanaminium IUPAC serine cation JCBN -1 C5H10NO2 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/p-1 KZSNJWFQEVHDMF-UHFFFAOYSA-M 116.13844 116.07170 CC(C)C(N)C([O-])=O Gmelin:49876 valinate chebi_ontology 2-amino-3-methylbutanoate val(-) valine anion CHEBI:32859 valinate Gmelin:49876 Gmelin valinate IUPAC 2-amino-3-methylbutanoate IUPAC val(-) IUPAC valine anion JCBN +1 C5H12NO2 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/p+1 KZSNJWFQEVHDMF-UHFFFAOYSA-O 118.15432 118.08626 CC(C)C([NH3+])C(O)=O Gmelin:1651060 valinium chebi_ontology 1-carboxy-2-methylpropan-1-aminium H2val(+) valine cation CHEBI:32860 valinium Gmelin:1651060 Gmelin valinium IUPAC 1-carboxy-2-methylpropan-1-aminium IUPAC H2val(+) IUPAC valine cation JCBN A compound formally derived from ammonia by replacing three hydrogen atoms by hydrocarbyl groups. 0 NR3 14.00670 14.00307 [*]N([*])[*] CHEBI:26879 CHEBI:9458 KEGG:C02196 Tertiary amine tertiary amines chebi_ontology R3N tertiaeres Amin CHEBI:32876 tertiary amine Tertiary amine KEGG_COMPOUND tertiary amines IUPAC R3N IUPAC tertiaeres Amin ChEBI A compound formally derived from ammonia by replacing one hydrogen atom by a hydrocarbyl group. 0 H2NR 16.02260 16.01872 N[*] CHEBI:26263 CHEBI:26265 CHEBI:8407 CHEBI:8409 KEGG:C00375 KEGG:C00893 KEGG:C02580 Primary amine primary amines chebi_ontology Primary monoamine R-NH2 RCH2NH2 primaeres Amin CHEBI:32877 primary amine Primary amine KEGG_COMPOUND primary amines IUPAC Primary monoamine KEGG_COMPOUND R-NH2 IUPAC RCH2NH2 KEGG_COMPOUND primaeres Amin ChEBI 0 C3H8 InChI=1S/C3H8/c1-3-2/h3H2,1-2H3 ATUOYWHBWRKTHZ-UHFFFAOYSA-N 44.09562 44.06260 CCC Beilstein:1730718 CAS:74-98-6 Gmelin:25044 propane chebi_ontology CH3-CH2-CH3 E944 Propan CHEBI:32879 propane Beilstein:1730718 Beilstein CAS:74-98-6 ChemIDplus CAS:74-98-6 NIST Chemistry WebBook Gmelin:25044 Gmelin propane IUPAC propane UniProt CH3-CH2-CH3 IUPAC E944 ChEBI Propan ChEBI A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups. CHEBI:13814 CHEBI:22474 CHEBI:2641 KEGG:C00706 Amine amines chebi_ontology Amin Substituted amine CHEBI:32952 amine Amine KEGG_COMPOUND amines IUPAC Amin ChEBI Substituted amine KEGG_COMPOUND -1 C5H11N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p-1 AHLPHDHHMVZTML-UHFFFAOYSA-M 131.15312 131.08260 NCCCC(N)C([O-])=O CHEBI:11448 CHEBI:19370 Gmelin:1242186 2,5-diaminopentanoate ornithinate chebi_ontology ornithine anion CHEBI:32964 ornithinate Gmelin:1242186 Gmelin 2,5-diaminopentanoate IUPAC ornithinate IUPAC ornithine anion JCBN An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. CHEBI:22473 CHEBI:2633 KEGG:C00241 Amide amides chebi_ontology CHEBI:32988 amide Amide KEGG_COMPOUND amides IUPAC A calcium salt with formula CCaO3. calcium carbonate http://langual.org 0 CCaO3 CO3.Ca InChI=1S/CH2O3.Ca/c2-1(3)4;/h(H2,2,3,4);/q;+2/p-2 VTYYLEPIZMXCLO-UHFFFAOYSA-L 100.087 99.94733 [Ca+2].C(=O)([O-])[O-] BPDB:108 CAS:471-34-1 Codex::170(i) DrugBank:DB06724 Europe::170 KEGG:C08129 KEGG:D00932 PPDB:108 Reaxys:8008338 Wikipedia:Calcium_carbonate http://www.langual.org/langual_thesaurus.asp?termid=B3031 Calcium carbonate calcium carbonate calcium trioxidocarbonate chebi_ontology CaCO3 Calciumcarbonat E 170 Kalziumkarbonat Precipitated calcium carbonate calcium carbonate (1:1) carbonate de calcium carbonato de calcio carbonic acid calcium salt (1:1) kohlensaurer Kalk CHEBI:3311 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): acidity regulator, anticaking agent, stabilizer, surface colourant. calcium carbonate CAS:471-34-1 ChemIDplus CAS:471-34-1 KEGG COMPOUND CAS:471-34-1 NIST Chemistry WebBook Reaxys:8008338 Reaxys Calcium carbonate KEGG_COMPOUND calcium carbonate IUPAC calcium trioxidocarbonate IUPAC CaCO3 IUPAC Calciumcarbonat ChEBI E 170 ChEBI Kalziumkarbonat ChEBI Precipitated calcium carbonate KEGG_COMPOUND calcium carbonate (1:1) ChemIDplus carbonate de calcium ChEBI carbonato de calcio ChEBI carbonic acid calcium salt (1:1) ChemIDplus kohlensaurer Kalk ChEBI vitamin role A biochemical role played by any micronutrient that is an organic compound. Vitamins are present in foods in small amounts and are essential to normal metabolism and biochemical functions, usually as coenzymes. The term "vitamines" (from vita + amines) was coined in 1912 by Casimir Funk, who believed that these compounds were amines. Any micronutrient that is an organic compound. The term "vitamines" (from vita + amines) was coined in 1912 by Casimir Funk, who believed that these compounds were amines. CHEBI:10004 CHEBI:27305 Wikipedia:Vitamin Vitamin chebi_ontology vitamina vitaminas vitamine vitamines vitamins vitaminum CHEBI:33229 vitamin Vitamin ChEBI vitamina ChEBI vitaminas ChEBI vitamine ChEBI vitamines ChEBI vitamins ChEBI vitaminum ChEBI A substance that kills or slows the growth of Mycobacterium tuberculosis and is used in the treatment of tuberculosis. chebi_ontology antitubercular antitubercular agents antitubercular drug antitubercular drugs tuberculostatic agent CHEBI:33231 antitubercular agent antitubercular ChEBI antitubercular agents ChEBI antitubercular drug ChEBI antitubercular drugs ChEBI tuberculostatic agent ChEBI application role Intended use of the molecular entity or part thereof by humans. chebi_ontology CHEBI:33232 application A particle not known to have substructure. elementary particle chebi_ontology elementary particles CHEBI:33233 fundamental particle elementary particle IUPAC elementary particles ChEBI A monoatomic entity is a molecular entity consisting of a single atom. chebi_ontology atomic entity monoatomic entities CHEBI:33238 monoatomic entity atomic entity ChEBI monoatomic entities ChEBI An assembly consisting of a central atom (usually metallic) to which is attached a surrounding array of other groups of atoms (ligands). coordination entities coordination entity chebi_ontology coordination compounds CHEBI:33240 coordination entity coordination entities IUPAC coordination entity IUPAC coordination compounds ChEBI chebi_ontology oxoacid derivatives CHEBI:33241 oxoacid derivative oxoacid derivatives ChEBI chebi_ontology inorganic hydrides CHEBI:33242 inorganic hydride inorganic hydrides ChEBI An organic fundamental parent is a structure used as a basis for substitutive names in organic nomenclature, containing, in addition to one or more hydrogen atoms, a single atom of an element, a number of atoms (alike or different) linked together to form an unbranched chain, a monocyclic or polycyclic ring system, or a ring assembly or ring/chain system. chebi_ontology organic fundamental parents organic parent hydrides CHEBI:33245 organic fundamental parent organic fundamental parents ChEBI organic parent hydrides ChEBI Any substituent group which does not contain carbon. chebi_ontology inorganic groups CHEBI:33246 inorganic group inorganic groups ChEBI Any substituent group or skeleton containing carbon. chebi_ontology organic groups CHEBI:33247 organic group organic groups ChEBI A univalent group formed by removing a hydrogen atom from a hydrocarbon. hydrocarbyl group hydrocarbyl groups chebi_ontology groupe hydrocarbyle grupo hidrocarbilo grupos hidrocarbilo CHEBI:33248 hydrocarbyl group hydrocarbyl group IUPAC hydrocarbyl groups IUPAC groupe hydrocarbyle IUPAC grupo hidrocarbilo IUPAC grupos hidrocarbilo IUPAC Any organic substituent group, regardless of functional type, having one free valence at a carbon atom. organyl group organyl groups chebi_ontology groupe organyle grupo organilo grupos organilo CHEBI:33249 organyl group organyl group IUPAC organyl groups IUPAC groupe organyle IUPAC grupo organilo IUPAC grupos organilo IUPAC A chemical entity constituting the smallest component of an element having the chemical properties of the element. CHEBI:22671 CHEBI:23907 atom chebi_ontology atome atomo atoms atomus element elements CHEBI:33250 atom atom IUPAC atome IUPAC atomo IUPAC atoms ChEBI atomus ChEBI element ChEBI elements ChEBI A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. nucleus chebi_ontology Atomkern Kern noyau noyau atomique nuclei nucleo nucleo atomico nucleus atomi CHEBI:33252 atomic nucleus nucleus IUPAC Atomkern ChEBI Kern ChEBI noyau IUPAC noyau atomique ChEBI nuclei ChEBI nucleo IUPAC nucleo atomico ChEBI nucleus atomi ChEBI Heavy nuclear particle: proton or neutron. nucleon chebi_ontology Nukleon Nukleonen nucleons CHEBI:33253 nucleon nucleon IUPAC nucleon IUPAC Nukleon ChEBI Nukleonen ChEBI nucleons ChEBI A derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group. primary amide primary amides chebi_ontology CHEBI:33256 primary amide primary amide IUPAC primary amides IUPAC A molecular entity all atoms of which have the same atomic number. chebi_ontology homoatomic entity homoatomic molecular entities homoatomic molecular entity CHEBI:33259 elemental molecular entity homoatomic entity ChEBI homoatomic molecular entities ChEBI homoatomic molecular entity ChEBI An organosulfur compound is a compound containing at least one carbon-sulfur bond. CHEBI:23010 CHEBI:25714 Wikipedia:Organosulfur_compounds organosulfur compound chebi_ontology organosulfur compounds CHEBI:33261 organosulfur compound organosulfur compound ChEBI organosulfur compounds ChEBI An anion consisting of more than one atom. chebi_ontology polyatomic anions CHEBI:33273 polyatomic anion polyatomic anions ChEBI chebi_ontology chemical messenger CHEBI:33280 molecular messenger chemical messenger ChEBI A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans. CHEBI:22582 PMID:12964249 PMID:22117953 PMID:22439833 PMID:22849268 PMID:22849276 PMID:22958833 chebi_ontology Antibiotika Antibiotikum antibiotic antibiotics antibiotique antimicrobial antimicrobial agents antimicrobials microbicide microbicides CHEBI:33281 antimicrobial agent PMID:12964249 Europe PMC PMID:22117953 Europe PMC PMID:22439833 Europe PMC PMID:22849268 Europe PMC PMID:22849276 Europe PMC PMID:22958833 Europe PMC Antibiotika ChEBI Antibiotikum ChEBI antibiotic ChEBI antibiotics ChEBI antibiotique IUPAC antimicrobial ChEBI antimicrobial agents ChEBI antimicrobials ChEBI microbicide ChEBI microbicides ChEBI A substance (or active part thereof) that kills or slows the growth of bacteria. chebi_ontology antibacterial agents antibacterials bactericide bactericides CHEBI:33282 antibacterial agent antibacterial agents ChEBI antibacterials ChEBI bactericide ChEBI bactericides ChEBI nutrient role A nutrient is a food component that an organism uses to survive and grow. chebi_ontology nutrients CHEBI:33284 nutrient nutrients ChEBI A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms. chebi_ontology heteroorganic entities organoelement compounds CHEBI:33285 heteroorganic entity heteroorganic entities ChEBI organoelement compounds ChEBI An agrochemical is a substance that is used in agriculture or horticulture. Wikipedia:Agrochemical chebi_ontology agrichemical agrichemicals agricultural chemicals agrochemicals CHEBI:33286 agrochemical agrichemical ChEBI agrichemicals ChEBI agricultural chemicals ChEBI agrochemicals ChEBI A fertilizer is any substance that is added to soil or water to assist the growth of plants. chebi_ontology fertiliser fertilizers CHEBI:33287 fertilizer fertiliser ChEBI fertilizers ChEBI food role Any material that can be ingested by an organism. food An energy-rich substance that can be transformed with release of usable energy. chebi_ontology CHEBI:33292 fuel A molecular entity containing one or more atoms of an alkali metal. chebi_ontology alkali metal molecular entities CHEBI:33296 alkali metal molecular entity alkali metal molecular entities ChEBI An alkaline earth molecular entity is a molecular entity containing one or more atoms of an alkaline earth metal. alkaline earth molecular entity chebi_ontology alkaline earth compounds alkaline earth molecular entities alkaline-earth compounds CHEBI:33299 alkaline earth molecular entity alkaline earth molecular entity ChEBI alkaline earth compounds ChEBI alkaline earth molecular entities ChEBI alkaline-earth compounds ChEBI Any p-block element atom that is in group 15 of the periodic table: nitrogen, phosphorus, arsenic, antimony and bismuth. pnictogens chebi_ontology group 15 elements group V elements nitrogenoideos nitrogenoides pnictogene pnictogenes CHEBI:33300 pnictogen pnictogens IUPAC group 15 elements ChEBI group V elements ChEBI nitrogenoideos ChEBI nitrogenoides ChEBI pnictogene ChEBI pnictogenes ChEBI A p-block molecular entity containing any pnictogen. pnictogen molecular entity chebi_ontology pnictogen molecular entities CHEBI:33302 pnictogen molecular entity pnictogen molecular entity ChEBI pnictogen molecular entities ChEBI Any p-block element belonging to the group 16 family of the periodic table. PMID:17084588 chalcogen chalcogens chebi_ontology Chalkogen Chalkogene anfigeno anfigenos calcogeno calcogenos chalcogene chalcogenes group 16 elements group VI elements CHEBI:33303 chalcogen PMID:17084588 Europe PMC chalcogen IUPAC chalcogens IUPAC Chalkogen ChEBI Chalkogene ChEBI anfigeno ChEBI anfigenos ChEBI calcogeno ChEBI calcogenos ChEBI chalcogene ChEBI chalcogenes ChEBI group 16 elements ChEBI group VI elements ChEBI Any p-block molecular entity containing a chalcogen. chalcogen molecular entity chebi_ontology chalcogen compounds chalcogen molecular entities CHEBI:33304 chalcogen molecular entity chalcogen molecular entity ChEBI chalcogen compounds ChEBI chalcogen molecular entities ChEBI group 14 elements chebi_ontology carbon group element carbon group elements carbonoides cristallogene cristallogenes group IV elements CHEBI:33306 carbon group element atom group 14 elements IUPAC carbon group element ChEBI carbon group elements ChEBI carbonoides ChEBI cristallogene ChEBI cristallogenes ChEBI group IV elements ChEBI An ester of a carboxylic acid, R(1)C(=O)OR(2), where R(1) = H or organyl and R(2) = organyl. 0 CO2R2 44.010 43.98983 [*]C(=O)O[*] CHEBI:13204 CHEBI:23028 CHEBI:3408 KEGG:C02391 Wikipedia:Ester Carboxylic ester carboxylic esters chebi_ontology a carboxylic ester carboxylic acid esters CHEBI:33308 carboxylic ester Carboxylic ester KEGG_COMPOUND carboxylic esters IUPAC a carboxylic ester UniProt carboxylic acid esters ChEBI An atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table. main group elements chebi_ontology Hauptgruppenelement Hauptgruppenelemente main group element CHEBI:33318 main group element atom main group elements IUPAC Hauptgruppenelement ChEBI Hauptgruppenelemente ChEBI main group element ChEBI group 12 elements chebi_ontology zinc group element zinc group elements CHEBI:33340 zinc group element atom group 12 elements IUPAC zinc group element ChEBI zinc group elements ChEBI group 8 elements chebi_ontology iron group element iron group elements CHEBI:33356 iron group element atom group 8 elements IUPAC iron group element ChEBI iron group elements ChEBI group 9 elements chebi_ontology cobalt group element cobalt group elements CHEBI:33358 cobalt group element atom group 9 elements IUPAC cobalt group element ChEBI cobalt group elements ChEBI A serine zwitterion obtained by transfer of a proton from the carboxy to the amino group of L-serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1 MTCFGRXMJLQNBG-REOHCLBHSA-N 105.09262 105.04259 [NH3+][C@@H](CO)C([O-])=O MetaCyc:SER (2S)-2-ammonio-3-hydroxypropanoate L-serine zwitterion chebi_ontology L-serine CHEBI:33384 L-serine zwitterion (2S)-2-ammonio-3-hydroxypropanoate IUPAC L-serine zwitterion IUPAC L-serine UniProt chebi_ontology oxoacids of sulfur sulfur oxoacids CHEBI:33402 sulfur oxoacid oxoacids of sulfur ChEBI sulfur oxoacids ChEBI A hydracid is a compound which contains hydrogen that is not bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). hydracid chebi_ontology hydracids CHEBI:33405 hydracid hydracid IUPAC hydracids ChEBI chebi_ontology pnictogen oxoacids CHEBI:33408 pnictogen oxoacid pnictogen oxoacids ChEBI sulfur oxoacid derivative chebi_ontology sulfur oxoacid derivatives CHEBI:33424 sulfur oxoacid derivative sulfur oxoacid derivative ChEBI sulfur oxoacid derivatives ChEBI -1 0.00000 [*-] chebi_ontology monoatomic monoanions CHEBI:33429 monoatomic monoanion monoatomic monoanions ChEBI elemental halogen chebi_ontology elemental halogens CHEBI:33434 elemental halogen elemental halogen ChEBI elemental halogens ChEBI Arylmethyl groups and derivatives formed by substitution: ArCR2-. benzylic group benzylic groups chebi_ontology benzylic groups groupe benzylique CHEBI:33452 benzylic group benzylic group IUPAC benzylic groups IUPAC benzylic groups ChEBI groupe benzylique IUPAC A pnictogen oxoacid which contains phosphorus and oxygen, at least one hydrogen atom bound to oxygen, and forms an ion by the loss of one or more protons. phosphorus oxoacid chebi_ontology Oxosaeure des Phosphors oxoacids of phosphorus phosphorus oxoacids CHEBI:33457 phosphorus oxoacid phosphorus oxoacid ChEBI Oxosaeure des Phosphors ChEBI oxoacids of phosphorus ChEBI phosphorus oxoacids ChEBI pnictogen oxoanion chebi_ontology pnictogen oxoanions CHEBI:33459 pnictogen oxoanion pnictogen oxoanion ChEBI pnictogen oxoanions ChEBI phosphorus oxoanion chebi_ontology oxoanions of phosphorus phosphorus oxoanions CHEBI:33461 phosphorus oxoanion phosphorus oxoanion ChEBI oxoanions of phosphorus ChEBI phosphorus oxoanions ChEBI sulfur oxoanion chebi_ontology oxoanions of sulfur sulfur oxoanions CHEBI:33482 sulfur oxoanion sulfur oxoanion ChEBI oxoanions of sulfur ChEBI sulfur oxoanions ChEBI chalcogen oxoacid chebi_ontology chalcogen oxoacids CHEBI:33484 chalcogen oxoacid chalcogen oxoacid ChEBI chalcogen oxoacids ChEBI chalcogen oxoanion chebi_ontology chalcogen oxoanions CHEBI:33485 chalcogen oxoanion chalcogen oxoanion ChEBI chalcogen oxoanions ChEBI A molecular entity containing one or more atoms of a transition element. chebi_ontology transition element molecular entities transition metal molecular entity CHEBI:33497 transition element molecular entity transition element molecular entities ChEBI transition metal molecular entity ChEBI chebi_ontology alkali metal cations CHEBI:33504 alkali metal cation alkali metal cations ChEBI chebi_ontology alkaline earth cations alkaline earth metal cation alkaline-earth metal cations CHEBI:33513 alkaline earth cation alkaline earth cations ChEBI alkaline earth metal cation ChEBI alkaline-earth metal cations ChEBI chebi_ontology transition element cations transition metal cation CHEBI:33515 transition element cation transition element cations ChEBI transition metal cation ChEBI An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. CHEBI:25217 CHEBI:6788 KEGG:C00050 PMID:21784043 Wikipedia:Metal chebi_ontology elemental metal elemental metals metal element metal elements metals CHEBI:33521 metal atom PMID:21784043 Europe PMC elemental metal ChEBI elemental metals ChEBI metal element ChEBI metal elements ChEBI metals ChEBI The sulfur oxoanion formed by deprotonation of sulfonic acid. -1 HO3S InChI=1S/H2O3S/c1-4(2)3/h4H,(H,1,2,3)/p-1 BDHFUVZGWQCTTF-UHFFFAOYSA-M 81.07214 80.96519 [H]S([O-])(=O)=O Gmelin:971569 hydridotrioxidosulfate(1-) chebi_ontology SHO3(-) [SHO3](-) sulfonates CHEBI:33543 sulfonate Gmelin:971569 Gmelin hydridotrioxidosulfate(1-) IUPAC SHO3(-) IUPAC [SHO3](-) IUPAC sulfonates ChEBI sulfonic acid derivative chebi_ontology derivatives of sulfonic acid sulfonic acid derivatives CHEBI:33552 sulfonic acid derivative sulfonic acid derivative ChEBI derivatives of sulfonic acid ChEBI sulfonic acid derivatives ChEBI An amino-acid anion obtained by deprotonation of any alpha-amino acid. alpha-amino-acid anion chebi_ontology alpha-amino acid anions alpha-amino-acid anions CHEBI:33558 alpha-amino-acid anion alpha-amino-acid anion ChEBI alpha-amino acid anions ChEBI alpha-amino-acid anions ChEBI chebi_ontology s-block element s-block elements CHEBI:33559 s-block element atom s-block element ChEBI s-block elements ChEBI Any main group element atom belonging to the p-block of the periodic table. chebi_ontology p-block element p-block elements CHEBI:33560 p-block element atom p-block element ChEBI p-block elements ChEBI chebi_ontology d-block element d-block elements CHEBI:33561 d-block element atom d-block element ChEBI d-block elements ChEBI A carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid. 0 CHO2R 45.01740 44.99765 OC([*])=O CHEBI:13428 CHEBI:13627 CHEBI:23027 PMID:17147560 PMID:18433345 Wikipedia:Carboxylic_acid carboxylic acid carboxylic acids chebi_ontology Carbonsaeure Carbonsaeuren Karbonsaeure RC(=O)OH acide carboxylique acides carboxyliques acido carboxilico acidos carboxilicos CHEBI:33575 carboxylic acid PMID:17147560 Europe PMC PMID:18433345 Europe PMC carboxylic acid IUPAC carboxylic acids IUPAC Carbonsaeure ChEBI Carbonsaeuren ChEBI Karbonsaeure ChEBI RC(=O)OH IUPAC acide carboxylique IUPAC acides carboxyliques IUPAC acido carboxilico IUPAC acidos carboxilicos IUPAC Any carboxylic acid having a sulfur substituent. chebi_ontology S-containing carboxylic acid S-containing carboxylic acids sulfur-containing carboxylic acids CHEBI:33576 sulfur-containing carboxylic acid S-containing carboxylic acid ChEBI S-containing carboxylic acids ChEBI sulfur-containing carboxylic acids ChEBI A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table. chebi_ontology main group compounds main group molecular entities CHEBI:33579 main group molecular entity main group compounds ChEBI main group molecular entities ChEBI carbon group molecular entity chebi_ontology carbon group molecular entities CHEBI:33582 carbon group molecular entity carbon group molecular entity ChEBI carbon group molecular entities ChEBI Any molecule that consists of a series of atoms joined together to form a ring. Wikipedia:Cyclic_compound chebi_ontology cyclic compounds CHEBI:33595 cyclic compound cyclic compounds ChEBI A cyclic compound having as ring members atoms of the same element only. homocyclic compound homocyclic compounds chebi_ontology isocyclic compounds CHEBI:33597 homocyclic compound homocyclic compound IUPAC homocyclic compounds IUPAC isocyclic compounds IUPAC A homocyclic compound in which all of the ring members are carbon atoms. carbocyclic compound carbocyclic compounds chebi_ontology carbocycle CHEBI:33598 carbocyclic compound carbocyclic compound IUPAC carbocyclic compounds IUPAC carbocycle ChEBI chebi_ontology hydrogen compounds hydrogen molecular entities CHEBI:33608 hydrogen molecular entity hydrogen compounds ChEBI hydrogen molecular entities ChEBI chebi_ontology polycyclic compounds CHEBI:33635 polycyclic compound polycyclic compounds ChEBI A molecule that features two fused rings. chebi_ontology bicyclic compounds CHEBI:33636 bicyclic compound bicyclic compounds ChEBI A polycyclic compound in which two rings have two, and only two, atoms in common. Such compounds have n common faces and 2n common atoms. ortho-fused polycyclic compounds chebi_ontology ortho-fused compounds CHEBI:33637 ortho-fused compound ortho-fused polycyclic compounds IUPAC ortho-fused compounds ChEBI Any acyclic or cyclic, saturated or unsaturated carbon compound, excluding aromatic compounds. aliphatic compounds chebi_ontology CHEBI:33653 aliphatic compound aliphatic compounds IUPAC A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character. aromatic compounds aromatic molecular entity chebi_ontology aromatics aromatische Verbindungen CHEBI:33655 aromatic compound aromatic compounds IUPAC aromatic molecular entity IUPAC aromatics ChEBI aromatische Verbindungen ChEBI Any monocyclic or polycyclic aromatic hydrocarbon. arene arenes chebi_ontology aromatic hydrocarbons CHEBI:33658 arene arene IUPAC arenes IUPAC aromatic hydrocarbons IUPAC chebi_ontology organic aromatic compounds CHEBI:33659 organic aromatic compound organic aromatic compounds ChEBI chebi_ontology monocyclic compounds CHEBI:33661 monocyclic compound monocyclic compounds ChEBI A mancude monocyclic hydrocarbon without side chains of the general formula CnHn (n is an even number) or CnHn+1 (n is an odd number). In systematic nomenclature an annulene with seven or more carbon atoms may be named [n]annulene, where n is the number of carbon atoms. annulene annulenes chebi_ontology CHEBI:33662 annulene annulene IUPAC annulenes IUPAC cyclic hydrocarbon chebi_ontology cyclic hydrocarbons CHEBI:33663 cyclic hydrocarbon cyclic hydrocarbon ChEBI cyclic hydrocarbons ChEBI monocyclic hydrocarbon monocyclic hydrocarbons chebi_ontology monocyclic hydrocarbons CHEBI:33664 monocyclic hydrocarbon monocyclic hydrocarbon ChEBI monocyclic hydrocarbons IUPAC monocyclic hydrocarbons ChEBI polycyclic hydrocarbon polycyclic hydrocarbons chebi_ontology CHEBI:33666 polycyclic hydrocarbon polycyclic hydrocarbon IUPAC polycyclic hydrocarbons IUPAC heteromonocyclic compound heteromonocyclic compounds chebi_ontology CHEBI:33670 heteromonocyclic compound heteromonocyclic compound IUPAC heteromonocyclic compounds IUPAC A polycyclic compound in which at least one of the rings contains at least one non-carbon atom. heteropolycyclic compounds chebi_ontology polyheterocyclic compounds CHEBI:33671 heteropolycyclic compound heteropolycyclic compounds IUPAC polyheterocyclic compounds ChEBI A bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom. heterobicyclic compounds chebi_ontology CHEBI:33672 heterobicyclic compound heterobicyclic compounds IUPAC chebi_ontology zinc group molecular entities CHEBI:33673 zinc group molecular entity zinc group molecular entities ChEBI An s-block molecular entity is a molecular entity containing one or more atoms of an s-block element. s-block molecular entity chebi_ontology s-block compounds s-block molecular entities CHEBI:33674 s-block molecular entity s-block molecular entity ChEBI s-block compounds ChEBI s-block molecular entities ChEBI A main group molecular entity that contains one or more atoms of a p-block element. chebi_ontology p-block compounds p-block molecular entities p-block molecular entitiy CHEBI:33675 p-block molecular entity p-block compounds ChEBI p-block molecular entities ChEBI p-block molecular entitiy ChEBI A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element. d-block molecular entity chebi_ontology d-block compounds d-block molecular entities CHEBI:33676 d-block molecular entity d-block molecular entity ChEBI d-block compounds ChEBI d-block molecular entities ChEBI Hydrides are chemical compounds of hydrogen with other chemical elements. chebi_ontology CHEBI:33692 hydrides A cation consisting of more than one atom. chebi_ontology polyatomic cations CHEBI:33702 polyatomic cation polyatomic cations ChEBI amino-acid cation chebi_ontology amino acid cation amino-acid cations CHEBI:33703 amino-acid cation amino-acid cation ChEBI amino acid cation ChEBI amino-acid cations ChEBI An amino acid in which the amino group is located on the carbon atom at the position alpha to the carboxy group. 0 C2H4NO2R 74.05870 74.02420 NC([*])C(O)=O CHEBI:10208 CHEBI:13779 CHEBI:22442 CHEBI:2642 KEGG:C00045 KEGG:C05167 alpha-amino acid chebi_ontology Amino acid Amino acids alpha-amino acids alpha-amino carboxylic acids CHEBI:33704 alpha-amino acid alpha-amino acid IUPAC Amino acid KEGG_COMPOUND Amino acids KEGG_COMPOUND alpha-amino acids ChEBI alpha-amino acids JCBN alpha-amino carboxylic acids IUPAC A non-proteinogenic amino-acid in which the amino group is located on the carbon atom at the position gamma to the carboxy group. gamma-amino acid chebi_ontology gamma-amino acids CHEBI:33707 gamma-amino acid gamma-amino acid ChEBI gamma-amino acids ChEBI amino acid A carboxylic acid containing one or more amino groups. CHEBI:13815 CHEBI:22477 Wikipedia:Amino_acid chebi_ontology Aminocarbonsaeure Aminokarbonsaeure Aminosaeure amino acids CHEBI:33709 amino acid Aminocarbonsaeure ChEBI Aminokarbonsaeure ChEBI Aminosaeure ChEBI amino acids ChEBI alpha-amino-acid cation chebi_ontology alpha-amino acid cations alpha-amino-acid cations CHEBI:33719 alpha-amino-acid cation alpha-amino-acid cation ChEBI alpha-amino acid cations ChEBI alpha-amino-acid cations ChEBI carbohydrate acid chebi_ontology carbohydrate acids CHEBI:33720 carbohydrate acid carbohydrate acid ChEBI carbohydrate acids ChEBI carbohydrate acid anion chebi_ontology carbohydrate acid anions CHEBI:33721 carbohydrate acid anion carbohydrate acid anion ChEBI carbohydrate acid anions ChEBI iron group molecular entity chebi_ontology iron group molecular entities CHEBI:33744 iron group molecular entity iron group molecular entity ChEBI iron group molecular entities ChEBI cobalt group molecular entity chebi_ontology cobalt group molecular entities CHEBI:33767 cobalt group molecular entity cobalt group molecular entity ChEBI cobalt group molecular entities ChEBI An organic compound having at least one hydroxy group attached to a carbon atom. CHEBI:64710 hydroxy compounds chebi_ontology organic alcohol organic hydroxy compounds CHEBI:33822 organic hydroxy compound hydroxy compounds IUPAC organic alcohol ChEBI organic hydroxy compounds ChEBI Alkenols; the term refers specifically to vinylic alcohols, which have the structure HOCR'=CR2. Enols are tautomeric with aldehydes (R' = H) or ketones (R' =/= H). 0 C2HOR3 41.029 41.00274 OC(=C(*)*)* enol enols chebi_ontology alkenols enols CHEBI:33823 enol enol IUPAC enols IUPAC alkenols IUPAC enols ChEBI Any organic molecule that consists of atoms connected in the form of a ring. chebi_ontology organic cyclic compounds CHEBI:33832 organic cyclic compound organic cyclic compounds ChEBI A heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2). heteroarenes chebi_ontology hetarenes CHEBI:33833 heteroarene heteroarenes IUPAC hetarenes IUPAC chebi_ontology benzenoid aromatic compounds benzenoid compound CHEBI:33836 benzenoid aromatic compound benzenoid aromatic compounds ChEBI benzenoid compound ChEBI An N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents. 0 C5H8O3R2 116.115 116.04734 [C@H]1([C@H]([C@@H](*)[C@@H](O1)*)O)CO CHEBI:13661 CHEBI:25611 CHEBI:7647 KEGG:C00801 Nucleoside nucleosides chebi_ontology a nucleoside nucleosides CHEBI:33838 nucleoside Nucleoside KEGG_COMPOUND nucleosides IUPAC a nucleoside UniProt nucleosides ChEBI macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer macromolecule chebi_ontology aromatic annulenes CHEBI:33842 aromatic annulene aromatic annulenes ChEBI A monocyclic aromatic hydrocarbon. chebi_ontology monocyclic arenes CHEBI:33847 monocyclic arene monocyclic arenes ChEBI A polycyclic aromatic hydrocarbon. PMID:15198916 PMID:25679824 Wikipedia:Polycyclic_aromatic_hydrocarbon chebi_ontology PAH PAHs polycyclic arenes polycyclic aromatic hydrocarbons CHEBI:33848 polycyclic arene PMID:15198916 Europe PMC PMID:25679824 Europe PMC PAH ChEBI PAHs ChEBI polycyclic arenes ChEBI polycyclic aromatic hydrocarbons ChEBI An amino acid whose structure includes an aromatic ring. 0 C2H4NO2R 88.085 74.02420 CHEBI:13820 CHEBI:22623 CHEBI:2835 KEGG:C01021 Wikipedia:Aromatic_amino_acid Aromatic amino acid chebi_ontology aromatic amino acids CHEBI:33856 aromatic amino acid Aromatic amino acid KEGG_COMPOUND aromatic amino acids ChEBI Any carboxylic acid in which the carboxy group is directly bonded to an aromatic ring. CHEBI:13817 CHEBI:13821 CHEBI:2830 chebi_ontology aromatic carboxylic acids CHEBI:33859 aromatic carboxylic acid aromatic carboxylic acids ChEBI An amino compound in which the amino group is linked directly to an aromatic system. CHEBI:13827 CHEBI:22622 CHEBI:22646 CHEBI:2834 CHEBI:2863 chebi_ontology aromatic amines aryl amine aryl amines arylamine arylamines CHEBI:33860 aromatic amine aromatic amines ChEBI aryl amine ChEBI aryl amines ChEBI arylamine ChEBI arylamines ChEBI chebi_ontology transition element coordination entities transition metal coordination compounds transition metal coordination entities CHEBI:33861 transition element coordination entity transition element coordination entities ChEBI transition metal coordination compounds ChEBI transition metal coordination entities ChEBI cobalt molecular entity chebi_ontology cobalt compounds cobalt molecular entities CHEBI:33888 cobalt molecular entity cobalt molecular entity ChEBI cobalt compounds ChEBI cobalt molecular entities ChEBI cobalt coordination entity chebi_ontology cobalt coordination compounds cobalt coordination entities CHEBI:33890 cobalt coordination entity cobalt coordination entity ChEBI cobalt coordination compounds ChEBI cobalt coordination entities ChEBI A substance used in a chemical reaction to detect, measure, examine, or produce other substances. reagent chebi_ontology reactif reactivo reagents CHEBI:33893 reagent reagent IUPAC reactif IUPAC reactivo IUPAC reagents ChEBI chebi_ontology cobalt corrinoids cobalt-corrinoids CHEBI:33906 cobalt corrinoid cobalt corrinoids ChEBI cobalt-corrinoids ChEBI chebi_ontology metal-tetrapyrrole metal-tetrapyrrole complex metallotetrapyrroles CHEBI:33909 metallotetrapyrrole metal-tetrapyrrole ChEBI metal-tetrapyrrole complex ChEBI metallotetrapyrroles ChEBI A derivative of the corrin nucleus, which contains four reduced or partly reduced pyrrole rings joined in a macrocycle by three =C- groups and one direct carbon-carbon bond linking alpha positions. 0 C19HN4R21 285.239 285.02012 CHEBI:23391 CHEBI:3890 KEGG:C06021 Corrinoid corrinoid corrinoids chebi_ontology Corrinoid protein Corrinoid protein Co+ Korrinoid corrinoide corrinoides CHEBI:33913 corrinoid Corrinoid KEGG_COMPOUND corrinoid UniProt corrinoids IUPAC Corrinoid protein KEGG_COMPOUND Corrinoid protein Co+ KEGG_COMPOUND Korrinoid ChEBI corrinoide IUPAC corrinoides IUPAC A pentose with a (potential) aldehyde group at one end. PMID:10723607 aldopentose chebi_ontology aldopentoses CHEBI:33916 aldopentose PMID:10723607 Europe PMC aldopentose ChEBI aldopentoses ChEBI A hexose with a (potential) aldehyde group at one end. CHEBI:2558 aldohexose chebi_ontology aldohexoses CHEBI:33917 aldohexose aldohexose ChEBI aldohexoses ChEBI chebi_ontology CHEBI:33937 macronutrient Any aldopentose where the open-chain form has all the hydroxy groups on the same side in the Fischer projection. Occurrs in two enantiomeric forms, D- and L-ribose, of which only the former is found in nature. 0 C5H10O5 150.130 150.05282 CHEBI:26564 ribo-pentose ribose chebi_ontology Rib CHEBI:33942 ribose ribo-pentose IUPAC ribose IUPAC Rib JCBN A quaternary ammonium ion that is the the conjugate acid of carnitine. +1 C7H16NO3 InChI=1S/C7H15NO3/c1-8(2,3)5-6(9)4-7(10)11/h6,9H,4-5H2,1-3H3/p+1 PHIQHXFUZVPYII-UHFFFAOYSA-O 162.20688 162.11247 C[N+](C)(C)CC(O)CC(O)=O CAS:406-76-8 CAS:461-06-3 KEGG:C00487 3-carboxy-2-hydroxy-N,N,N-trimethylpropan-1-aminium chebi_ontology 3-hydroxy-4-(trimethylammonio)butanoic acid Carnitine CHEBI:3424 carnitinium CAS:406-76-8 KEGG COMPOUND CAS:461-06-3 KEGG COMPOUND 3-carboxy-2-hydroxy-N,N,N-trimethylpropan-1-aminium IUPAC 3-hydroxy-4-(trimethylammonio)butanoic acid ChEBI Carnitine KEGG_COMPOUND chebi_ontology nitrogen hydrides CHEBI:35106 nitrogen hydride nitrogen hydrides ChEBI Saturated acyclic nitrogen hydrides having the general formula NnHn+2. chebi_ontology azanes CHEBI:35107 azane azanes ChEBI 0 C40H56 InChI=1S/C40H56/c1-31(19-13-21-33(3)25-27-37-35(5)23-15-29-39(37,7)8)17-11-12-18-32(2)20-14-22-34(4)26-28-38-36(6)24-16-30-40(38,9)10/h11-14,17-23,25-28,37H,15-16,24,29-30H2,1-10H3/b12-11+,19-13+,20-14+,27-25+,28-26+,31-17+,32-18+,33-21+,34-22+/t37-/m0/s1 ANVAOWXLWRTKGA-NTXLUARGSA-N 536.87264 536.43820 CC(\C=C\C=C(C)\C=C\[C@H]1C(C)=CCCC1(C)C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C Beilstein:2067409 CAS:7488-99-5 LIPID_MAPS_instance:LMPR01070011 (6'R)-beta,epsilon-carotene chebi_ontology (+)-alpha-carotene alpha-carotene (natural) CHEBI:35147 (6'R)-beta,epsilon-carotene Beilstein:2067409 Beilstein CAS:7488-99-5 ChemIDplus LIPID_MAPS_instance:LMPR01070011 LIPID MAPS (6'R)-beta,epsilon-carotene IUPAC (+)-alpha-carotene ChemIDplus alpha-carotene (natural) ChemIDplus 0 C40H56 InChI=1S/C40H56/c1-31(19-13-21-33(3)25-27-37-35(5)23-15-29-39(37,7)8)17-11-12-18-32(2)20-14-22-34(4)26-28-38-36(6)24-16-30-40(38,9)10/h11-14,17-23,25-28,37H,15-16,24,29-30H2,1-10H3/b12-11+,19-13+,20-14+,27-25+,28-26+,31-17+,32-18+,33-21+,34-22+/t37-/m1/s1 ANVAOWXLWRTKGA-QTRZAOAUSA-N 536.87264 536.43820 CC(\C=C\C=C(C)\C=C\[C@@H]1C(C)=CCCC1(C)C)=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C Beilstein:2682045 (6'S)-beta,epsilon-carotene chebi_ontology CHEBI:35148 (6'S)-beta,epsilon-carotene Beilstein:2682045 Beilstein (6'S)-beta,epsilon-carotene IUPAC chebi_ontology CHEBI:35155 elemental calcium chebi_ontology Kalziumsalz Kalziumsalze calcium salts CHEBI:35156 calcium salt Kalziumsalz ChEBI Kalziumsalze ChEBI calcium salts ChEBI cyclic carotene chebi_ontology cyclic carotenes CHEBI:35163 cyclic carotene cyclic carotene ChEBI cyclic carotenes ChEBI An oxo monocarboxylic acid anion in which the oxo group is located at the 2-position. -1 C2O3R 72.020 71.98474 [O-]C(=O)C([*])=O CHEBI:70795 MetaCyc:2-Oxo-carboxylates PMID:10850983 chebi_ontology 2-oxo monocarboxylate 2-oxo monocarboxylic acid anions a 2-oxocarboxylate CHEBI:35179 2-oxo monocarboxylic acid anion MetaCyc:2-Oxo-carboxylates SUBMITTER PMID:10850983 SUBMITTER 2-oxo monocarboxylate ChEBI 2-oxo monocarboxylic acid anions ChEBI a 2-oxocarboxylate UniProt A hydrocarbon of biological origin having carbon skeleton formally derived from isoprene [CH2=C(CH3)CH=CH2]. terpene terpenes chebi_ontology Terpen terpenes terpeno terpenos CHEBI:35186 terpene terpene IUPAC terpenes IUPAC Terpen ChEBI terpenes IUPAC terpeno IUPAC terpenos IUPAC A C20 terpene. diterpenes chebi_ontology Diterpen diterpenes diterpeno diterpenos CHEBI:35190 diterpene diterpenes IUPAC Diterpen ChEBI diterpenes IUPAC diterpeno IUPAC diterpenos IUPAC A C40 terpene. tetraterpenes chebi_ontology tetraterpenes tetraterpeno tetraterpenos CHEBI:35193 tetraterpene tetraterpenes IUPAC tetraterpenes IUPAC tetraterpeno IUPAC tetraterpenos IUPAC A substance which lowers the surface tension of the medium in which it is dissolved, and/or the interfacial tension with other phases, and, accordingly, is positively adsorbed at the liquid/vapour and/or at other interfaces. surfactant chebi_ontology surface active agent surfactants CHEBI:35195 surfactant surfactant IUPAC surface active agent IUPAC surfactants ChEBI A substance that diminishes the rate of a chemical reaction. inhibitor chebi_ontology inhibidor inhibiteur inhibitors CHEBI:35222 inhibitor inhibitor IUPAC inhibidor ChEBI inhibiteur ChEBI inhibitors ChEBI 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1 XUJNEKJLAYXESH-REOHCLBHSA-N 121.15922 121.01975 [NH3+][C@@H](CS)C([O-])=O Gmelin:49993 (2R)-2-ammonio-3-sulfanylpropanoate L-cysteine zwitterion chebi_ontology (2R)-2-ammonio-3-mercaptopropanoate L-cysteine CHEBI:35235 L-cysteine zwitterion Gmelin:49993 Gmelin (2R)-2-ammonio-3-sulfanylpropanoate IUPAC L-cysteine zwitterion IUPAC (2R)-2-ammonio-3-mercaptopropanoate ChEBI L-cysteine UniProt 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m1/s1 XUJNEKJLAYXESH-UWTATZPHSA-N 121.15922 121.01975 [NH3+][C@H](CS)C([O-])=O Gmelin:2352354 (2S)-2-ammonio-3-sulfanylpropanoate D-cysteine zwitterion chebi_ontology (2S)-2-ammonio-3-mercaptopropanoate D-cysteine CHEBI:35236 D-cysteine zwitterion Gmelin:2352354 Gmelin (2S)-2-ammonio-3-sulfanylpropanoate IUPAC D-cysteine zwitterion IUPAC (2S)-2-ammonio-3-mercaptopropanoate ChEBI D-cysteine UniProt 0 C3H7NO2S InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6) XUJNEKJLAYXESH-UHFFFAOYSA-N 121.15922 121.01975 [NH3+]C(CS)C([O-])=O Gmelin:49992 2-ammonio-3-sulfanylpropanoate cysteine zwitterion chebi_ontology (+)H3N-CH(CH2SH)-COO(-) 2-ammonio-3-mercaptopropanoate CHEBI:35237 cysteine zwitterion Gmelin:49992 Gmelin 2-ammonio-3-sulfanylpropanoate IUPAC cysteine zwitterion IUPAC (+)H3N-CH(CH2SH)-COO(-) ChEBI 2-ammonio-3-mercaptopropanoate ChEBI The zwitterionic form of an amino acid having a negatively charged carboxyl group and a positively charged amino group. amino acid zwitterion chebi_ontology CHEBI:35238 amino acid zwitterion amino acid zwitterion ChEBI An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amnio group of serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7) MTCFGRXMJLQNBG-UHFFFAOYSA-N 105.09262 105.04259 [NH3+]C(CO)C([O-])=O Beilstein:3935647 Gmelin:2060272 2-ammonio-3-hydroxypropanoate serine zwitterion chebi_ontology CHEBI:35243 serine zwitterion Beilstein:3935647 Beilstein Gmelin:2060272 Gmelin 2-ammonio-3-hydroxypropanoate IUPAC serine zwitterion IUPAC A serine zwitterion obtained by transfer of a proton from the carboxy to the amino group of D-serine. 0 C3H7NO3 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m1/s1 MTCFGRXMJLQNBG-UWTATZPHSA-N 105.09262 105.04259 [NH3+][C@H](CO)C([O-])=O MetaCyc:D-SERINE (2R)-2-ammonio-3-hydroxypropanoate D-serine zwitterion chebi_ontology D-serine CHEBI:35247 D-serine zwitterion (2R)-2-ammonio-3-hydroxypropanoate IUPAC D-serine zwitterion IUPAC D-serine UniProt A derivative of ammonium, NH4(+), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually organyl) groups. +1 NR4 14.00670 14.00307 [*][N+]([*])([*])[*] CHEBI:26470 CHEBI:8693 KEGG:C06703 quaternary ammonium ion chebi_ontology Quaternary amine quaternary ammonium quaternary ammonium ions CHEBI:35267 quaternary ammonium ion quaternary ammonium ion IUPAC Quaternary amine KEGG_COMPOUND quaternary ammonium UniProt quaternary ammonium ions ChEBI A derivative of ammonium, NH4(+), in which one (or more) of the hydrogens bonded to the nitrogen have been replaced with univalent organyl groups. The substituting carbon of the organyl group must not itself be directly attached to a heteroatom (thereby excluding protonated amides, hemiaminals, etc). chebi_ontology ammonium ion derivatives azanium ion derivative azanium ion derivatives CHEBI:35274 ammonium ion derivative ammonium ion derivatives ChEBI azanium ion derivative ChEBI azanium ion derivatives ChEBI Neutral molecules having charge-separated forms with an onium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. betaines chebi_ontology onium betaines CHEBI:35281 onium betaine betaines IUPAC onium betaines ChEBI Neutral molecules having charge-separated forms with an sulfonium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. chebi_ontology sulfonium betaines CHEBI:35282 sulfonium betaine sulfonium betaines ChEBI Any neutral molecule having charge-separated forms with a quaternary ammonium atom which bears no hydrogen atoms and that is not adjacent to the anionic atom. chebi_ontology ammonium betaines CHEBI:35284 ammonium betaine ammonium betaines ChEBI chebi_ontology fused compounds fused polycyclic compounds fused-ring polycyclic compound fused-ring polycyclic compounds polycyclic fused-ring compounds CHEBI:35293 fused compound fused compounds ChEBI fused polycyclic compounds ChEBI fused-ring polycyclic compound ChEBI fused-ring polycyclic compounds ChEBI polycyclic fused-ring compounds ChEBI A polyclic compound in which all of the ring members are carbon atoms. chebi_ontology carbopolycyclic compounds CHEBI:35294 carbopolycyclic compound carbopolycyclic compounds ChEBI chebi_ontology homopolycyclic compounds CHEBI:35295 homopolycyclic compound homopolycyclic compounds ChEBI chebi_ontology ortho-fused polycyclic arenes CHEBI:35296 ortho-fused polycyclic arene ortho-fused polycyclic arenes ChEBI A polycyclic aromatic hydrocarbon consisting of fused benzene rings in a rectilinear arrangement. 0 C10H8.(C4H2)n Wikipedia:Acene acene acenes chebi_ontology Acen Azen polyacenes CHEBI:35297 acene acene IUPAC acenes IUPAC Acen ChEBI Azen ChEBI polyacenes ChEBI Any drug that enhances the activity of the central nervous system. Wikipedia:Central_nervous_system_stimulants central nervous system stimulant chebi_ontology CNS stimulant analeptic analeptic agent analeptic drug analeptics central stimulant CHEBI:35337 central nervous system stimulant central nervous system stimulant ChEBI CNS stimulant ChEBI analeptic ChEBI analeptic agent ChEBI analeptic drug ChEBI analeptics ChEBI central stimulant ChEBI Amines that constitute a class of central nervous system stimulants based on the structure of the parent amphetamine 1-phenylpropan-2-amine. chebi_ontology amphetamine drug CHEBI:35338 amphetamines amphetamine drug ChEBI Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene, so may be considered as triterpenoids. 0 C19H31R 259.450 259.24258 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCCC4)C CHEBI:13687 CHEBI:26768 CHEBI:9263 KEGG:C00377 MetaCyc:Steroids Steroid steroids chebi_ontology a steroid CHEBI:35341 steroid Steroid KEGG_COMPOUND steroids IUPAC a steroid UniProt A sterol in which the hydroxy group at position 3 has beta- configuration. 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CC[C@@H](C4)O)C CHEBI:13609 CHEBI:1725 CHEBI:1726 CHEBI:20248 chebi_ontology 3beta-hydroxysteroids 3beta-sterols CHEBI:35348 3beta-sterol 3beta-hydroxysteroids ChEBI 3beta-sterols ChEBI CHEBI:24748 CHEBI:5814 KEGG:C02159 chebi_ontology Hydroxysteroid hydroxy steroids hydroxysteroids CHEBI:35350 hydroxy steroid Hydroxysteroid KEGG_COMPOUND hydroxy steroids ChEBI hydroxysteroids ChEBI Any heteroorganic entity containing at least one carbon-nitrogen bond. organonitrogen compounds chebi_ontology organonitrogens CHEBI:35352 organonitrogen compound organonitrogen compounds IUPAC organonitrogens ChEBI An amide of a sulfonic acid RS(=O)2NR'2. 0 NO2SR3 78.07100 77.96497 [*]S(=O)(=O)N([*])[*] PMID:11498380 PMID:2434548 PMID:26811268 PMID:26832216 Wikipedia:Sulfonamide sulfonamides chebi_ontology sulfonamides CHEBI:35358 sulfonamide PMID:11498380 Europe PMC PMID:2434548 Europe PMC PMID:26811268 Europe PMC PMID:26832216 Europe PMC sulfonamides IUPAC sulfonamides ChEBI Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. fatty acids http://langual.org 0 CHO2R 45.01740 44.99765 OC([*])=O CHEBI:13633 CHEBI:24024 CHEBI:4984 Codex::570 Europe::570 KEGG:C00162 PMID:14287444 PMID:14300208 PMID:14328676 Wikipedia:Fatty_acid http://www.langual.org/langual_thesaurus.asp?termid=B3098 Fatty acid fatty acids chebi_ontology Fettsaeure Fettsaeuren acide gras acides gras acido graso acidos grasos fatty acids CHEBI:35366 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): antifoaming agent. foam stabilizer, glazing agent. fatty acid PMID:14287444 Europe PMC PMID:14300208 Europe PMC PMID:14328676 Europe PMC Fatty acid KEGG_COMPOUND fatty acids IUPAC Fettsaeure ChEBI Fettsaeuren ChEBI acide gras ChEBI acides gras ChemIDplus acido graso ChEBI acidos grasos ChEBI fatty acids ChEBI Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group. CHEBI:25407 CHEBI:6984 KEGG:C06698 Monosaccharide monosaccharides chebi_ontology Monosaccharid Monosacharid monosacarido monosacaridos CHEBI:35381 monosaccharide Monosaccharide KEGG_COMPOUND monosaccharides IUPAC Monosaccharid ChEBI Monosacharid ChEBI monosacarido ChEBI monosacaridos IUPAC An oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen. CHEBI:33274 CHEBI:33436 oxoanion chebi_ontology oxoacid anions oxoanions CHEBI:35406 oxoanion oxoanion ChEBI oxoacid anions ChEBI oxoanions ChEBI ortho-fused polycyclic hydrocarbon chebi_ontology ortho-fused polycyclic hydrocarbons CHEBI:35427 ortho-fused polycyclic hydrocarbon ortho-fused polycyclic hydrocarbon ChEBI ortho-fused polycyclic hydrocarbons ChEBI A substance used in the prophylaxis or therapy of infectious diseases. chebi_ontology anti-infective agents anti-infective drugs antiinfective agents antiinfective drug CHEBI:35441 antiinfective agent anti-infective agents ChEBI anti-infective drugs ChEBI antiinfective agents ChEBI antiinfective drug ChEBI A substance used to treat or prevent parasitic infections. Wikipedia:Antiparasitic chebi_ontology antiparasitic drugs antiparasitics parasiticides CHEBI:35442 antiparasitic agent antiparasitic drugs ChEBI antiparasitics ChEBI parasiticides ChEBI An EC 3.4.15.* (peptidyl-dipeptidase) inhibitor that interferes with the action of peptidyl-dipeptidase A (EC 3.4.15.1). Wikipedia:ACE_inhibitor chebi_ontology ACE inhibitor ACE inhibitors DCP inhibitor DCP inhibitors EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitors EC 3.4.15.1 inhibitor EC 3.4.15.1 inhibitors PDH inhibitor PDH inhibitors angiotensin I-converting enzyme inhibitor angiotensin I-converting enzyme inhibitors angiotensin-converting enzyme inhibitor angiotensin-converting enzyme inhibitors carboxycathepsin inhibitor carboxycathepsin inhibitors dipeptidase inhibitor dipeptidase inhibitors dipeptide hydrolase inhibitor dipeptide hydrolase inhibitors dipeptidyl carboxypeptidase I inhibitor dipeptidyl carboxypeptidase I inhibitors dipeptidyl carboxypeptidase inhibitor dipeptidyl carboxypeptidase inhibitors endothelial cell peptidyl dipeptidase inhibitor endothelial cell peptidyl dipeptidase inhibitors kininase II inhibitor kininase II inhibitors peptidase P inhibitor peptidase P inhibitors peptidyl dipeptidase A inhibitor peptidyl dipeptidase A inhibitors peptidyl dipeptidase I inhibitor peptidyl dipeptidase I inhibitors peptidyl dipeptidase-4 inhibitor peptidyl dipeptidase-4 inhibitors peptidyl dipeptide hydrolase inhibitor peptidyl dipeptide hydrolase inhibitors peptidyl-dipeptidase A (EC 3.4.15.1) inhibitor peptidyl-dipeptidase A (EC 3.4.15.1) inhibitors peptidyl-dipeptidase A inhibitor peptidyl-dipeptidase A inhibitors peptidyl-dipeptide hydrolase inhibitor peptidyl-dipeptide hydrolase inhibitors peptidyldipeptide hydrolase inhibitor peptidyldipeptide hydrolase inhibitors CHEBI:35457 EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor ACE inhibitor ChEBI ACE inhibitors ChEBI DCP inhibitor ChEBI DCP inhibitors ChEBI EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitors ChEBI EC 3.4.15.1 inhibitor ChEBI EC 3.4.15.1 inhibitors ChEBI PDH inhibitor ChEBI PDH inhibitors ChEBI angiotensin I-converting enzyme inhibitor ChEBI angiotensin I-converting enzyme inhibitors ChEBI angiotensin-converting enzyme inhibitor ChEBI angiotensin-converting enzyme inhibitors ChEBI carboxycathepsin inhibitor ChEBI carboxycathepsin inhibitors ChEBI dipeptidase inhibitor ChEBI dipeptidase inhibitors ChEBI dipeptide hydrolase inhibitor ChEBI dipeptide hydrolase inhibitors ChEBI dipeptidyl carboxypeptidase I inhibitor ChEBI dipeptidyl carboxypeptidase I inhibitors ChEBI dipeptidyl carboxypeptidase inhibitor ChEBI dipeptidyl carboxypeptidase inhibitors ChEBI endothelial cell peptidyl dipeptidase inhibitor ChEBI endothelial cell peptidyl dipeptidase inhibitors ChEBI kininase II inhibitor ChEBI kininase II inhibitors ChEBI peptidase P inhibitor ChEBI peptidase P inhibitors ChEBI peptidyl dipeptidase A inhibitor ChEBI peptidyl dipeptidase A inhibitors ChEBI peptidyl dipeptidase I inhibitor ChEBI peptidyl dipeptidase I inhibitors ChEBI peptidyl dipeptidase-4 inhibitor ChEBI peptidyl dipeptidase-4 inhibitors ChEBI peptidyl dipeptide hydrolase inhibitor ChEBI peptidyl dipeptide hydrolase inhibitors ChEBI peptidyl-dipeptidase A (EC 3.4.15.1) inhibitor ChEBI peptidyl-dipeptidase A (EC 3.4.15.1) inhibitors ChEBI peptidyl-dipeptidase A inhibitor ChEBI peptidyl-dipeptidase A inhibitors ChEBI peptidyl-dipeptide hydrolase inhibitor ChEBI peptidyl-dipeptide hydrolase inhibitors ChEBI peptidyldipeptide hydrolase inhibitor ChEBI peptidyldipeptide hydrolase inhibitors ChEBI Antidepressants are mood-stimulating drugs used primarily in the treatment of affective disorders and related conditions. chebi_ontology antidepressant drugs antidepressants thymoanaleptics thymoleptic drugs thymoleptics CHEBI:35469 antidepressant antidepressant drugs ChEBI antidepressants ChEBI thymoanaleptics ChEBI thymoleptic drugs ChEBI thymoleptics ChEBI A class of drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system. chebi_ontology CNS agent CNS drugs central nervous system agents CHEBI:35470 central nervous system drug CNS agent ChEBI CNS drugs ChEBI central nervous system agents ChEBI A loosely defined grouping of drugs that have effects on psychological function. Wikipedia:Psychotropic_drug chebi_ontology psychoactive agent psychoactive drugs psychopharmaceuticals psychotropic drugs CHEBI:35471 psychotropic drug psychoactive agent ChEBI psychoactive drugs ChEBI psychopharmaceuticals ChEBI psychotropic drugs ChEBI A substance that reduces or suppresses inflammation. chebi_ontology anti-inflammatory drugs antiinflammatory agent antiinflammatory drug antiinflammatory drugs CHEBI:35472 anti-inflammatory drug anti-inflammatory drugs ChEBI antiinflammatory agent ChEBI antiinflammatory drug ChEBI antiinflammatory drugs ChEBI A traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behaviour. chebi_ontology ataractics tranquilising drug tranquilizing drugs tranquillising agent tranquillizing agents CHEBI:35473 tranquilizing drug ataractics ChEBI tranquilising drug ChEBI tranquilizing drugs ChEBI tranquillising agent ChEBI tranquillizing agents ChEBI Anxiolytic drugs are agents that alleviate anxiety, tension, and anxiety disorders, promote sedation, and have a calming effect without affecting clarity of consciousness or neurologic conditions. chebi_ontology anti-anxiety agents anti-anxiety drugs anxiolytic agents anxiolytics minor tranquilisers minor tranquilizers minor tranquilizing agents CHEBI:35474 anxiolytic drug anti-anxiety agents ChEBI anti-anxiety drugs ChEBI anxiolytic agents ChEBI anxiolytics ChEBI minor tranquilisers ChEBI minor tranquilizers ChEBI minor tranquilizing agents ChEBI Antipsychotic drugs are agents that control agitated psychotic behaviour, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect. chebi_ontology Neuroleptikum antipsychotic agents antipsychotic drug antipsychotic drugs antipsychotics antipsychotiques grosser Tranquilizer major tranquilizers major tranquilizing agents neuroleptic neuroleptic agents neuroleptics neuroleptique neuroleptiques CHEBI:35476 antipsychotic agent Neuroleptikum ChEBI antipsychotic agents ChEBI antipsychotic drug ChEBI antipsychotic drugs ChEBI antipsychotics ChEBI antipsychotiques ChEBI grosser Tranquilizer ChEBI major tranquilizers ChEBI major tranquilizing agents ChEBI neuroleptic ChEBI neuroleptic agents ChEBI neuroleptics ChEBI neuroleptique ChEBI neuroleptiques ChEBI Antimanic drugs are agents used to treat bipolar disorders or mania associated with other affective disorders. chebi_ontology antimanic agent antimanic drugs antimanics CHEBI:35477 antimanic drug antimanic agent ChEBI antimanic drugs ChEBI antimanics ChEBI chebi_ontology alkali metal salts CHEBI:35479 alkali metal salt alkali metal salts ChEBI An agent capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms. chebi_ontology CHEBI:35480 analgesic A drug that has principally analgesic, antipyretic and anti-inflammatory actions. Non-narcotic analgesics do not bind to opioid receptors. chebi_ontology CHEBI:35481 non-narcotic analgesic A narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. chebi_ontology narcotic narcotic analgesic narcotic analgesics narcotics opioid analgesics CHEBI:35482 opioid analgesic narcotic ChEBI narcotic analgesic ChEBI narcotic analgesics ChEBI narcotics ChEBI opioid analgesics ChEBI A loosely defined group of drugs that tend to reduce the activity of the central nervous system. chebi_ontology CNS depressants central nervous system depressants CHEBI:35488 central nervous system depressant CNS depressants ChEBI central nervous system depressants ChEBI A compound which inhibits or antagonises the biosynthesis or actions of androgens. Wikipedia:Antiandrogen chebi_ontology antiandrogen CHEBI:35497 androgen antagonist antiandrogen ChEBI An agent that promotes the excretion of urine through its effects on kidney function. chebi_ontology diuretics CHEBI:35498 diuretic diuretics ChEBI natural product fundamental parents chebi_ontology CHEBI:35507 natural product fundamental parent natural product fundamental parents IUPAC chebi_ontology steroid fundamental parents CHEBI:35508 steroid fundamental parent steroid fundamental parents ChEBI 0 C27H48 InChI=1S/C27H48/c1-19(2)9-8-10-20(3)23-14-15-24-22-13-12-21-11-6-7-17-26(21,4)25(22)16-18-27(23,24)5/h19-25H,6-18H2,1-5H3/t20-,21?,22+,23-,24+,25+,26+,27-/m1/s1 XIIAYQZJNBULGD-LDHZKLTISA-N 372.67002 372.37560 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCCC(C)C Beilstein:5334741 CAS:14982-53-7 LIPID_MAPS_instance:LMST01010000 Wikipedia:Cholestane cholestane chebi_ontology CHEBI:35516 cholestane Beilstein:5334741 Beilstein CAS:14982-53-7 ChemIDplus CAS:14982-53-7 NIST Chemistry WebBook LIPID_MAPS_instance:LMST01010000 LIPID MAPS cholestane IUPAC 0 C24H42 InChI=1S/C24H42/c1-5-8-17(2)20-12-13-21-19-11-10-18-9-6-7-15-23(18,3)22(19)14-16-24(20,21)4/h17-22H,5-16H2,1-4H3/t17-,18?,19+,20-,21+,22+,23+,24-/m1/s1 QSHQKIURKJITMZ-BRPMRXRMSA-N 330.59028 330.32865 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC cholane chebi_ontology CHEBI:35519 cholane cholane IUPAC An agent that selectively binds to and activates beta-adrenergic receptors. chebi_ontology beta-adrenergic agonists beta-adrenergic receptor agonist beta-adrenoceptor agonists CHEBI:35522 beta-adrenergic agonist beta-adrenergic agonists ChEBI beta-adrenergic receptor agonist ChEBI beta-adrenoceptor agonists IUPHAR An agent that causes an increase in the expansion of a bronchus or bronchial tubes. chebi_ontology bronchodilator bronchodilator agents broncholytic agent CHEBI:35523 bronchodilator agent bronchodilator ChEBI bronchodilator agents ChEBI broncholytic agent ChEBI A drug which lowers the blood glucose level. chebi_ontology antidiabetic antihyperglycemic antihyperglycemic agent antihyperglycemic agents antihyperglycemic drug antihyperglycemic drugs antihyperglycemics hypoglycemic agents hypoglycemic drug hypoglycemic drugs CHEBI:35526 hypoglycemic agent antidiabetic ChEBI antihyperglycemic ChEBI antihyperglycemic agent ChEBI antihyperglycemic agents ChEBI antihyperglycemic drug ChEBI antihyperglycemic drugs ChEBI antihyperglycemics ChEBI hypoglycemic agents ChEBI hypoglycemic drug ChEBI hypoglycemic drugs ChEBI An agent that binds to but does not activate beta-adrenergic receptors thereby blocking the actions of endogenous or exogenous beta-adrenergic agonists. beta-Adrenergic antagonists are used for treatment of hypertension, cardiac arrhythmias, angina pectoris, glaucoma, migraine headaches and anxiety. chebi_ontology beta-adrenergic antagonists beta-adrenergic blocker beta-adrenergic blockers beta-adrenergic receptor blockaders beta-adrenoceptor antagonists beta-blocker beta-blockers CHEBI:35530 beta-adrenergic antagonist beta-adrenergic antagonists ChEBI beta-adrenergic blocker ChEBI beta-adrenergic blockers ChEBI beta-adrenergic receptor blockaders ChEBI beta-adrenoceptor antagonists IUPHAR beta-blocker ChEBI beta-blockers ChEBI heterocyclic parent hydrides chebi_ontology heterocyclic fundamental parent heterocyclic organic fundamental parents organic heterocyclic fundamental parents CHEBI:35552 heterocyclic organic fundamental parent heterocyclic parent hydrides IUPAC heterocyclic fundamental parent ChEBI heterocyclic organic fundamental parents ChEBI organic heterocyclic fundamental parents ChEBI A drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. chebi_ontology cardiovascular agent cardiovascular drugs CHEBI:35554 cardiovascular drug cardiovascular agent ChEBI cardiovascular drugs ChEBI Any molecular entity that consists of a ring having (formally) the maximum number of noncumulative double bonds. mancude-ring systems chebi_ontology mancude rings mancunide-ring systems CHEBI:35568 mancude ring mancude-ring systems IUPAC mancude rings ChEBI mancunide-ring systems IUPAC chebi_ontology mancude organic heterobicyclic parents mancude-ring organic heterobicyclic parents CHEBI:35570 mancude organic heterobicyclic parent mancude organic heterobicyclic parents ChEBI mancude-ring organic heterobicyclic parents ChEBI chebi_ontology mancude organic heterocyclic parents mancude-ring organic heterocyclic parents CHEBI:35571 mancude organic heterocyclic parent mancude organic heterocyclic parents ChEBI mancude-ring organic heterocyclic parents ChEBI chebi_ontology organic mancude parents organic mancude-ring parents CHEBI:35573 organic mancude parent organic mancude parents ChEBI organic mancude-ring parents ChEBI N-oxide chebi_ontology N-oxides CHEBI:35580 N-oxide N-oxide ChEBI N-oxides ChEBI A heterobicyclic aromatic organic compound comprising a pyrimidine ring fused to an imidazole ring; the parent compound of the purines. 0 C5H4N4 120.112 120.04360 HMDB:HMDB0001366 KEGG:C15587 MetaCyc:PURINE PMID:12865945 PMID:24088627 purine chebi_ontology CHEBI:35584 purine PMID:12865945 Europe PMC PMID:24088627 Europe PMC purine IUPAC A negative ion consisting solely of carbon and oxygen atoms, and therefore having the general formula CxOy(n-) for some integers x, y and n. carbon oxoanion chebi_ontology carbon oxoanions oxocarbon anion oxocarbon anions CHEBI:35604 carbon oxoanion carbon oxoanion ChEBI carbon oxoanions ChEBI oxocarbon anion ChEBI oxocarbon anions ChEBI chebi_ontology carbon oxoacids oxoacids of carbon CHEBI:35605 carbon oxoacid carbon oxoacids ChEBI oxoacids of carbon ChEBI A substance that inhibits or prevents the proliferation of neoplasms. chebi_ontology anticancer agent anticancer agents antineoplastic antineoplastic agents cytostatic CHEBI:35610 antineoplastic agent anticancer agent ChEBI anticancer agents ChEBI antineoplastic ChEBI antineoplastic agents ChEBI cytostatic ChEBI A food additive that is used to added improve the taste or odour of a food. chebi_ontology flavoring agent flavoring agents flavour enhancer flavour enhancers flavouring agents CHEBI:35617 flavouring agent flavoring agent ChEBI flavoring agents ChEBI flavour enhancer ChEBI flavour enhancers ChEBI flavouring agents ChEBI A drug used to cause dilation of the blood vessels. chebi_ontology vasodilator vasodilator agents CHEBI:35620 vasodilator agent vasodilator ChEBI vasodilator agents ChEBI A drug used to prevent seizures or reduce their severity. chebi_ontology Antiepileptika Antiepileptikum Antikonvulsiva Antikonvulsivum anti-convulsant anti-convulsants anti-convulsive agent anti-convulsive agents anticonvulsants anticonvulsive agent anticonvulsive agents antiepileptic antiepileptics antiepileptique antiepileptiques CHEBI:35623 anticonvulsant Antiepileptika ChEBI Antiepileptikum ChEBI Antikonvulsiva ChEBI Antikonvulsivum ChEBI anti-convulsant ChEBI anti-convulsants ChEBI anti-convulsive agent ChEBI anti-convulsive agents ChEBI anticonvulsants ChEBI anticonvulsive agent ChEBI anticonvulsive agents ChEBI antiepileptic ChEBI antiepileptics ChEBI antiepileptique ChEBI antiepileptiques ChEBI A lactam in which the amide bond is contained within a four-membered ring, which includes the amide nitrogen and the carbonyl carbon. 0 C3H2NOR3 68.054 68.01364 C1(C(N(*)C1*)=O)* CHEBI:10426 CHEBI:13203 CHEBI:22845 KEGG:C01866 Wikipedia:Beta-lactam beta-Lactam chebi_ontology a beta-lactam beta-lactams CHEBI:35627 beta-lactam beta-Lactam KEGG_COMPOUND a beta-lactam UniProt beta-lactams ChEBI An inhibitor of HIV protease, an enzyme required for production of proteins needed for viral assembly. Wikipedia:Protease_inhibitor_(pharmacology) chebi_ontology HIV protease inhibitors CHEBI:35660 HIV protease inhibitor HIV protease inhibitors ChEBI Any EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that inhibits HMG-CoA reductases. Hydroxymethylglutaryl-CoA reductase inhibitors have been shown to lower directly cholesterol synthesis. The Enzyme Commission designation is EC 1.1.1.34 for the NADPH-dependent enzyme and EC 1.1.1.88 for an NADH-dependent enzyme. PMID:1464741 PMID:15531285 PMID:20467214 Wikipedia:HMG-CoA_reductase chebi_ontology HMG-CoA reductase inhibitor HMG-CoA reductase inhibitors hydroxymethylglutaryl-CoA reductase inhibitor hydroxymethylglutaryl-CoA reductase inhibitors CHEBI:35664 EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor PMID:1464741 Europe PMC PMID:15531285 Europe PMC PMID:20467214 Europe PMC HMG-CoA reductase inhibitor ChEBI HMG-CoA reductase inhibitors ChEBI hydroxymethylglutaryl-CoA reductase inhibitor ChEBI hydroxymethylglutaryl-CoA reductase inhibitors ChEBI Any drug used in the treatment of acute or chronic vascular hypertension regardless of pharmacological mechanism. Wikipedia:Antihypertensive_drug chebi_ontology antihypertensive antihypertensive agents antihypertensive drug antihypertensive drugs CHEBI:35674 antihypertensive agent antihypertensive ChEBI antihypertensive agents ChEBI antihypertensive drug ChEBI antihypertensive drugs ChEBI A substance used to treat hyperlipidemia (an excess of lipids in the blood). Wikipedia:Hypolipidemic_agent chebi_ontology antihyperlipemic antihyperlipemics antihyperlipidaemic agent antihyperlipidaemic agents antihyperlipidaemic drug antihyperlipidaemic drugs antihyperlipidemic antihyperlipidemic agent antihyperlipidemic agents antihyperlipidemic drug antihyperlipidemic drugs antihyperlipidemics antilipemic antilipemic drugs antilipemics hypolipidemic agent hypolipidemic agents lipid-lowering agent lipid-lowering agents lipid-lowering drug lipid-lowering drugs CHEBI:35679 antilipemic drug antihyperlipemic ChEBI antihyperlipemics ChEBI antihyperlipidaemic agent ChEBI antihyperlipidaemic agents ChEBI antihyperlipidaemic drug ChEBI antihyperlipidaemic drugs ChEBI antihyperlipidemic ChEBI antihyperlipidemic agent ChEBI antihyperlipidemic agents ChEBI antihyperlipidemic drug ChEBI antihyperlipidemic drugs ChEBI antihyperlipidemics ChEBI antilipemic ChEBI antilipemic drugs ChEBI antilipemics ChEBI hypolipidemic agent ChEBI hypolipidemic agents ChEBI lipid-lowering agent ChEBI lipid-lowering agents ChEBI lipid-lowering drug ChEBI lipid-lowering drugs ChEBI A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it. 0 CH2OR2 30.026 30.01056 *C(*)O CHEBI:13425 CHEBI:13686 CHEBI:26617 CHEBI:58662 CHEBI:8741 CHEBI:9077 KEGG:C00432 KEGG:C01612 Secondary alcohol chebi_ontology R-CHOH-R' a secondary alcohol secondary alcohols CHEBI:35681 secondary alcohol Secondary alcohol KEGG_COMPOUND R-CHOH-R' KEGG_COMPOUND a secondary alcohol UniProt secondary alcohols ChEBI Any carboxylic acid containing two carboxy groups. CHEBI:23692 CHEBI:36172 CHEBI:4501 KEGG:C02028 Dicarboxylic acid chebi_ontology dicarboxylic acids CHEBI:35692 dicarboxylic acid Dicarboxylic acid KEGG_COMPOUND dicarboxylic acids ChEBI dicarboxylic acid anion chebi_ontology dicarboxylic acid anions CHEBI:35693 dicarboxylic acid anion dicarboxylic acid anion ChEBI dicarboxylic acid anions ChEBI Any dicarboxylic acid anion that is a monoanion obtained by the deprotonation of only one of the carboxy groups of the dicarboxylic acid. chebi_ontology dicarboxylic acid monoanions CHEBI:35695 dicarboxylic acid monoanion dicarboxylic acid monoanions ChEBI A compound formally derived from an oxoacid RkE(=O)l(OH)m (l > 0) and an alcohol, phenol, heteroarenol, or enol by linking with formal loss of water from an acidic hydroxy group of the former and a hydroxy group of the latter. CHEBI:23960 CHEBI:4859 KEGG:C00287 Wikipedia:Ester Ester chebi_ontology esters CHEBI:35701 ester Ester KEGG_COMPOUND esters ChEBI An agent that suppresses immune function by one of several mechanisms of action. Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response. chebi_ontology immunosuppressant immunosuppressive agents inmunosupresor CHEBI:35705 immunosuppressive agent immunosuppressant ChEBI immunosuppressive agents ChEBI inmunosupresor ChEBI A central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. chebi_ontology hypnotics hypnotics and sedatives sedative drug sedatives sedatives and hypnotics CHEBI:35717 sedative hypnotics ChEBI hypnotics and sedatives ChEBI sedative drug ChEBI sedatives ChEBI sedatives and hypnotics ChEBI An antimicrobial agent that destroys fungi by suppressing their ability to grow or reproduce. chebi_ontology antifungal antifungal agents antifungal drug antifungal drugs antifungals CHEBI:35718 antifungal agent antifungal ChEBI antifungal agents ChEBI antifungal drug ChEBI antifungal drugs ChEBI antifungals ChEBI Any member of the group of lipids containing a common glycerol backbone to which at least one fatty acid-derived group is attached. PMID:18606873 chebi_ontology glycerolipids CHEBI:35741 glycerolipid PMID:18606873 Europe PMC glycerolipids ChEBI A carboxylic acid anion formed when the carboxy group of a monocarboxylic acid is deprotonated. -1 CO2R 44.01000 43.98983 [O-]C([*])=O CHEBI:13657 CHEBI:25382 CHEBI:3407 KEGG:C00060 chebi_ontology Carboxylate Monocarboxylate a monocarboxylate monocarboxylates monocarboxylic acid anions CHEBI:35757 monocarboxylic acid anion Carboxylate KEGG_COMPOUND Monocarboxylate KEGG_COMPOUND a monocarboxylate UniProt monocarboxylates ChEBI monocarboxylic acid anions ChEBI A phosphorus oxoanion that is the conjugate base of phosphoric acid. chebi_ontology Pi phosphate phosphate ions CHEBI:35780 phosphate ion Pi ChEBI phosphate ChEBI phosphate ions ChEBI chebi_ontology seco-steroids CHEBI:35788 seco-steroid seco-steroids ChEBI A substance that suppresses Mycobacterium leprae, ameliorates the clinical manifestations of leprosy, and/or reduces the incidence and severity of leprous reactions. chebi_ontology leprostatic leprostatic agent leprostatic drugs CHEBI:35816 leprostatic drug leprostatic ChEBI leprostatic agent ChEBI leprostatic drugs ChEBI Any fatty acid in which the parent hydrocarbon chain has one or more alkyl substituents; a common component in animal and bacterial lipids. The fatty acyl chain is usually saturated and the substituent a methyl group; however, unsaturated BCFAs are found in marine animals, and branches other than methyl are found in microbial lipids. CHEBI:22919 CHEBI:3166 KEGG:C05996 PMID:18318842 chebi_ontology BCFA BCFAs Branched chain fatty acid branched fatty acid branched fatty acids branched-chain fatty acids CHEBI:35819 branched-chain fatty acid PMID:18318842 Europe PMC BCFA ChEBI BCFAs ChEBI Branched chain fatty acid KEGG_COMPOUND branched fatty acid ChEBI branched fatty acids ChEBI branched-chain fatty acids ChEBI Any antimicrobial drug which is used to treat or prevent protozoal infections. Wikipedia:Antiprotozoal_agent chebi_ontology antiprotozoal agent antiprotozoal agents antiprotozoal drugs CHEBI:35820 antiprotozoal drug antiprotozoal agent ChEBI antiprotozoal agents ChEBI antiprotozoal drugs ChEBI A substance used to lower plasma cholesterol levels. CHEBI:64906 chebi_ontology anticholesteremic anticholesteremic agent anticholesteremic drugs antihypercholesterolemic antihypercholesterolemic agent antihypercholesterolemic agents antihypercholesterolemic drug antihypercholesterolemic drugs antihypercholesterolemics cholesterol inhibitor cholesterol-lowering agent cholesterol-lowering agents cholesterol-lowering drug cholesterol-lowering drugs hypocholesteremic agent CHEBI:35821 anticholesteremic drug anticholesteremic ChEBI anticholesteremic agent ChEBI anticholesteremic drugs ChEBI antihypercholesterolemic ChEBI antihypercholesterolemic agent ChEBI antihypercholesterolemic agents ChEBI antihypercholesterolemic drug ChEBI antihypercholesterolemic drugs ChEBI antihypercholesterolemics ChEBI cholesterol inhibitor ChEBI cholesterol-lowering agent ChEBI cholesterol-lowering agents ChEBI cholesterol-lowering drug ChEBI cholesterol-lowering drugs ChEBI hypocholesteremic agent ChEBI A gout suppressant that acts directly on the renal tubule to increase the excretion of uric acid, thus reducing its concentrations in plasma. chebi_ontology uricosuric agent uricosuric drugs CHEBI:35841 uricosuric drug uricosuric agent ChEBI uricosuric drugs ChEBI A drug used to treat rheumatoid arthritis. chebi_ontology anti-rheumatic drugs antirheumatic agent antirheumatic drugs CHEBI:35842 antirheumatic drug anti-rheumatic drugs ChEBI antirheumatic agent ChEBI antirheumatic drugs ChEBI A drug that increases uric acid excretion by the kidney (uricosuric drug), decreases uric acid production (antihyperuricemic), or alleviates the pain and inflammation of acute attacks of gout. chebi_ontology gout suppressants CHEBI:35845 gout suppressant gout suppressants ChEBI A drug used for its effect on the kidneys' regulation of body fluid composition and volume. chebi_ontology renal agents CHEBI:35846 renal agent renal agents ChEBI Any monocarboxylic acid which also contains a separate (alcoholic or phenolic) hydroxy substituent. chebi_ontology hydroxy acid hydroxy monocarboxylic acids CHEBI:35868 hydroxy monocarboxylic acid hydroxy acid ChEBI hydroxy monocarboxylic acids ChEBI Any monocarboxylic acid having at least one additional oxo functional group. chebi_ontology oxo monocarboxylic acids CHEBI:35871 oxo monocarboxylic acid oxo monocarboxylic acids ChEBI chebi_ontology imidazopyrimidines CHEBI:35875 imidazopyrimidine imidazopyrimidines ChEBI pnictogen hydride chebi_ontology pnictogen hydrides CHEBI:35881 pnictogen hydride pnictogen hydride ChEBI pnictogen hydrides ChEBI CHEBI:35178 CHEBI:35901 chebi_ontology oxo monocarboxylic acid anions CHEBI:35902 oxo monocarboxylic acid anion oxo monocarboxylic acid anions ChEBI Any carboxylic acid anion containing at least one oxo group. chebi_ontology oxo carboxylic acid anions CHEBI:35903 oxo carboxylic acid anion oxo carboxylic acid anions ChEBI Any monocarboxylic acid having a 2-oxo substituent. 0 C2HO3R 73.02750 72.99257 OC(=O)C([*])=O CHEBI:11634 CHEBI:1238 CHEBI:13195 CHEBI:13594 CHEBI:19736 CHEBI:35909 KEGG:C00161 2-oxo carboxylic acids chebi_ontology 2-Oxo acid 2-Oxocarboxylate 2-oxo acid 2-oxo monocarboxylic acids CHEBI:35910 2-oxo monocarboxylic acid 2-oxo carboxylic acids IUPAC 2-Oxo acid KEGG_COMPOUND 2-Oxocarboxylate KEGG_COMPOUND 2-oxo acid UniProt 2-oxo monocarboxylic acids ChEBI A substance used for its pharmacological action on any aspect of neurotransmitter systems. Neurotransmitter agents include agonists, antagonists, degradation inhibitors, uptake inhibitors, depleters, precursors, and modulators of receptor function. chebi_ontology neurotransmitter agents CHEBI:35942 neurotransmitter agent neurotransmitter agents ChEBI A hydroxy monocarboxylic acid that has a hydroxy group beta to the carboxy group. chebi_ontology 3-hydroxy acid 3-hydroxy monocarboxylic acids beta-hydroxy acid beta-hydroxy acids beta-hydroxy carboxylic acid beta-hydroxy carboxylic acids CHEBI:35969 3-hydroxy monocarboxylic acid 3-hydroxy acid ChEBI 3-hydroxy monocarboxylic acids ChEBI beta-hydroxy acid ChEBI beta-hydroxy acids ChEBI beta-hydroxy carboxylic acid ChEBI beta-hydroxy carboxylic acids ChEBI Any amino acid carrying two amino groups. chebi_ontology CHEBI:35987 diamino acid Natural and synthetic antibiotics containing the 4-thia-1-azabicyclo[3.2.0]heptan-7-one structure, generally assumed to have the 5R configuration unless otherwise specified. penams chebi_ontology CHEBI:35992 penams penams IUPAC Any C22 polyunsaturated fatty acid containing six double bonds. 0 C22H32O2 328.489 328.24023 docosahexaenoic acid chebi_ontology DHA docosahexaenoic acids CHEBI:36005 docosahexaenoic acid docosahexaenoic acid IUPAC DHA ChEBI docosahexaenoic acids ChEBI A drug used to treat or prevent microbial infections. chebi_ontology antimicrobial drugs CHEBI:36043 antimicrobial drug antimicrobial drugs ChEBI A substance used in the prophylaxis or therapy of virus diseases. chebi_ontology anti-viral drug anti-virus drug antiviral drugs CHEBI:36044 antiviral drug anti-viral drug ChEBI anti-virus drug ChEBI antiviral drugs ChEBI A drug used to treat or prevent bacterial infections. Wikipedia:Antibacterial chebi_ontology antibacterial drugs CHEBI:36047 antibacterial drug antibacterial drugs ChEBI Any monocarboxylic acid anion carrying at least one hydroxy substituent. chebi_ontology hydroxy monocarboxylic acid anions hydroxymonocarboxylic acid anion hydroxymonocarboxylic acid anions CHEBI:36059 hydroxy monocarboxylic acid anion hydroxy monocarboxylic acid anions ChEBI hydroxymonocarboxylic acid anion ChEBI hydroxymonocarboxylic acid anions ChEBI CHEBI:22867 CHEBI:50419 LIPID_MAPS_class:LMST04 chebi_ontology bile acids and derivatives cholanoids CHEBI:36078 cholanoid LIPID_MAPS_class:LMST04 LIPID MAPS bile acids and derivatives LIPID_MAPS cholanoids ChEBI Compounds having a fully conjugated cyclic dione structure, such as that of benzoquinones, derived from aromatic compounds by conversion of an even number of -CH= groups into -C(=O)- groups with any necessary rearrangement of double bonds (polycyclic and heterocyclic analogues are included). CHEBI:13684 CHEBI:26517 Wikipedia:Quinone quinone quinones chebi_ontology Chinon quinones CHEBI:36141 quinone quinone IUPAC quinones IUPAC Chinon ChEBI quinones ChEBI A compound in which two monosaccharides are joined by a glycosidic bond. CHEBI:23844 CHEBI:4654 KEGG:C01911 Disaccharide disaccharides chebi_ontology Disaccharid Disacharid disacarido disacaridos CHEBI:36233 disaccharide Disaccharide KEGG_COMPOUND disaccharides IUPAC Disaccharid ChEBI Disacharid ChEBI disacarido ChEBI disacaridos IUPAC Conjugate base of chenodeoxycholic acid; major species at pH 7.3. -1 C24H39O4 InChI=1S/C24H40O4/c1-14(4-7-21(27)28)17-5-6-18-22-19(9-11-24(17,18)3)23(2)10-8-16(25)12-15(23)13-20(22)26/h14-20,22,25-26H,4-13H2,1-3H3,(H,27,28)/p-1/t14-,15+,16-,17-,18+,19+,20-,22+,23+,24-/m1/s1 RUDATBOHQWOJDD-BSWAIDMHSA-M 391.56406 391.28538 [H][C@@]12C[C@H](O)CC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])[C@H](O)C2)[C@H](C)CCC([O-])=O CHEBI:13960 CHEBI:23093 CHEBI:57884 Beilstein:3703074 3alpha,7alpha-dihydroxy-5beta-cholan-24-oate chenodeoxycholate chebi_ontology chenodeoxycholate anion chenodeoxycholate(1-) CHEBI:36234 chenodeoxycholate Beilstein:3703074 Beilstein 3alpha,7alpha-dihydroxy-5beta-cholan-24-oate IUPAC chenodeoxycholate UniProt chenodeoxycholate anion ChEBI chenodeoxycholate(1-) ChEBI chebi_ontology bile acid anions CHEBI:36235 bile acid anion bile acid anions ChEBI A steroid acid that consists of cholane having a carboxy group in place of the methyl group at position 24. 0 C24H40O2 InChI=1S/C24H40O2/c1-16(7-12-22(25)26)19-10-11-20-18-9-8-17-6-4-5-14-23(17,2)21(18)13-15-24(19,20)3/h16-21H,4-15H2,1-3H3,(H,25,26)/t16-,17?,18+,19-,20+,21+,23+,24-/m1/s1 RPKLZQLYODPWTM-KBMWBBLPSA-N 360.57320 360.30283 [H][C@@]1(CC[C@@]2([H])[C@]3([H])CCC4CCCC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCC(O)=O CAS:25312-65-6 Patent:JP2008069152 Reaxys:13246008 cholan-24-oic acid chebi_ontology CHEBI:36237 cholanic acid CAS:25312-65-6 ChemIDplus Reaxys:13246008 Reaxys cholan-24-oic acid IUPAC 0 C24H40O2 InChI=1S/C24H40O2/c1-16(7-12-22(25)26)19-10-11-20-18-9-8-17-6-4-5-14-23(17,2)21(18)13-15-24(19,20)3/h16-21H,4-15H2,1-3H3,(H,25,26)/t16-,17+,18+,19-,20+,21+,23+,24-/m1/s1 RPKLZQLYODPWTM-LVVAJZGHSA-N 360.57320 360.30283 [H][C@@]12CCCC[C@]1(C)[C@@]1([H])CC[C@]3(C)[C@]([H])(CC[C@@]3([H])[C@]1([H])CC2)[C@H](C)CCC(O)=O Beilstein:3214794 CAS:546-18-9 LIPID_MAPS_instance:LMST04010441 5beta-cholan-24-oic acid 5beta-cholanic acid chebi_ontology (5beta)-cholan-24-oic acid (5beta,17beta)-gamma-methylandrostane-17-butanoic acid 5beta-cholanoic acid ursocholanic acid CHEBI:36238 5beta-cholanic acid Beilstein:3214794 Beilstein CAS:546-18-9 ChemIDplus LIPID_MAPS_instance:LMST04010441 LIPID MAPS 5beta-cholan-24-oic acid IUPAC 5beta-cholanic acid ChemIDplus (5beta)-cholan-24-oic acid ChemIDplus (5beta,17beta)-gamma-methylandrostane-17-butanoic acid ChemIDplus 5beta-cholanoic acid ChemIDplus ursocholanic acid ChemIDplus Members of the class of cholanic acids based on a 5beta-cholane skeleton. chebi_ontology CHEBI:36248 5beta-cholanic acids CHEBI:23166 CHEBI:23211 chebi_ontology CHEBI:36278 cholanic acids macrocyclic tetrapyrroles chebi_ontology cyclic tetrapyrroles macrocyclic tetrapyrrole CHEBI:36309 cyclic tetrapyrrole macrocyclic tetrapyrroles IUPAC cyclic tetrapyrroles ChEBI macrocyclic tetrapyrrole ChEBI Any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block. local anaesthetic chebi_ontology Lokalanaesthetikum anesthesique local local anaesthetics local anesthetics CHEBI:36333 local anaesthetic local anaesthetic IUPAC Lokalanaesthetikum ChEBI anesthesique local ChEBI local anaesthetics ChEBI local anesthetics ChEBI Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin). chebi_ontology leptons CHEBI:36338 lepton leptons ChEBI Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy). chebi_ontology baryons CHEBI:36339 baryon baryons ChEBI Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi. fermion chebi_ontology fermions CHEBI:36340 fermion fermion IUPAC fermions ChEBI A particle smaller than an atom. Wikipedia:Subatomic_particle chebi_ontology subatomic particles CHEBI:36342 subatomic particle subatomic particles ChEBI A subatomic particle known to have substructure (i.e. consisting of smaller particles). chebi_ontology composite particles CHEBI:36343 composite particle composite particles ChEBI Hadron is a subatomic particle which experiences the strong force. chebi_ontology hadrons CHEBI:36344 hadron hadrons ChEBI A nucleus or any of its constituents in any of their energy states. nuclear particle chebi_ontology CHEBI:36347 nuclear particle nuclear particle IUPAC Any molecular entity consisting of more than one atom. chebi_ontology polyatomic entities CHEBI:36357 polyatomic entity polyatomic entities ChEBI An ion consisting of more than one atom. chebi_ontology polyatomic ions CHEBI:36358 polyatomic ion polyatomic ions ChEBI phosphorus oxoacid derivative chebi_ontology CHEBI:36359 phosphorus oxoacid derivative phosphorus oxoacid derivative ChEBI chebi_ontology CHEBI:36360 phosphorus oxoacids and derivatives chebi_ontology alkaline earth salts CHEBI:36364 alkaline earth salt alkaline earth salts ChEBI Any compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives. carbonyl compounds chebi_ontology CHEBI:36586 carbonyl compound carbonyl compounds IUPAC Organic compounds containing an oxygen atom, =O, doubly bonded to carbon or another element. oxo compounds chebi_ontology organic oxo compounds CHEBI:36587 organic oxo compound oxo compounds IUPAC organic oxo compounds ChEBI heterotricyclic compound heterotricyclic compounds chebi_ontology heterotricyclic compounds CHEBI:36688 heterotricyclic compound heterotricyclic compound ChEBI heterotricyclic compounds IUPAC heterotricyclic compounds ChEBI Any of a class of steroid hormones that are produced in the adrenal cortex. chebi_ontology adrenal cortex hormones corticosteroid hormones CHEBI:36699 corticosteroid hormone adrenal cortex hormones ChEBI corticosteroid hormones ChEBI -1 chebi_ontology monoanions CHEBI:36830 monoanion monoanions ChEBI Any hydroxy steroid carrying a hydroxy group at position 3. chebi_ontology 3-hydroxy steroids CHEBI:36834 3-hydroxy steroid 3-hydroxy steroids ChEBI A 3-hydroxy steroid in which the 3-hydroxy substituent is in the beta-position. 0 C19H31OR 275.450 275.23749 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CC[C@@H](C4)O)C CHEBI:71195 KEGG:C02945 MetaCyc:3-Beta-Hydroxysterols PMID:10535978 PMID:12829805 chebi_ontology 3beta-hydroxy steroids a 3beta-hydroxysteroid CHEBI:36836 3beta-hydroxy steroid PMID:10535978 SUBMITTER PMID:12829805 SUBMITTER 3beta-hydroxy steroids ChEBI a 3beta-hydroxysteroid UniProt chebi_ontology hydroxy seco-steroids CHEBI:36853 hydroxy seco-steroid hydroxy seco-steroids ChEBI chebi_ontology CHEBI:36892 elemental fluorine 0 F 18.998 18.99840 chebi_ontology atomic fluorine CHEBI:36895 monoatomic fluorine atomic fluorine ChEBI chebi_ontology inorganic ions CHEBI:36914 inorganic ion inorganic ions ChEBI chebi_ontology inorganic cations CHEBI:36915 inorganic cation inorganic cations ChEBI A monoatomic or polyatomic species having one or more elementary charges of the proton. CHEBI:23058 CHEBI:3473 KEGG:C01373 Cation cation chebi_ontology Kation Kationen cationes cations CHEBI:36916 cation Cation KEGG_COMPOUND cation ChEBI cation IUPAC Kation ChEBI Kationen ChEBI cationes ChEBI cations ChEBI chalcocarbonic acid chalcocarbonic acids chebi_ontology chalcocarbonic acids CHEBI:36961 chalcocarbonic acid chalcocarbonic acid ChEBI chalcocarbonic acids IUPAC chalcocarbonic acids ChEBI An organochalcogen compound is a compound containing at least one carbon-chalcogen bond. organochalcogen compound chebi_ontology organochalcogen compounds CHEBI:36962 organochalcogen compound organochalcogen compound ChEBI organochalcogen compounds ChEBI An organochalcogen compound containing at least one carbon-oxygen bond. PMID:17586126 organooxygen compound chebi_ontology organooxygen compounds CHEBI:36963 organooxygen compound PMID:17586126 Europe PMC organooxygen compound ChEBI organooxygen compounds ChEBI amino-acid anion chebi_ontology amino acid anions amino-acid anions CHEBI:37022 amino-acid anion amino-acid anion ChEBI amino acid anions ChEBI amino-acid anions ChEBI chebi_ontology organic hydrides CHEBI:37175 organic hydride organic hydrides ChEBI mononuclear parent hydrides chebi_ontology mononuclear hydride mononuclear hydrides CHEBI:37176 mononuclear parent hydride mononuclear parent hydrides IUPAC mononuclear hydride ChEBI mononuclear hydrides IUPAC chebi_ontology CHEBI:37246 elemental sodium chebi_ontology CHEBI:37247 elemental potassium chebi_ontology CHEBI:37253 elemental zinc A branched-chain saturated fatty acid anion that is the conjugate base of phytanic acid, arising from deprotonation of the carboxylic acid group. -1 C20H39O2 InChI=1S/C20H40O2/c1-16(2)9-6-10-17(3)11-7-12-18(4)13-8-14-19(5)15-20(21)22/h16-19H,6-15H2,1-5H3,(H,21,22)/p-1 RLCKHJSFHOZMDR-UHFFFAOYSA-M 311.52246 311.29555 CC(C)CCCC(C)CCCC(C)CCCC(C)CC([O-])=O CHEBI:14834 CHEBI:26109 Beilstein:3669982 KEGG:C01607 PMID:5130448 Reaxys:3669982 3,7,11,15-tetramethylhexadecanoate chebi_ontology 3,7,11,15-tetramethylhexadecanoate 3,7,11,15-tetramethylpalmitate phytanate anion CHEBI:37257 phytanate Beilstein:3669982 Beilstein PMID:5130448 Europe PMC Reaxys:3669982 Reaxys 3,7,11,15-tetramethylhexadecanoate IUPAC 3,7,11,15-tetramethylhexadecanoate UniProt 3,7,11,15-tetramethylpalmitate ChEBI phytanate anion ChEBI A 7,8-dimethylbenzo[g]pteridine-2,4-dione that is isoalloxazine substituted by methyl groups at positions 7 and 8. 0 C12H10N4O2 InChI=1S/C12H10N4O2/c1-5-3-7-8(4-6(5)2)14-10-9(13-7)11(17)16-12(18)15-10/h3-4H,1-2H3,(H2,14,15,16,17,18) ZJTJUVIJVLLGSP-UHFFFAOYSA-N 242.23356 242.08038 Cc1cc2nc3c(nc(=O)[nH]c3=O)[nH]c2cc1C Beilstein:539579 PMID:16128574 Reaxys:539579 7,8-dimethylbenzo[g]pteridine-2,4(3H,10H)-dione chebi_ontology dimethylisoalloxazine CHEBI:37323 7,8-dimethylisoalloxazine Beilstein:539579 Beilstein PMID:16128574 Europe PMC Reaxys:539579 Reaxys 7,8-dimethylbenzo[g]pteridine-2,4(3H,10H)-dione IUPAC dimethylisoalloxazine IUPAC 0 C12H10N4O2 242.234 242.08038 7,8-dimethylbenzo[g]pteridine-2,4-dione chebi_ontology CHEBI:37324 7,8-dimethylbenzo[g]pteridine-2,4-dione 7,8-dimethylbenzo[g]pteridine-2,4-dione IUPAC 0 C10H6N4O2 InChI=1S/C10H6N4O2/c15-9-7-8(13-10(16)14-9)12-6-4-2-1-3-5(6)11-7/h1-4H,(H2,12,13,14,15,16) HAUGRYOERYOXHX-UHFFFAOYSA-N 214.18040 214.04908 O=c1[nH]c2nc3ccccc3nc2c(=O)[nH]1 Beilstein:85819 CAS:490-59-5 LINCS:LSM-2889 alloxazine benzo[g]pteridine-2,4(1H,3H)-dione chebi_ontology Alloxazin CHEBI:37325 alloxazine Beilstein:85819 Beilstein CAS:490-59-5 NIST Chemistry WebBook alloxazine NIST_Chemistry_WebBook benzo[g]pteridine-2,4(1H,3H)-dione IUPAC Alloxazin NIST_Chemistry_WebBook 0 C10H6N4O2 214.181 214.04908 benzo[g]pteridine-2,4-dione chebi_ontology CHEBI:37326 benzo[g]pteridine-2,4-dione benzo[g]pteridine-2,4-dione IUPAC 0 C10H6N4O2 InChI=1S/C10H6N4O2/c15-9-7-8(13-10(16)14-9)12-6-4-2-1-3-5(6)11-7/h1-4H,(H2,12,13,14,15,16) HAUGRYOERYOXHX-UHFFFAOYSA-N 214.18040 214.04908 O=c1nc2[nH]c3ccccc3nc2c(=O)[nH]1 Beilstein:991206 benzo[g]pteridine-2,4(3H,10H)-dione chebi_ontology CHEBI:37327 isoalloxazine Beilstein:991206 Beilstein benzo[g]pteridine-2,4(3H,10H)-dione IUPAC A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. CHEBI:24074 CHEBI:24076 folates chebi_ontology folate folates CHEBI:37445 folic acids folates IUPAC folate ChEBI folates ChEBI An acid is a molecular entity capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid). CHEBI:13800 CHEBI:13801 CHEBI:22209 CHEBI:2426 KEGG:C00174 Acid acid chebi_ontology Saeure Saeuren acide acido acids CHEBI:37527 acid Acid KEGG_COMPOUND acid IUPAC Saeure ChEBI Saeuren ChEBI acide IUPAC acido ChEBI acids ChEBI A molecular entity consisting of two or more chemical elements. chebi_ontology chemical compound heteroatomic molecular entities CHEBI:37577 heteroatomic molecular entity chemical compound ChEBI heteroatomic molecular entities ChEBI An amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom. 0 CNOR3 42.01680 41.99799 [*]C(=O)N([*])[*] CHEBI:35354 CHEBI:35355 carboxamides chebi_ontology carboxamides primary carboxamide CHEBI:37622 carboxamide carboxamides IUPAC carboxamides ChEBI primary carboxamide ChEBI A compound which inhibits or antagonizes the biosynthesis or actions of proteases (endopeptidases). Wikipedia:Protease_inhibitor_(biology) chebi_ontology protease inhibitors CHEBI:37670 protease inhibitor protease inhibitors ChEBI An EC 3.1.1.* (carboxylic ester hydrolase) inhibitor that interferes with the action of cholinesterase (EC 3.1.1.8). chebi_ontology BChE inhibitor BChE inhibitors BtChoEase inhibitor BtChoEase inhibitors EC 3.1.1.8 (cholinesterase) inhibitors EC 3.1.1.8 inhibitor EC 3.1.1.8 inhibitors anticholineesterase inhibitor anticholineesterase inhibitors anticholinesterase anticholinesterases benzoylcholinesterase inhibitor benzoylcholinesterase inhibitors butyrylcholine esterase inhibitor butyrylcholine esterase inhibitors butyrylcholinesterase inhibitor butyrylcholinesterase inhibitors choline esterase II (unspecific) inhibitor choline esterase II (unspecific) inhibitors choline esterase inhibitor choline esterase inhibitors cholinesterase (EC 3.1.1.8) inhibitor cholinesterase (EC 3.1.1.8) inhibitors cholinesterase inhibitor non-specific cholinesterase inhibitor non-specific cholinesterase inhibitors propionylcholinesterase inhibitor propionylcholinesterase inhibitors pseudocholinesterase inhibitor pseudocholinesterase inhibitors CHEBI:37733 EC 3.1.1.8 (cholinesterase) inhibitor BChE inhibitor ChEBI BChE inhibitors ChEBI BtChoEase inhibitor ChEBI BtChoEase inhibitors ChEBI EC 3.1.1.8 (cholinesterase) inhibitors ChEBI EC 3.1.1.8 inhibitor ChEBI EC 3.1.1.8 inhibitors ChEBI anticholineesterase inhibitor ChEBI anticholineesterase inhibitors ChEBI anticholinesterase ChEBI anticholinesterases ChEBI benzoylcholinesterase inhibitor ChEBI benzoylcholinesterase inhibitors ChEBI butyrylcholine esterase inhibitor ChEBI butyrylcholine esterase inhibitors ChEBI butyrylcholinesterase inhibitor ChEBI butyrylcholinesterase inhibitors ChEBI choline esterase II (unspecific) inhibitor ChEBI choline esterase II (unspecific) inhibitors ChEBI choline esterase inhibitor ChEBI choline esterase inhibitors ChEBI cholinesterase (EC 3.1.1.8) inhibitor ChEBI cholinesterase (EC 3.1.1.8) inhibitors ChEBI cholinesterase inhibitor ChEBI non-specific cholinesterase inhibitor ChEBI non-specific cholinesterase inhibitors ChEBI propionylcholinesterase inhibitor ChEBI propionylcholinesterase inhibitors ChEBI pseudocholinesterase inhibitor ChEBI pseudocholinesterase inhibitors ChEBI A penam that consists of 3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane bearing a carboxy group at position 2 and having (2S,5R)-configuration. 0 C8H11NO3S InChI=1S/C8H11NO3S/c1-8(2)6(7(11)12)9-4(10)3-5(9)13-8/h5-6H,3H2,1-2H3,(H,11,12)/t5-,6+/m1/s1 RBKMMJSQKNKNEV-RITPCOANSA-N 201.24388 201.04596 [H][C@@]12CC(=O)N1[C@@H](C(O)=O)C(C)(C)S2 Beilstein:4677775 CAS:87-53-6 Reaxys:4677775 2,2-dimethylpenam-3alpha-carboxylic acid penicillanic acid chebi_ontology (2S,5R)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid CHEBI:37806 penicillanic acid Beilstein:4677775 Beilstein CAS:87-53-6 ChemIDplus Reaxys:4677775 Reaxys 2,2-dimethylpenam-3alpha-carboxylic acid IUPAC penicillanic acid ChemIDplus (2S,5R)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid IUPAC A straight chain alkane composed of 4 carbon atoms. 0 C4H10 InChI=1S/C4H10/c1-3-4-2/h3-4H2,1-2H3 IJDNQMDRQITEOD-UHFFFAOYSA-N 58.12220 58.07825 CCCC CHEBI:22945 CHEBI:25462 CHEBI:44430 Beilstein:969129 CAS:106-97-8 Gmelin:1148 PDBeChem:NBU PMID:24179026 Reaxys:969129 Wikipedia:Butane butane chebi_ontology E 943a E-943a E943a N-BUTANE R-600 n-Butan n-C4H10 n-butane CHEBI:37808 butane Beilstein:969129 Beilstein CAS:106-97-8 ChemIDplus CAS:106-97-8 NIST Chemistry WebBook Gmelin:1148 Gmelin PMID:24179026 Europe PMC Reaxys:969129 Reaxys butane IUPAC butane UniProt E 943a ChEBI E-943a ChEBI E943a ChEBI N-BUTANE PDBeChem R-600 ChEBI n-Butan ChEBI n-C4H10 NIST_Chemistry_WebBook n-butane NIST_Chemistry_WebBook A carboacyl group is a group formed by loss of at least one OH from the carboxy group of a carboxylic acid. carboacyl groups carboxylic acyl group chebi_ontology carboxylic acyl groups CHEBI:37838 carboacyl group carboacyl groups IUPAC carboxylic acyl group IUPAC carboxylic acyl groups IUPAC An agent that selectively binds to and activates adrenergic receptors. chebi_ontology adrenergic agonists adrenergic receptor agonist adrenoceptor agonists adrenomimetic adrenomimetics CHEBI:37886 adrenergic agonist adrenergic agonists ChEBI adrenergic receptor agonist ChEBI adrenoceptor agonists IUPHAR adrenomimetic ChEBI adrenomimetics ChEBI An agent that binds to but does not activate adrenergic receptors thereby blocking the actions of endogenous or exogenous adrenergic agonists. chebi_ontology adrenergic antagonists adrenergic blockaders adrenergic blocker adrenergic blockers adrenergic receptor blockaders adrenoceptor antagonists CHEBI:37887 adrenergic antagonist adrenergic antagonists ChEBI adrenergic blockaders ChEBI adrenergic blocker ChEBI adrenergic blockers ChEBI adrenergic receptor blockaders ChEBI adrenoceptor antagonists IUPHAR An agent that binds to but does not activate alpha-adrenergic receptors thereby blocking the actions of endogenous or exogenous alpha-adrenergic agonists. alpha-Adrenergic antagonists are used in the treatment of hypertension, vasospasm, peripheral vascular disease, shock, and pheochromocytoma. chebi_ontology alpha-adrenergic antagonists alpha-adrenergic blocker alpha-adrenergic blockers alpha-adrenergic receptor blockaders alpha-adrenoceptor antagonists CHEBI:37890 alpha-adrenergic antagonist alpha-adrenergic antagonists ChEBI alpha-adrenergic blocker ChEBI alpha-adrenergic blockers ChEBI alpha-adrenergic receptor blockaders ChEBI alpha-adrenoceptor antagonists IUPHAR Histamine antagonists are the drugs that bind to but do not activate histamine receptors, thereby blocking the actions of histamine or histamine agonists. PMID:22035879 Wikipedia:Antihistamines chebi_ontology antihistamine antihistamines antihistaminico antihistaminics histamine receptor blocker histamine receptor blockers CHEBI:37956 histamine antagonist PMID:22035879 Europe PMC antihistamine ChEBI antihistamines ChEBI antihistaminico ChEBI antihistaminics ChEBI histamine receptor blocker ChEBI histamine receptor blockers ChEBI Drugs used for their actions on histaminergic systems. chebi_ontology histamine agents histamine drugs histaminergic agent histaminergic agents histaminergic drugs CHEBI:37957 histaminergic drug histamine agents ChEBI histamine drugs ChEBI histaminergic agent ChEBI histaminergic agents ChEBI histaminergic drugs ChEBI Any agent that acts on an adrenergic receptor or affects the life cycle of an adrenergic transmitter. chebi_ontology adrenergic agents adrenergic drug adrenergic drugs adrenergic neuron agents adrenergics CHEBI:37962 adrenergic agent adrenergic agents ChEBI adrenergic drug ChEBI adrenergic drugs ChEBI adrenergic neuron agents ChEBI adrenergics ChEBI A drug used for the treatment or prevention of cardiac arrhythmias. Anti-arrhythmia drugs may affect the polarisation-repolarisation phase of the action potential, its excitability or refractoriness, or impulse conduction or membrane responsiveness within cardiac fibres. chebi_ontology anti-arrhythmia agent antiarrhythmic agent CHEBI:38070 anti-arrhythmia drug anti-arrhythmia agent ChEBI antiarrhythmic agent ChEBI A compound composed of two or more pyrrole units. Beilstein:8538310 chebi_ontology PPys poly(pyrrole)s polypyrroles CHEBI:38077 polypyrrole Beilstein:8538310 Beilstein PPys ChEBI poly(pyrrole)s ChEBI polypyrroles ChEBI Any organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms. chebi_ontology heterocyclic organonitrogen compounds organonitrogen heterocyclic compounds CHEBI:38101 organonitrogen heterocyclic compound heterocyclic organonitrogen compounds ChEBI organonitrogen heterocyclic compounds ChEBI Any organic heterocyclic compound containing at least one ring oxygen atom. PMID:17134300 chebi_ontology heterocyclic organooxygen compounds organooxygen heterocyclic compounds oxacycles CHEBI:38104 oxacycle PMID:17134300 Europe PMC heterocyclic organooxygen compounds ChEBI organooxygen heterocyclic compounds ChEBI oxacycles ChEBI chebi_ontology heterocyclic organosulfur compounds organosulfur heterocyclic compounds CHEBI:38106 organosulfur heterocyclic compound heterocyclic organosulfur compounds ChEBI organosulfur heterocyclic compounds ChEBI CHEBI:25429 CHEBI:38075 chebi_ontology organic heteropolycyclic compounds CHEBI:38166 organic heteropolycyclic compound organic heteropolycyclic compounds ChEBI chebi_ontology monocyclic heteroarenes CHEBI:38179 monocyclic heteroarene monocyclic heteroarenes ChEBI A monocarboxylic acid anion resulting from the removal of a proton from the carboxy group of a pyridinemonocarboxylic acid. A 'closed class'. chebi_ontology pyridinemonocarboxylates CHEBI:38181 pyridinemonocarboxylate pyridinemonocarboxylates ChEBI A hydroxypyridine carrying a single hydroxy substituent. chebi_ontology monohydroxypyridines CHEBI:38182 monohydroxypyridine monohydroxypyridines ChEBI Any member of the class of pyridines carrying a hydroxymethyl substituent at unspecified position. chebi_ontology hydroxymethylpyridines CHEBI:38196 hydroxymethylpyridine hydroxymethylpyridines ChEBI One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools. chebi_ontology calcium channel antagonist calcium channel antagonists calcium channel blockers CHEBI:38215 calcium channel blocker calcium channel antagonist ChEBI calcium channel antagonists ChEBI calcium channel blockers ChEBI A branched chain amino acid that consists of 3-methylpentanoic acid bearing an amino substituent at position 2. 0 C6H13NO2 InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9) AGPKZVBTJJNPAG-UHFFFAOYSA-N 131.17296 131.09463 CCC(C)C(N)C(O)=O CAS:443-79-8 KEGG:C16434 PMID:10944265 Reaxys:1721790 2-amino-3-methylpentanoic acid chebi_ontology CHEBI:38264 2-amino-3-methylpentanoic acid CAS:443-79-8 ChemIDplus CAS:443-79-8 KEGG COMPOUND PMID:10944265 Europe PMC Reaxys:1721790 Reaxys 2-amino-3-methylpentanoic acid IUPAC chebi_ontology azabicycloalkanes CHEBI:38295 azabicycloalkane azabicycloalkanes ChEBI chebi_ontology thiabicycloalkanes CHEBI:38297 thiabicycloalkane thiabicycloalkanes ChEBI chebi_ontology cephems CHEBI:38311 cephem cephems ChEBI Any organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure). chebi_ontology CHEBI:38313 diazines Any drug used for its actions on cholinergic systems. Included here are agonists and antagonists, drugs that affect the life cycle of acetylcholine, and drugs that affect the survival of cholinergic neurons. chebi_ontology cholinergic agent cholinergic drugs cholinomimetic CHEBI:38323 cholinergic drug cholinergic agent ChEBI cholinergic drugs ChEBI cholinomimetic ChEBI A pyrimidine carrying one or more oxo substituents. chebi_ontology pyrimidones CHEBI:38337 pyrimidone pyrimidones ChEBI A member of the class of pyrimidines that is pyrimidine substituted by at least one amino group and its derivatives. chebi_ontology aminopyrimidines CHEBI:38338 aminopyrimidine aminopyrimidines ChEBI CHEBI:26949 CHEBI:38417 1,3-thiazoles chebi_ontology CHEBI:38418 1,3-thiazoles 1,3-thiazoles ChEBI An EC 3.1.1.* (carboxylic ester hydrolase) inhibitor that interferes with the action of enzyme acetylcholinesterase (EC 3.1.1.7), which helps breaking down of acetylcholine into choline and acetic acid. Wikipedia:Acetylcholinesterase_inhibitor chebi_ontology AChEI AcCholE inhibitor AcCholE inhibitors EC 3.1.1.7 (acetylcholinesterase) inhibitors EC 3.1.1.7 inhibitor EC 3.1.1.7 inhibitors acetyl.beta-methylcholinesterase inhibitor acetyl.beta-methylcholinesterase inhibitors acetylcholine acetylhydrolase inhibitor acetylcholine acetylhydrolase inhibitors acetylcholine esterase inhibitor acetylcholine hydrolase inhibitor acetylcholine hydrolase inhibitors acetylcholinesterase (EC 3.1.1.7) inhibitor acetylcholinesterase (EC 3.1.1.7) inhibitors acetylcholinesterase inhibitor acetylcholinesterase inhibitors acetylthiocholinesterase inhibitor acetylthiocholinesterase inhibitors choline esterase I inhibitor choline esterase I inhibitors cholinesterase inhibitor cholinesterase inhibitors true cholinesterase inhibitor true cholinesterase inhibitors CHEBI:38462 EC 3.1.1.7 (acetylcholinesterase) inhibitor AChEI ChEBI AcCholE inhibitor ChEBI AcCholE inhibitors ChEBI EC 3.1.1.7 (acetylcholinesterase) inhibitors ChEBI EC 3.1.1.7 inhibitor ChEBI EC 3.1.1.7 inhibitors ChEBI acetyl.beta-methylcholinesterase inhibitor ChEBI acetyl.beta-methylcholinesterase inhibitors ChEBI acetylcholine acetylhydrolase inhibitor ChEBI acetylcholine acetylhydrolase inhibitors ChEBI acetylcholine esterase inhibitor ChEBI acetylcholine hydrolase inhibitor ChEBI acetylcholine hydrolase inhibitors ChEBI acetylcholinesterase (EC 3.1.1.7) inhibitor ChEBI acetylcholinesterase (EC 3.1.1.7) inhibitors ChEBI acetylcholinesterase inhibitor ChEBI acetylcholinesterase inhibitors ChEBI acetylthiocholinesterase inhibitor ChEBI acetylthiocholinesterase inhibitors ChEBI choline esterase I inhibitor ChEBI choline esterase I inhibitors ChEBI cholinesterase inhibitor ChEBI cholinesterase inhibitors ChEBI true cholinesterase inhibitor ChEBI true cholinesterase inhibitors ChEBI An EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitor that interferes with the action of monoamine oxidase (EC 1.4.3.4). Wikipedia:Monoamine_oxidase_inhibitor chebi_ontology EC 1.4.3.4 (monoamine oxidase) inhibitors EC 1.4.3.4 inhibitor EC 1.4.3.4 inhibitors MAO A inhibitor MAO A inhibitors MAO B inhibitor MAO B inhibitors MAO inhibitor MAO inhibitors MAO-A inhibitor MAO-A inhibitors MAO-B inhibitor MAO-B inhibitors adrenalin oxidase inhibitor adrenalin oxidase inhibitors adrenaline oxidase inhibitor adrenaline oxidase inhibitors amine oxidase (flavin-containing) inhibitor amine oxidase (flavin-containing) inhibitors amine:oxygen oxidoreductase (deaminating) (flavin-containing) inhibitor amine:oxygen oxidoreductase (deaminating) (flavin-containing) inhibitors amine:oxygen oxidoreductase (deaminating) inhibitor amine:oxygen oxidoreductase (deaminating) inhibitors epinephrine oxidase inhibitor epinephrine oxidase inhibitors monoamine oxidase (EC 1.4.3.4) inhibitor monoamine oxidase (EC 1.4.3.4) inhibitors monoamine oxidase A inhibitor monoamine oxidase A inhibitors monoamine oxidase B inhibitor monoamine oxidase B inhibitors monoamine oxidase inhibitor monoamine oxidase inhibitors monoamine:O2 oxidoreductase (deaminating) inhibitor monoamine:O2 oxidoreductase (deaminating) inhibitors serotonin deaminase inhibitor serotonin deaminase inhibitors tyraminase inhibitor tyraminase inhibitors tyramine oxidase inhibitor tyramine oxidase inhibitors CHEBI:38623 EC 1.4.3.4 (monoamine oxidase) inhibitor EC 1.4.3.4 (monoamine oxidase) inhibitors ChEBI EC 1.4.3.4 inhibitor ChEBI EC 1.4.3.4 inhibitors ChEBI MAO A inhibitor ChEBI MAO A inhibitors ChEBI MAO B inhibitor ChEBI MAO B inhibitors ChEBI MAO inhibitor ChEBI MAO inhibitors ChEBI MAO-A inhibitor ChEBI MAO-A inhibitors ChEBI MAO-B inhibitor ChEBI MAO-B inhibitors ChEBI adrenalin oxidase inhibitor ChEBI adrenalin oxidase inhibitors ChEBI adrenaline oxidase inhibitor ChEBI adrenaline oxidase inhibitors ChEBI amine oxidase (flavin-containing) inhibitor ChEBI amine oxidase (flavin-containing) inhibitors ChEBI amine:oxygen oxidoreductase (deaminating) (flavin-containing) inhibitor ChEBI amine:oxygen oxidoreductase (deaminating) (flavin-containing) inhibitors ChEBI amine:oxygen oxidoreductase (deaminating) inhibitor ChEBI amine:oxygen oxidoreductase (deaminating) inhibitors ChEBI epinephrine oxidase inhibitor ChEBI epinephrine oxidase inhibitors ChEBI monoamine oxidase (EC 1.4.3.4) inhibitor ChEBI monoamine oxidase (EC 1.4.3.4) inhibitors ChEBI monoamine oxidase A inhibitor ChEBI monoamine oxidase A inhibitors ChEBI monoamine oxidase B inhibitor ChEBI monoamine oxidase B inhibitors ChEBI monoamine oxidase inhibitor ChEBI monoamine oxidase inhibitors ChEBI monoamine:O2 oxidoreductase (deaminating) inhibitor ChEBI monoamine:O2 oxidoreductase (deaminating) inhibitors ChEBI serotonin deaminase inhibitor ChEBI serotonin deaminase inhibitors ChEBI tyraminase inhibitor ChEBI tyraminase inhibitors ChEBI tyramine oxidase inhibitor ChEBI tyramine oxidase inhibitors ChEBI Any agent that affects the transport of molecular entities across a biological membrane. chebi_ontology membrane transport modulators CHEBI:38632 membrane transport modulator membrane transport modulators ChEBI An agent that inhibits sodium influx through cell membranes. chebi_ontology Na channel blocker sodium channel blockers CHEBI:38633 sodium channel blocker Na channel blocker ChEBI sodium channel blockers ChEBI organic sodium salt chebi_ontology organic sodium salts CHEBI:38700 organic sodium salt organic sodium salt ChEBI organic sodium salts ChEBI Any dianion containing at least one carboxy group. carboxylic acid dianion chebi_ontology carboxylic acid dianions CHEBI:38716 carboxylic acid dianion carboxylic acid dianion ChEBI carboxylic acid dianions ChEBI 0 C14H11N6O3 311.276 311.08926 CHEBI:37074 chebi_ontology CHEBI:38793 pteroate 0 C14H12N6O3 312.284 312.09709 CHEBI:26378 CAS:119-24-4 DrugBank:DB04196 Pteroic acid chebi_ontology Pteroinsaeure CHEBI:38794 pteroic acid CAS:119-24-4 ChemIDplus Pteroic acid ChemIDplus Pteroinsaeure ChEBI chebi_ontology CHEBI:38795 pteroic acids chebi_ontology CHEBI:38796 pteroates A membrane transport modulator that is able to regulate intracellular calcium levels. chebi_ontology calcium channel modulators CHEBI:38808 calcium channel modulator calcium channel modulators ChEBI Substance which produces loss of feeling or sensation. anaesthetic chebi_ontology Anaesthetika Anaesthetikum anaesthetics anesthetic agent anesthetic drug anesthetics CHEBI:38867 anaesthetic anaesthetic IUPAC Anaesthetika ChEBI Anaesthetikum ChEBI anaesthetics ChEBI anesthetic agent ChEBI anesthetic drug ChEBI anesthetics ChEBI Substance that produces loss of consciousness. general anaesthetic chebi_ontology Allgemeinanaesthetika Allgemeinanaesthetikum general anaesthetics general anesthetics CHEBI:38869 general anaesthetic general anaesthetic IUPAC Allgemeinanaesthetika ChEBI Allgemeinanaesthetikum ChEBI general anaesthetics ChEBI general anesthetics ChEBI chebi_ontology Inhalationsanaesthetika Inhalationsanaesthetikum Inhalationsnarkotika Inhalationsnarkotikum anesthetic gases inhalation anesthetics CHEBI:38870 inhalation anaesthetic Inhalationsanaesthetika ChEBI Inhalationsanaesthetikum ChEBI Inhalationsnarkotika ChEBI Inhalationsnarkotikum ChEBI anesthetic gases ChEBI inhalation anesthetics ChEBI chebi_ontology i.v.-Anaesthetika i.v.-Anaesthetikum intravenous anesthetics CHEBI:38877 intravenous anaesthetic i.v.-Anaesthetika ChEBI i.v.-Anaesthetikum ChEBI intravenous anesthetics ChEBI chebi_ontology benzopteridines CHEBI:38925 benzopteridine benzopteridines ChEBI Any alkylbenzene that is benzene substituted with one or more methyl groups. chebi_ontology methylbenzenes CHEBI:38975 methylbenzene methylbenzenes ChEBI A monocyclic arene that is benzene substituted with one or more alkyl groups. alkylbenzene chebi_ontology Alkylbenzol alkylbenzenes CHEBI:38976 alkylbenzene alkylbenzene ChEBI Alkylbenzol ChEBI alkylbenzenes ChEBI chebi_ontology sodium channel modulators CHEBI:39000 sodium channel modulator sodium channel modulators ChEBI Ca 40.078 39.96259 calcium cation chebi_ontology calcium cations CHEBI:39123 calcium cation calcium cation ChEBI calcium cations ChEBI 0 Ca 40.078 39.96259 calcium ion chebi_ontology calcium ions CHEBI:39124 calcium ion calcium ion ChEBI calcium ions ChEBI A molecular entity capable of donating a hydron to an acceptor (Bronsted base). Bronsted acid chebi_ontology Bronsted-Saeure acide de Bronsted donneur d'hydron hydron donor CHEBI:39141 Bronsted acid Bronsted acid IUPAC Bronsted-Saeure ChEBI acide de Bronsted IUPAC donneur d'hydron IUPAC hydron donor IUPAC A molecular entity capable of accepting a hydron from a donor (Bronsted acid). Bronsted base chebi_ontology Bronsted-Base accepteur d'hydron base de Bronsted hydron acceptor CHEBI:39142 Bronsted base Bronsted base IUPAC Bronsted-Base ChEBI accepteur d'hydron IUPAC base de Bronsted IUPAC hydron acceptor IUPAC A molecular entity able to provide a pair of electrons and thus capable of forming a covalent bond with an electron-pair acceptor (Lewis acid), thereby producing a Lewis adduct. Lewis base chebi_ontology Lewis-Base base de Lewis donneur d'une paire d'electrons electron donor CHEBI:39144 Lewis base Lewis base IUPAC Lewis-Base ChEBI base de Lewis IUPAC donneur d'une paire d'electrons ChEBI electron donor ChEBI Any saturated fatty acid with a carbon side-chain or isopropyl termination. branched-chain saturated fatty acid chebi_ontology branched saturated fatty acid branched saturated fatty acids branched-chain saturated fatty acids CHEBI:39417 branched-chain saturated fatty acid branched-chain saturated fatty acid ChEBI branched saturated fatty acid ChEBI branched saturated fatty acids ChEBI branched-chain saturated fatty acids ChEBI Any saturated fatty acid lacking a side-chain. PMID:15644336 straight-chain saturated fatty acid chebi_ontology straight-chain saturated fatty acids CHEBI:39418 straight-chain saturated fatty acid PMID:15644336 Europe PMC straight-chain saturated fatty acid ChEBI straight-chain saturated fatty acids ChEBI CHEBI:13784 CHEBI:26445 CHEBI:7263 chebi_ontology CHEBI:39446 pyrimidine ribonucleosides Any compound having a pyrimidine as part of its structure. CHEBI:13681 CHEBI:26448 chebi_ontology CHEBI:39447 pyrimidines Any drug which can be used to prevent or alleviate glaucoma, a disease in which the optic nerve is damaged, resulting in progressive, irreversible loss of vision. It is often, though not always, associated with increased pressure of the fluid in the eye. chebi_ontology anti-glaucoma agent anti-glaucoma agents anti-glaucoma drug anti-glaucoma drugs antiglaucoma agent antiglaucoma drugs CHEBI:39456 antiglaucoma drug anti-glaucoma agent ChEBI anti-glaucoma agents ChEBI anti-glaucoma drug ChEBI anti-glaucoma drugs ChEBI antiglaucoma agent ChEBI antiglaucoma drugs ChEBI A monovalent inorganic anion that consists of phosphoric acid in which one of the three OH groups has been deprotonated. -1 H2O4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-1 NBIIXXVUZAFLBC-UHFFFAOYSA-M 96.98724 96.96962 [H]OP([O-])(=O)O[H] CHEBI:29137 CHEBI:39739 DrugBank:DB02831 Gmelin:1999 PDBeChem:2HP dihydrogen(tetraoxidophosphate)(1-) dihydrogenphosphate dihydrogentetraoxophosphate(1-) dihydrogentetraoxophosphate(V) dihydroxidodioxidophosphate(1-) chebi_ontology DIHYDROGENPHOSPHATE ION H2PO4(-) [PO2(OH)2](-) CHEBI:39745 dihydrogenphosphate Gmelin:1999 Gmelin dihydrogen(tetraoxidophosphate)(1-) IUPAC dihydrogenphosphate IUPAC dihydrogentetraoxophosphate(1-) IUPAC dihydrogentetraoxophosphate(V) IUPAC dihydroxidodioxidophosphate(1-) IUPAC DIHYDROGENPHOSPHATE ION PDBeChem H2PO4(-) IUPAC [PO2(OH)2](-) IUPAC KEGG:C02019 Cyclic ketone cyclic ketones chebi_ontology CHEBI:3992 cyclic ketone Cyclic ketone KEGG_COMPOUND cyclic ketones IUPAC -2 CO3 InChI=1S/CH2O3/c2-1(3)4/h(H2,2,3,4)/p-2 BVKZGUZCCUSVTD-UHFFFAOYSA-L 60.00890 59.98584 [O-]C([O-])=O CHEBI:29201 CHEBI:41605 Beilstein:3600898 CAS:3812-32-6 Gmelin:1559 PDBeChem:CO3 carbonate trioxidocarbonate(2-) chebi_ontology CARBONATE ION CO3(2-) Karbonat [CO3](2-) CHEBI:41609 carbonate Beilstein:3600898 Beilstein CAS:3812-32-6 ChemIDplus Gmelin:1559 Gmelin carbonate IUPAC trioxidocarbonate(2-) IUPAC CARBONATE ION PDBeChem CO3(2-) ChEBI Karbonat ChEBI [CO3](2-) IUPAC 0 HO 17.00734 17.00274 *O[H] CHEBI:24706 CHEBI:43171 PDBeChem:OH HYDROXY GROUP hydroxy hydroxy group chebi_ontology -OH hydroxyl hydroxyl group CHEBI:43176 hydroxy group HYDROXY GROUP PDBeChem hydroxy IUPAC hydroxy group UniProt -OH IUPAC hydroxyl ChEBI hydroxyl group ChEBI chebi_ontology CHEBI:43254 (4S)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one A phosphate ion that is the conjugate base of dihydrogenphosphate. -2 HO4P InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-2 NBIIXXVUZAFLBC-UHFFFAOYSA-L 95.97930 95.96234 OP([O-])([O-])=O CHEBI:29139 CHEBI:43470 Gmelin:1998 MolBase:1628 PDBeChem:PI PDBeChem:PO4 hydrogen(tetraoxidophosphate)(2-) hydrogenphosphate hydrogentetraoxophosphate(2-) hydrogentetraoxophosphate(V) hydroxidotrioxidophosphate(2-) chebi_ontology HPO4(2-) HYDROGENPHOSPHATE ION INORGANIC PHOSPHATE GROUP [P(OH)O3](2-) [PO3(OH)](2-) hydrogen phosphate phosphate CHEBI:43474 hydrogenphosphate Gmelin:1998 Gmelin hydrogen(tetraoxidophosphate)(2-) IUPAC hydrogenphosphate IUPAC hydrogentetraoxophosphate(2-) IUPAC hydrogentetraoxophosphate(V) IUPAC hydroxidotrioxidophosphate(2-) IUPAC HPO4(2-) IUPAC HYDROGENPHOSPHATE ION PDBeChem INORGANIC PHOSPHATE GROUP PDBeChem [P(OH)O3](2-) MolBase [PO3(OH)](2-) IUPAC hydrogen phosphate ChEBI phosphate UniProt A primary aliphatic amine that is butane substituted by an amino group at position 1. 0 C4H11N InChI=1S/C4H11N/c1-2-3-4-5/h2-5H2,1H3 HQABUPZFAYXKJW-UHFFFAOYSA-N 73.13680 73.08915 CCCCN Beilstein:605269 CAS:109-73-9 DrugBank:DB03659 Gmelin:1784 MetaCyc:BUTYLAMINE PDBeChem:LYT PMID:16387436 PMID:23470444 PMID:23734590 Reaxys:605269 Wikipedia:N-Butylamine butan-1-amine chebi_ontology 1-Aminobutan 1-aminobutane 1-butanamine 1-butylamine BUTYLAMINE butanamine butylamine mono-n-butylamine monobutylamine n-Butylamin n-C4H9NH2 n-butylamine CHEBI:43799 butan-1-amine Beilstein:605269 Beilstein CAS:109-73-9 ChemIDplus CAS:109-73-9 NIST Chemistry WebBook Gmelin:1784 Gmelin PMID:16387436 Europe PMC PMID:23470444 Europe PMC PMID:23734590 Europe PMC Reaxys:605269 Reaxys butan-1-amine IUPAC 1-Aminobutan ChemIDplus 1-aminobutane ChemIDplus 1-butanamine NIST_Chemistry_WebBook 1-butylamine NIST_Chemistry_WebBook BUTYLAMINE PDBeChem butanamine NIST_Chemistry_WebBook butylamine ChemIDplus mono-n-butylamine ChemIDplus monobutylamine NIST_Chemistry_WebBook n-Butylamin ChemIDplus n-C4H9NH2 NIST_Chemistry_WebBook n-butylamine ChemIDplus 0 C4H9 57.11426 57.07043 CC(*)CC CHEBI:30352 CHEBI:45554 PDBeChem:NBU 1-methylpropyl SEC-BUTYL GROUP butan-2-ido butan-2-yl sec-butyl chebi_ontology -CH(CH3)-CH2-CH3 CH3-CH2-CH(CH3)- but-2-yl isoleucine side-chain s-butyl CHEBI:45557 sec-butyl group 1-methylpropyl IUPAC SEC-BUTYL GROUP PDBeChem butan-2-ido IUPAC butan-2-yl IUPAC sec-butyl IUPAC -CH(CH3)-CH2-CH3 ChEBI CH3-CH2-CH(CH3)- IUPAC but-2-yl ChEBI isoleucine side-chain ChEBI s-butyl ChEBI A ubiquinone having a side chain of 10 isoprenoid units. In the naturally occurring isomer, all isoprenyl double bonds are in the E- configuration. 0 C59H90O4 InChI=1S/C59H90O4/c1-44(2)24-15-25-45(3)26-16-27-46(4)28-17-29-47(5)30-18-31-48(6)32-19-33-49(7)34-20-35-50(8)36-21-37-51(9)38-22-39-52(10)40-23-41-53(11)42-43-55-54(12)56(60)58(62-13)59(63-14)57(55)61/h24,26,28,30,32,34,36,38,40,42H,15-23,25,27,29,31,33,35,37,39,41,43H2,1-14H3/b45-26+,46-28+,47-30+,48-32+,49-34+,50-36+,51-38+,52-40+,53-42+ ACTIUHUUMQJHFO-UPTCCGCDSA-N 863.34350 862.68391 COC1=C(OC)C(=O)C(C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)=C(C)C1=O CHEBI:46241 CHEBI:9854 Beilstein:1900141 CAS:303-98-0 Drug_Central:4607 HMDB:HMDB0001072 KEGG:C11378 KEGG:D01065 KNApSAcK:C00002866 LIPID_MAPS_instance:LMPR02010001 PDBeChem:U10 PMID:10953455 PMID:13445756 PMID:17192765 PMID:17605305 PMID:18787645 PMID:18843432 PMID:20367194 PMID:25544601 PMID:26741866 PMID:27012265 PMID:7599208 PMID:7718355 Reaxys:1900141 Wikipedia:Coenzyme_Q10 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione Coenzyme Q10 coenzyme Q10 chebi_ontology 2-((all-E)-3,7,11,15,19,23,27,31,35,39-decamethyl-2,6,10,14,18,22,26,30,34,38-tetracontadecaenyl)-5,6-dimethoxy-3-methyl-p-benzoquinone 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methyl-1,4-benzoquinone Adelir CoQ CoQ10 Q Q 199 Q10 UBIQUINONE-10 Ubidecarenone Ubiquinone-10 all-trans-ubiquinone ubiquinone ubiquinone 10 ubiquinone 50 ubiquinone-10 CHEBI:46245 coenzyme Q10 Beilstein:1900141 Beilstein CAS:303-98-0 ChemIDplus CAS:303-98-0 KEGG COMPOUND Drug_Central:4607 DrugCentral LIPID_MAPS_instance:LMPR02010001 LIPID MAPS PMID:10953455 Europe PMC PMID:13445756 Europe PMC PMID:17192765 Europe PMC PMID:17605305 Europe PMC PMID:18787645 Europe PMC PMID:18843432 Europe PMC PMID:20367194 Europe PMC PMID:25544601 Europe PMC PMID:26741866 Europe PMC PMID:27012265 Europe PMC PMID:7599208 Europe PMC PMID:7718355 Europe PMC Reaxys:1900141 Reaxys 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione IUPAC Coenzyme Q10 KEGG_COMPOUND coenzyme Q10 ChemIDplus 2-((all-E)-3,7,11,15,19,23,27,31,35,39-decamethyl-2,6,10,14,18,22,26,30,34,38-tetracontadecaenyl)-5,6-dimethoxy-3-methyl-p-benzoquinone ChemIDplus 2-[(2E,6E,10E,14E,18E,22E,26E,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methyl-1,4-benzoquinone ChEBI Adelir KEGG_DRUG CoQ ChEBI CoQ10 ChEBI Q ChEBI Q 199 ChemIDplus Q10 ChEBI UBIQUINONE-10 PDBeChem Ubidecarenone KEGG_COMPOUND Ubiquinone-10 KEGG_COMPOUND all-trans-ubiquinone ChEBI ubiquinone ChEBI ubiquinone 10 ChemIDplus ubiquinone 50 ChemIDplus ubiquinone-10 UniProt 0 O 15.99940 15.99491 O=* CHEBI:29353 CHEBI:44607 PDBeChem:O OXO GROUP oxo chebi_ontology =O CHEBI:46629 oxo group OXO GROUP PDBeChem oxo IUPAC =O IUPAC 0 C7H6O4 InChI=1S/C7H6O4/c1-3-2-4(8)6(10)7(11)5(3)9/h2,10-11H,1H3 DUPLFIFGNDSGBB-UHFFFAOYSA-N 154.12014 154.02661 CC1=CC(=O)C(O)=C(O)C1=O Beilstein:2254950 2,3-dihydroxy-5-methylcyclohexa-2,5-diene-1,4-dione chebi_ontology CHEBI:46691 2,3-dihydroxy-5-methyl-1,4-benzoquinone Beilstein:2254950 Beilstein 2,3-dihydroxy-5-methylcyclohexa-2,5-diene-1,4-dione IUPAC chebi_ontology carbonate salts CHEBI:46721 carbonate salt carbonate salts ChEBI A liquid that can dissolve other substances (solutes) without any change in their chemical composition. Wikipedia:Solvent chebi_ontology Loesungsmittel solvant solvents CHEBI:46787 solvent Loesungsmittel ChEBI solvant ChEBI solvents ChEBI 0 CHO2 45.01744 44.99765 *C(=O)O CHEBI:23025 CHEBI:41420 PDBeChem:FMT CARBOXY GROUP carboxy chebi_ontology -C(O)OH -CO2H -COOH carboxyl group CHEBI:46883 carboxy group CARBOXY GROUP PDBeChem carboxy IUPAC -C(O)OH IUPAC -CO2H ChEBI -COOH IUPAC carboxyl group ChEBI A dicarboxylic acid monoanion that is the conjugate base of oxalic acid. -1 C2HO4 InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)/p-1 MUBZPKHOEPUJKR-UHFFFAOYSA-M 89.02694 88.98803 OC(=O)C([O-])=O Beilstein:3601755 Gmelin:49515 carboxyformate chebi_ontology Hox hydrogen ethanedioate hydrogen oxalate CHEBI:46904 oxalate(1-) Beilstein:3601755 Beilstein Gmelin:49515 Gmelin carboxyformate IUPAC Hox IUPAC hydrogen ethanedioate IUPAC hydrogen oxalate ChEBI +1 C5H13N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p+1 AHLPHDHHMVZTML-UHFFFAOYSA-O 133.16900 133.09715 [NH3+]CCCC([NH3+])C([O-])=O 2,5-diammoniopentanoate ornithinium ornithinium(1+) chebi_ontology ornithine monocation CHEBI:46912 ornithinium(1+) 2,5-diammoniopentanoate IUPAC ornithinium IUPAC ornithinium(1+) JCBN ornithine monocation JCBN +2 C5H14N2O2 InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p+2 AHLPHDHHMVZTML-UHFFFAOYSA-P 134.17694 134.10443 [NH3+]CCCC([NH3+])C(O)=O 1-carboxybutane-1,4-diaminium ornithinediium ornithinium(2+) chebi_ontology ornithine dication CHEBI:46913 ornithinium(2+) 1-carboxybutane-1,4-diaminium IUPAC ornithinediium IUPAC ornithinium(2+) JCBN ornithine dication JCBN chebi_ontology tetrahydrofuranols CHEBI:47017 tetrahydrofuranol tetrahydrofuranols ChEBI chebi_ontology dihydroxytetrahydrofurans CHEBI:47019 dihydroxytetrahydrofuran dihydroxytetrahydrofurans ChEBI Any ester resulting from the condensation of one or more of the hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. CHEBI:13730 CHEBI:22230 glyceride glycerides chebi_ontology acylglycerols glycerides CHEBI:47778 glyceride glyceride ChEBI glycerides IUPAC acylglycerols ChEBI glycerides ChEBI chebi_ontology penamcarboxylates CHEBI:47811 penamcarboxylate penamcarboxylates ChEBI CHEBI:27220 CHEBI:36947 chebi_ontology urea derivatives CHEBI:47857 ureas urea derivatives ChEBI A chemical compound that can be excited by light of a specific wavelength and subsequently transfer energy to a chosen reactant. This is commonly molecular oxygen within a cancer tissue, which is converted to (highly rective) singlet state oxygen. This rapidly reacts with any nearby biomolecules, ultimately killing the cancer cells. chebi_ontology photosensitising agent CHEBI:47868 photosensitizing agent photosensitising agent ChEBI macrocyclic polypyrroles chebi_ontology cyclic polypyrroles polypyrrole macrocycles CHEBI:47882 cyclic polypyrrole macrocyclic polypyrroles IUPAC cyclic polypyrroles ChEBI polypyrrole macrocycles ChEBI Any steroid substituted by at least one carboxy group. chebi_ontology steroid acids CHEBI:47891 steroid acid steroid acids ChEBI A compound, usually an anti-bacterial agent or a toxin, which inhibits the synthesis of a protein. chebi_ontology protein synthesis antagonist protein synthesis antagonists protein synthesis inhibitors CHEBI:48001 protein synthesis inhibitor protein synthesis antagonist ChEBI protein synthesis antagonists ChEBI protein synthesis inhibitors ChEBI chebi_ontology Schwefeloxide oxides of sulfur sulfur oxides CHEBI:48154 sulfur oxide Schwefeloxide ChEBI oxides of sulfur ChEBI sulfur oxides ChEBI chebi_ontology serotonergic agents serotonergic drugs serotonin drugs CHEBI:48278 serotonergic drug serotonergic agents ChEBI serotonergic drugs ChEBI serotonin drugs ChEBI A solvent that is composed of polar molecules. Polar solvents can dissolve ionic compounds or ionisable covalent compounds. polar solvent chebi_ontology polar solvents CHEBI:48354 polar solvent polar solvent IUPAC polar solvents ChEBI chebi_ontology CHEBI:48355 non-polar solvent A polar solvent that is capable of acting as a hydron (proton) donor. protogenic solvent chebi_ontology CHEBI:48356 protic solvent protogenic solvent IUPAC Solvent that is capable of acting as a hydron (proton) acceptor. protophilic solvent chebi_ontology HBA solvent hydrogen bond acceptor solvent CHEBI:48359 protophilic solvent protophilic solvent IUPAC HBA solvent ChEBI hydrogen bond acceptor solvent ChEBI Self-ionizing solvent possessing both characteristics of Bronsted acids and bases. amphiprotic solvent chebi_ontology CHEBI:48360 amphiprotic solvent amphiprotic solvent IUPAC 0 CH4N2O InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4) XSQUKJJJFZCRTK-UHFFFAOYSA-N 60.05534 60.03236 NC(O)=N Beilstein:773698 CAS:4744-36-9 carbamimidic acid chebi_ontology H2N-C(=NH)-OH H2N-C(OH)=NH HO-C(=NH)-NH2 Isoharnstoff carbamimic acid carbonamidimidic acid isourea pseudourea CHEBI:48376 carbamimidic acid Beilstein:773698 Beilstein CAS:4744-36-9 ChemIDplus carbamimidic acid IUPAC H2N-C(=NH)-OH IUPAC H2N-C(OH)=NH IUPAC HO-C(=NH)-NH2 IUPAC Isoharnstoff ChEBI carbamimic acid ChemIDplus carbonamidimidic acid IUPAC isourea ChemIDplus pseudourea ChemIDplus Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing =O by =NR; thus tautomers of amides. In organic chemistry an unspecified imidic acid is generally a carboximidic acid, RC(=NR)(OH). imidic acid imidic acids chebi_ontology imidic acids imino acids CHEBI:48377 imidic acid imidic acid ChEBI imidic acids IUPAC imidic acids ChEBI imino acids IUPAC carboximidic acid carboximidic acids chebi_ontology carboximidic acids CHEBI:48378 carboximidic acid carboximidic acid ChEBI carboximidic acids IUPAC carboximidic acids ChEBI A carboximidic acid that is the imidic acid tautomer of urea, H2NC(=NH)OH, and its hydrocarbyl derivatives. isoureas chebi_ontology isoureas CHEBI:48379 isourea isoureas IUPAC isoureas ChEBI A drug used in the treatment of Parkinson's disease. Wikipedia:Antiparkinson chebi_ontology antiparkinson agent CHEBI:48407 antiparkinson drug antiparkinson agent ChEBI An agent and endogenous substances that antagonize or inhibit the development of new blood vessels. CHEBI:67170 Wikipedia:Angiogenesis_inhibitor chebi_ontology angiogenesis antagonist angiostatic agents anti-angiogenic agent CHEBI:48422 angiogenesis inhibitor angiogenesis antagonist ChEBI angiostatic agents ChEBI anti-angiogenic agent ChEBI A local anesthetic that is used to numb the surface of a body part. chebi_ontology topical anaesthetics topical anesthetic CHEBI:48425 topical anaesthetic topical anaesthetics ChEBI topical anesthetic ChEBI Any drug that acts on an alpha-adrenergic receptor. chebi_ontology alpha-adrenergic drugs CHEBI:48539 alpha-adrenergic drug alpha-adrenergic drugs ChEBI Any of the drugs that act on beta-adrenergic receptors. chebi_ontology beta-adrenergic drugs CHEBI:48540 beta-adrenergic drug beta-adrenergic drugs ChEBI A role played by a substance that can react readily with, and thereby eliminate, radicals. chebi_ontology free radical scavengers free-radical scavenger CHEBI:48578 radical scavenger free radical scavengers ChEBI free-radical scavenger ChEBI Substance which binds to cell receptors normally responding to naturally occurring substances and which produces a response of its own. agonist chebi_ontology agonista agoniste agonists CHEBI:48705 agonist agonist IUPAC agonista ChEBI agoniste ChEBI agonists ChEBI Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances. antagonist chebi_ontology antagonista antagoniste antagonists CHEBI:48706 antagonist antagonist IUPAC antagonista ChEBI antagoniste ChEBI antagonists ChEBI 0 H2O3S InChI=1S/H2O3S/c1-4(2)3/h(H2,1,2,3) LSNNMFCWUKXFEE-UHFFFAOYSA-N 82.08008 81.97247 OS(O)=O CHEBI:26837 CHEBI:9344 CAS:7782-99-2 Gmelin:1458 KEGG:C00094 KNApSAcK:C00019662 PDBeChem:SO3 UM-BBD_compID:c0348 Sulfurous acid dihydrogen trioxosulfate dihydroxidooxidosulfur sulfurous acid trioxosulfuric acid chebi_ontology H2SO3 S(O)(OH)2 Sulfite [SO(OH)2] acide sulfureux acido sulfuroso schweflige Saeure sulphurous acid CHEBI:48854 sulfurous acid CAS:7782-99-2 ChemIDplus Gmelin:1458 Gmelin UM-BBD_compID:c0348 UM-BBD Sulfurous acid KEGG_COMPOUND dihydrogen trioxosulfate IUPAC dihydroxidooxidosulfur IUPAC sulfurous acid IUPAC trioxosulfuric acid IUPAC H2SO3 IUPAC S(O)(OH)2 IUPAC Sulfite KEGG_COMPOUND [SO(OH)2] IUPAC acide sulfureux ChEBI acido sulfuroso ChEBI schweflige Saeure ChemIDplus sulphurous acid ChemIDplus Any drug that binds to but does not activate cholinergic receptors, thereby blocking the actions of acetylcholine or cholinergic agonists. chebi_ontology Anticholinergika Anticholinergikum acetylcholine antagonists acetylcholine receptor antagonist agent anticholinergique agente anticolinergico agentes anticolinergicos anticholinergic agents anticholinergics anticholinergiques anticolinergicos cholinergic-blocking agents CHEBI:48873 cholinergic antagonist Anticholinergika ChEBI Anticholinergikum ChEBI acetylcholine antagonists ChEBI acetylcholine receptor antagonist IUPHAR agent anticholinergique ChEBI agente anticolinergico ChEBI agentes anticolinergicos ChEBI anticholinergic agents ChEBI anticholinergics ChEBI anticholinergiques ChEBI anticolinergicos ChEBI cholinergic-blocking agents ChEBI An azole in which the five-membered heterocyclic aromatic skeleton contains a N atom and one S atom. chebi_ontology thiazole CHEBI:48901 thiazoles thiazole ChEBI Any L-alpha-amino acid carrying an N-acyl substituent. 0 C3H3NO3R2 101.061 101.01129 CHEBI:13240 CHEBI:7232 KEGG:C02850 chebi_ontology N-Acyl-L-amino acid CHEBI:48927 N-acyl-L-alpha-amino acid N-Acyl-L-amino acid KEGG_COMPOUND 0 C20H42 InChI=1S/C20H42/c1-7-18(4)12-9-14-20(6)16-10-15-19(5)13-8-11-17(2)3/h17-20H,7-16H2,1-6H3 GGYKPYDKXLHNTI-UHFFFAOYSA-N 282.54748 282.32865 CCC(C)CCCC(C)CCCC(C)CCCC(C)C Beilstein:1744639 CAS:638-36-8 2,6,10,14-tetramethylhexadecane chebi_ontology Phytan CHEBI:48937 phytane Beilstein:1744639 Beilstein CAS:638-36-8 NIST Chemistry WebBook 2,6,10,14-tetramethylhexadecane IUPAC Phytan NIST_Chemistry_WebBook A chemical substance which inhibits the function of the endocrine glands, the biosynthesis of their secreted hormones, or the action of hormones upon their specific sites. chebi_ontology hormone antagonists CHEBI:49020 hormone antagonist hormone antagonists ChEBI chebi_ontology drug metabolites CHEBI:49103 drug metabolite drug metabolites ChEBI A drug designed to prevent leukotriene synthesis or activity by blocking binding at the receptor level. chebi_ontology LTRA leukotriene antagonists leukotriene receptor antagonist leukotriene receptor antagonists CHEBI:49159 leukotriene antagonist LTRA DrugBank leukotriene antagonists ChEBI leukotriene receptor antagonist ChEBI leukotriene receptor antagonists ChEBI A drug used to treat asthma. chebi_ontology anti-asthmatic agent anti-asthmatic agents anti-asthmatic drugs CHEBI:49167 anti-asthmatic drug anti-asthmatic agent ChEBI anti-asthmatic agents ChEBI anti-asthmatic drugs ChEBI One of various classes of drugs with different action mechanisms used to treat or ameliorate peptic ulcer or irritation of the gastrointestinal tract. chebi_ontology anti-ulcer agent anti-ulcer agents anti-ulcer drugs CHEBI:49201 anti-ulcer drug anti-ulcer agent ChEBI anti-ulcer agents ChEBI anti-ulcer drugs ChEBI 0 H InChI=1S/H YZCKVEUIGOORGS-UHFFFAOYSA-N 1.00794 1.00783 [H] CHEBI:24634 CHEBI:49636 WebElements:H hydrogen chebi_ontology 1H H Wasserstoff hidrogeno hydrogen hydrogene CHEBI:49637 hydrogen atom hydrogen IUPAC 1H IUPAC H IUPAC Wasserstoff ChEBI hidrogeno ChEBI hydrogen ChEBI hydrogene ChEBI A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups. chebi_ontology organic amino compounds CHEBI:50047 organic amino compound organic amino compounds ChEBI An agent that binds to and activates excitatory amino acid receptors. chebi_ontology excitatory amino acid agonists excitatory amino acid receptor agonist excitatory amino acid receptor agonists CHEBI:50103 excitatory amino acid agonist excitatory amino acid agonists ChEBI excitatory amino acid receptor agonist ChEBI excitatory amino acid receptor agonists ChEBI 0 C3H3NaO3 InChI=1S/C3H4O3.Na/c1-2(4)3(5)6;/h1H3,(H,5,6);/q;+1/p-1 DAEPDZWVDSPTHF-UHFFFAOYSA-M 110.04389 109.99799 [Na+].CC(=O)C([O-])=O Beilstein:3568341 CAS:113-24-6 Gmelin:97013 sodium 2-oxopropanoate chebi_ontology Natriumpyruvat pyruvic acid, sodium salt CHEBI:50144 sodium pyruvate Beilstein:3568341 Beilstein CAS:113-24-6 ChemIDplus Gmelin:97013 Gmelin sodium 2-oxopropanoate IUPAC Natriumpyruvat ChEBI pyruvic acid, sodium salt ChemIDplus Any anion formed by loss of a proton from a steroid acid. chebi_ontology steroid acid anions CHEBI:50160 steroid acid anion steroid acid anions ChEBI A drug used to treat or prevent skin disorders or for the routine care of skin. chebi_ontology dermatologic agent dermatologic drugs dermatological agent CHEBI:50177 dermatologic drug dermatologic agent ChEBI dermatologic drugs ChEBI dermatological agent ChEBI A substance that can be converted into a vitamin by animal tissues. Wikipedia:Provitamin chebi_ontology provitamins CHEBI:50188 provitamin provitamins ChEBI Any protective agent counteracting or neutralizing the action of poisons. chebi_ontology antidotes CHEBI:50247 antidote antidotes ChEBI Drug that acts on blood and blood-forming organs and those that affect the hemostatic system. chebi_ontology hematologic agents CHEBI:50248 hematologic agent hematologic agents ChEBI An agent that prevents blood clotting. chebi_ontology anticoagulante anticoagulants CHEBI:50249 anticoagulant anticoagulante ChEBI anticoagulants ChEBI A compound that, on administration, must undergo chemical conversion by metabolic processes before becoming the pharmacologically active drug for which it is a prodrug. PMID:23993918 PMID:23998799 PMID:24329110 PMID:24628402 PMID:24709544 PMID:25144792 PMID:25157234 PMID:25269430 PMID:25391982 PMID:25591121 PMID:25620096 PMID:25795057 PMID:26028253 PMID:26184144 PMID:28070577 PMID:28215138 PMID:28219047 PMID:28259775 PMID:28319647 PMID:28329729 PMID:28334528 Wikipedia:Prodrug chebi_ontology Prodrugs CHEBI:50266 prodrug PMID:23993918 Europe PMC PMID:23998799 Europe PMC PMID:24329110 Europe PMC PMID:24628402 Europe PMC PMID:24709544 Europe PMC PMID:25144792 Europe PMC PMID:25157234 Europe PMC PMID:25269430 Europe PMC PMID:25391982 Europe PMC PMID:25591121 Europe PMC PMID:25620096 Europe PMC PMID:25795057 Europe PMC PMID:26028253 Europe PMC PMID:26184144 Europe PMC PMID:28070577 Europe PMC PMID:28215138 Europe PMC PMID:28219047 Europe PMC PMID:28259775 Europe PMC PMID:28319647 Europe PMC PMID:28329729 Europe PMC PMID:28334528 Europe PMC Prodrugs ChEBI Synthetic or natural substance which is given to prevent a disease or disorder or are used in the process of treating a disease or injury due to a poisonous agent. chebi_ontology chemoprotectant chemoprotectants chemoprotective agent chemoprotective agents protective agents CHEBI:50267 protective agent chemoprotectant ChEBI chemoprotectants ChEBI chemoprotective agent ChEBI chemoprotective agents ChEBI protective agents ChEBI chebi_ontology CHEBI:50312 onium compound Mononuclear cations derived by addition of a hydron to a mononuclear parent hydride of the pnictogen, chalcogen and halogen families. onium cations chebi_ontology onium cations onium ion onium ions CHEBI:50313 onium cation onium cations IUPAC onium cations ChEBI onium ion ChEBI onium ions ChEBI +1 FH2 InChI=1S/FH2/h1H2/q+1 YNESUKSMQODWNS-UHFFFAOYSA-N 21.01428 21.01350 [H][F+][H] fluoranium fluoronium chebi_ontology H2F(+) [FH2](+) CHEBI:50314 fluoronium fluoranium IUPAC fluoronium IUPAC H2F(+) IUPAC [FH2](+) ChEBI A univalent organyl group obtained by cleaving the bond from C-2 to the side chain of a proteinogenic amino-acid. chebi_ontology canonical amino-acid side-chain canonical amino-acid side-chains proteinogenic amino-acid side-chain proteinogenic amino-acid side-chain groups proteinogenic amino-acid side-chains CHEBI:50325 proteinogenic amino-acid side-chain group canonical amino-acid side-chain ChEBI canonical amino-acid side-chains ChEBI proteinogenic amino-acid side-chain ChEBI proteinogenic amino-acid side-chain groups ChEBI proteinogenic amino-acid side-chains ChEBI 0 CH3S 47.10052 46.99555 SC* sulfanylmethyl chebi_ontology -CH2-SH HS-CH2- cysteine side-chain CHEBI:50326 sulfanylmethyl group sulfanylmethyl IUPAC -CH2-SH IUPAC HS-CH2- IUPAC cysteine side-chain ChEBI 0 C3H5O2 73.07060 73.02895 C(CC(=O)O)* 2-carboxyethyl chebi_ontology glutamic acid side-chain CHEBI:50329 2-carboxyethyl group 2-carboxyethyl IUPAC glutamic acid side-chain ChEBI 0 C7H7O 107.12988 107.04969 C1=C(C*)C=CC(=C1)O 4-hydroxybenzyl chebi_ontology tyrosine side-chain CHEBI:50336 4-hydroxybenzyl group 4-hydroxybenzyl IUPAC tyrosine side-chain ChEBI 0 C4H10N 72.12894 72.08132 NCCCC* 4-aminobutyl chebi_ontology lysine side-chain CHEBI:50339 4-aminobutyl group 4-aminobutyl IUPAC lysine side-chain ChEBI 0 C4H10N3 100.14242 100.08747 NC(=N)NCCC* 3-carbamimidamidopropyl chebi_ontology 3-(carbamimidoylamino)propyl 3-guanidinopropyl arginine side-chain CHEBI:50340 3-carbamimidamidopropyl group 3-carbamimidamidopropyl IUPAC 3-(carbamimidoylamino)propyl IUPAC 3-guanidinopropyl ChEBI arginine side-chain ChEBI Any steroid based on a cholestane skeleton and its derivatives. chebi_ontology cholestanoids CHEBI:50401 cholestanoid cholestanoids ChEBI A drug or agent which antagonizes or impairs any mechanism leading to blood platelet aggregation, whether during the phases of activation and shape change or following the dense-granule release reaction and stimulation of the prostaglandin-thromboxane system. chebi_ontology platelet aggregation inhibitors CHEBI:50427 platelet aggregation inhibitor platelet aggregation inhibitors ChEBI Substance that sweeten food, beverages, medications, etc. chebi_ontology sweetener sweeteners CHEBI:50505 sweetening agent sweetener ChEBI sweeteners ChEBI An aliphatic alcohol in which the aliphatic alkane chain is substituted by a hydroxy group at unspecified position. CHEBI:22937 CHEBI:50581 chebi_ontology alkyl alcohols hydroxyalkane hydroxyalkanes CHEBI:50584 alkyl alcohol alkyl alcohols ChEBI hydroxyalkane ChEBI hydroxyalkanes ChEBI A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues. oligosaccharide http://langual.org CHEBI:25679 CHEBI:35319 CHEBI:7758 KEGG:C00930 http://www.langual.org/langual_thesaurus.asp?termid=C0226 Oligosaccharide oligosaccharides chebi_ontology O-glycosylglycoside O-glycosylglycosides oligosacarido oligosacaridos CHEBI:50699 LanguaL term definition: Complex carbohydrate with molecules composed of three to ten saccharide units (specifically dextrin). May be slightly sweet to the taste. oligosaccharide Oligosaccharide KEGG_COMPOUND oligosaccharides IUPAC O-glycosylglycoside ChEBI O-glycosylglycosides ChEBI oligosacarido ChEBI oligosacaridos IUPAC A product in capsule, tablet or liquid form that provide essential nutrients, such as a vitamin, an essential mineral, a protein, an herb, or similar nutritional substance. chebi_ontology Dietary Supplement Food Supplementation Nutritional supplement CHEBI:50733 nutraceutical Dietary Supplement ChEBI Food Supplementation ChEBI Nutritional supplement ChEBI A substance that possess antiestrogenic actions but can also produce estrogenic effects as well. It acts as complete or partial agonist or as antagonist. It can be either steroidal or nonsteroidal in structure. chebi_ontology CHEBI:50739 estrogen receptor modulator An EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor which interferes with the action of aromatase (EC 1.14.14.14) and so reduces production of estrogenic steroid hormones. Wikipedia:Aromatase_inhibitor chebi_ontology EC 1.14.14.14 (aromatase) inhibitors EC 1.14.14.14 inhibitor EC 1.14.14.14 inhibitors aromatase (EC 1.14.14.14) inhibitor aromatase (EC 1.14.14.14) inhibitors aromatase inhibitor aromatase inhibitors estrogen synthase inhibitor estrogen synthase inhibitors estrogen synthetase inhibitor estrogen synthetase inhibitors oestrogen synthase inhibitor oestrogen synthase inhibitors oestrogen synthetase inhibitor oestrogen synthetase inhibitors CHEBI:50790 EC 1.14.14.14 (aromatase) inhibitor EC 1.14.14.14 (aromatase) inhibitors ChEBI EC 1.14.14.14 inhibitor ChEBI EC 1.14.14.14 inhibitors ChEBI aromatase (EC 1.14.14.14) inhibitor ChEBI aromatase (EC 1.14.14.14) inhibitors ChEBI aromatase inhibitor ChEBI aromatase inhibitors ChEBI estrogen synthase inhibitor ChEBI estrogen synthase inhibitors ChEBI estrogen synthetase inhibitor ChEBI estrogen synthetase inhibitors ChEBI oestrogen synthase inhibitor ChEBI oestrogen synthase inhibitors ChEBI oestrogen synthetase inhibitor ChEBI oestrogen synthetase inhibitors ChEBI A drug used to treat hyperparathyroidism by reducing the excessive production of parathyroid hormones. chebi_ontology antiparathyroid agent antiparathyroid agents antiparathyroid drugs CHEBI:50827 antiparathyroid drug antiparathyroid agent ChEBI antiparathyroid agents ChEBI antiparathyroid drugs ChEBI A compound which inhibits or antagonises the biosynthesis or actions of estrogens. chebi_ontology oestrogen antagonist CHEBI:50837 estrogen antagonist oestrogen antagonist ChEBI Biologically active substance whose activity affects or plays a role in the functioning of the immune system. Wikipedia:Immunotherapy chebi_ontology Biomodulator Immune factor Immunologic factor Immunological factor immunomodulators CHEBI:50846 immunomodulator Biomodulator ChEBI Immune factor ChEBI Immunologic factor ChEBI Immunological factor ChEBI immunomodulators ChEBI A substance that augments, stimulates, activates, potentiates, or modulates the immune response at either the cellular or humoral level. A classical agent (Freund's adjuvant, BCG, Corynebacterium parvum, et al.) contains bacterial antigens. It could also be endogenous (e.g., histamine, interferon, transfer factor, tuftsin, interleukin-1). Its mode of action is either non-specific, resulting in increased immune responsiveness to a wide variety of antigens, or antigen-specific, i.e., affecting a restricted type of immune response to a narrow group of antigens. The therapeutic efficacy is related to its antigen-specific immunoadjuvanticity. Wikipedia:Immunologic_adjuvant chebi_ontology Immunoactivator Immunoadjuvant Immunologic adjuvant Immunopotentiator Immunostimulant CHEBI:50847 immunological adjuvant Immunoactivator ChEBI Immunoadjuvant ChEBI Immunologic adjuvant ChEBI Immunopotentiator ChEBI Immunostimulant ChEBI A cardiovascular drug that prevents atherogenesis, the accumulation of lipid-containing plaques on the innermost layers of the arteries. Compare with antiatherosclerotic agent. PMID:14592471 PMID:16366593 PMID:17990280 PMID:20222342 PMID:21074432 PMID:21172387 PMID:21649483 PMID:3288054 PMID:9796331 antiatherogenic agent chebi_ontology anti-atherogenic agent anti-atherogenic agents anti-atherogenic drug anti-atherogenic drugs antiatherogenic agents antiatherogenic drug antiatherogenic drugs CHEBI:50855 antiatherogenic agent PMID:14592471 Europe PMC PMID:16366593 Europe PMC PMID:17990280 Europe PMC PMID:20222342 Europe PMC PMID:21074432 Europe PMC PMID:21172387 Europe PMC PMID:21649483 Europe PMC PMID:3288054 Europe PMC PMID:9796331 Europe PMC antiatherogenic agent ChEBI anti-atherogenic agent ChEBI anti-atherogenic agents ChEBI anti-atherogenic drug ChEBI anti-atherogenic drugs ChEBI antiatherogenic agents ChEBI antiatherogenic drug ChEBI antiatherogenic drugs ChEBI A drug used to treat allergic reactions. chebi_ontology anti-allergic agents anti-allergic drug anti-allergic drugs CHEBI:50857 anti-allergic agent anti-allergic agents ChEBI anti-allergic drug ChEBI anti-allergic drugs ChEBI A natural or synthetic analogue of the hormones secreted by the adrenal gland. chebi_ontology corticoides corticosteroides corticosteroids CHEBI:50858 corticosteroid corticoides ChEBI corticosteroides ChEBI corticosteroids ChEBI Any molecular entity that contains carbon. CHEBI:25700 CHEBI:33244 chebi_ontology organic compounds organic entity organic molecular entities CHEBI:50860 organic molecular entity organic compounds ChEBI organic entity ChEBI organic molecular entities ChEBI A role played by a chemical compound to induce direct or indirect DNA damage. Such damage can potentially lead to the formation of a malignant tumour, but DNA damage does not lead inevitably to the creation of cancerous cells. Wikipedia:Genotoxicity chebi_ontology genotoxic agent genotoxic agents genotoxins CHEBI:50902 genotoxin genotoxic agent ChEBI genotoxic agents ChEBI genotoxins ChEBI A role played by a chemical compound which is known to induce a process of carcinogenesis by corrupting normal cellular pathways, leading to the acquistion of tumoral capabilities. chebi_ontology agente carcinogeno cancerigene cancerogene carcinogen carcinogene carcinogenic agents carcinogeno carcinogens CHEBI:50903 carcinogenic agent agente carcinogeno ChEBI cancerigene ChEBI cancerogene ChEBI carcinogen ChEBI carcinogene ChEBI carcinogenic agents ChEBI carcinogeno ChEBI carcinogens ChEBI A chemical compound, or part thereof, which causes the onset of an allergic reaction by interacting with any of the molecular pathways involved in an allergy. Wikipedia:Allergen chebi_ontology alergeno allergene allergenic agent CHEBI:50904 allergen alergeno ChEBI allergene ChEBI allergenic agent ChEBI role (CHEBI) A role is particular behaviour which a material entity may exhibit. chebi_ontology CHEBI:50906 role A poison that interferes with the functions of the nervous system. CHEBI:50911 Wikipedia:Neurotoxin chebi_ontology agente neurotoxico nerve poison nerve poisons neurotoxic agent neurotoxic agents neurotoxicant neurotoxins CHEBI:50910 neurotoxin agente neurotoxico ChEBI nerve poison ChEBI nerve poisons ChEBI neurotoxic agent ChEBI neurotoxic agents ChEBI neurotoxicant ChEBI neurotoxins ChEBI A drug used to prevent nausea or vomiting. An antiemetic may act by a wide range of mechanisms: it might affect the medullary control centres (the vomiting centre and the chemoreceptive trigger zone) or affect the peripheral receptors. Wikipedia:Antiemetic chebi_ontology anti-emetic anti-emetics antiemetico antiemetics CHEBI:50919 antiemetic anti-emetic ChEBI anti-emetics ChEBI antiemetico ChEBI antiemetics ChEBI An agent that modulates the physiologic angiogenesis process. This is accomplished by endogenous angiogenic proteins and a variety of other chemicals and pharmaceutical agents. chebi_ontology CHEBI:50926 angiogenesis modulating agent An agent that induces or stimulates the physiologic angiogenesis process. chebi_ontology CHEBI:50927 angiogenesis inducing agent A compound that specifically inhibits the reuptake of serotonin in the brain. This increases the serotonin concentration in the synaptic cleft which then activates serotonin receptors to a greater extent. Wikipedia:Selective_serotonin_reuptake_inhibitor chebi_ontology SSRI serotonin reuptake inhibitor CHEBI:50949 serotonin uptake inhibitor SSRI ChEBI serotonin reuptake inhibitor ChEBI A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group. chebi_ontology primary amino compounds CHEBI:50994 primary amino compound primary amino compounds ChEBI A compound formally derived from ammonia by replacing three hydrogen atoms by organyl groups. chebi_ontology tertiary amino compounds CHEBI:50996 tertiary amino compound tertiary amino compounds ChEBI A cyclic compound containing nine or more atoms as part of the cyclic system. Wikipedia:Macrocycle macrocycle chebi_ontology Makrocyclen Makrozyklen macrocycles makrocyclische Verbindungen makrozyklische Verbindungen CHEBI:51026 macrocycle macrocycle IUPAC Makrocyclen ChEBI Makrozyklen ChEBI macrocycles ChEBI makrocyclische Verbindungen ChEBI makrozyklische Verbindungen ChEBI A drug that modulates the function of the endocrine glands, the biosynthesis of their secreted hormones, or the action of hormones upon their specific sites. chebi_ontology hormone receptor modulators CHEBI:51061 hormone receptor modulator hormone receptor modulators ChEBI A role played by the molecular entity or part thereof within a chemical context. chebi_ontology CHEBI:51086 chemical role nitrogen http://langual.org CHEBI:25556 CHEBI:7594 Codex::941 Europe::941 KEGG:C06061 http://www.langual.org/langual_thesaurus.asp?termid=B3173 chebi_ontology Nitrogenous compounds nitrogen compounds nitrogen molecular entities CHEBI:51143 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive; technological purpose(s): packaging gas, propellant. nitrogen molecular entity Nitrogenous compounds KEGG_COMPOUND nitrogen compounds ChEBI nitrogen molecular entities ChEBI An organic molecule that is electrically neutral carrying a positive and a negative charge in one of its major canonical descriptions. In most dipolar compounds the charges are delocalized; however the term is also applied to species where this is not the case. chebi_ontology dipolar compounds CHEBI:51151 dipolar compound dipolar compounds ChEBI Polycyclic aromatic hydrocarbons consisting of fused benzene rings in a rectilinear arrangement and their substitution derivatives. chebi_ontology CHEBI:51269 acenes Compounds containing a tetracene skeleton. chebi_ontology naphthacenes CHEBI:51270 tetracenes naphthacenes ChEBI Any anion formed by loss of a proton from the carboxy group of a penicillin. -1 C9H10N2O4SR 242.25200 242.03613 [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC([*])=O)C([O-])=O CHEBI:58108 chebi_ontology penicillin penicillin anion penicillin anions CHEBI:51356 penicillinate anion penicillin UniProt penicillin anion ChEBI penicillin anions ChEBI A drug used to produce muscle relaxation (excepting neuromuscular blocking agents). Its primary clinical and therapeutic use is the treatment of muscle spasm and immobility associated with strains, sprains, and injuries of the back and, to a lesser degree, injuries to the neck. Also used for the treatment of a variety of clinical conditions that have in common only the presence of skeletal muscle hyperactivity, for example, the muscle spasms that can occur in multiple sclerosis. chebi_ontology muscle relaxants CHEBI:51371 muscle relaxant muscle relaxants ChEBI A drug used for its actions on skeletal muscle. chebi_ontology CHEBI:51372 neuromuscular agent A substance, such as agonists, antagonists, degradation or uptake inhibitors, depleters, precursors, and modulators of receptor function, used for its pharmacological actions on GABAergic systems. chebi_ontology CHEBI:51374 GABA agent Any organic substituent group, regardless of functional type, having two free valences at carbon atom(s). chebi_ontology organodiyl groups CHEBI:51422 organodiyl group organodiyl groups ChEBI chebi_ontology CHEBI:51446 organic divalent group chebi_ontology CHEBI:51447 organic univalent group A carboxamide resulting from the formal condensation of a carboxylic acid with the amino group of an amino acid. CHEBI:21653 CHEBI:22226 chebi_ontology N-acyl amino acid N-acyl amino acids N-acyl-amino-acid N-acyl-amino-acids N-acylamino acid N-acylamino acids acyl-amino-acid acyl-amino-acids acylamino acids CHEBI:51569 N-acyl-amino acid N-acyl amino acid ChEBI N-acyl amino acids ChEBI N-acyl-amino-acid ChEBI N-acyl-amino-acids ChEBI N-acylamino acid ChEBI N-acylamino acids ChEBI acyl-amino-acid ChEBI acyl-amino-acids ChEBI acylamino acids ChEBI Compounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton. chebi_ontology CHEBI:51570 biotins chebi_ontology organic polycyclic compounds CHEBI:51958 organic polycyclic compound organic polycyclic compounds ChEBI chebi_ontology organic tricyclic compounds CHEBI:51959 organic tricyclic compound organic tricyclic compounds ChEBI An organic anion that is the conjugate base of methanol. -1 CH3O InChI=1S/CH3O/c1-2/h1H3/q-1 NBTOZLQBSIZIKS-UHFFFAOYSA-N 31.03390 31.01894 C[O-] Reaxys:1839368 chebi_ontology methoxide ion CHEBI:52090 methoxide Reaxys:1839368 Reaxys methoxide ion ChEBI A biological role played by the molecular entity or part thereof within a biochemical context. chebi_ontology CHEBI:52206 biochemical role chebi_ontology CHEBI:52208 biophysical role A role played by the molecular entity or part thereof which causes the development of a pathological process. chebi_ontology etiopathogenetic agent etiopathogenetic role CHEBI:52209 aetiopathogenetic role etiopathogenetic agent ChEBI etiopathogenetic role ChEBI A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties. chebi_ontology CHEBI:52210 pharmacological role chebi_ontology CHEBI:52211 physiological role Any substance introduced into a living organism with therapeutic or diagnostic purpose. CHEBI:33293 CHEBI:33294 chebi_ontology farmaco medicament pharmaceuticals CHEBI:52217 pharmaceutical farmaco ChEBI medicament ChEBI pharmaceuticals ChEBI A compound with the general formula R2C=O (R=/=H) where one or more of the R groups contains an oxy (-O-) group. chebi_ontology oxyketones CHEBI:52395 oxyketone oxyketones ChEBI An oxyketone with the general formula R2C(=O) (R=/=H) where one or more of the R groups contains an oxy (-O-) group and the oxy and carbonyl groups are bonded to the same carbon atom. chebi_ontology alpha-oxyketones CHEBI:52396 alpha-oxyketone alpha-oxyketones ChEBI Any fatty acid containing at least one C=C double bond. PMID:832335 chebi_ontology CHEBI:53339 olefinic fatty acid PMID:832335 Europe PMC Any drug found useful in the symptomatic treatment of diarrhoea. chebi_ontology antidiarrheal antidiarrheal agent antidiarrheal agents antidiarrheal drug antidiarrheal drugs antidiarrheals antidiarrhoeal antidiarrhoeal agent antidiarrhoeal agents antidiarrhoeal drugs antidiarrhoeals antiperistaltic antiperistaltic agent antiperistaltic agents antiperistaltic drug antiperistaltic drugs antiperistaltics CHEBI:55323 antidiarrhoeal drug antidiarrheal ChEBI antidiarrheal agent ChEBI antidiarrheal agents ChEBI antidiarrheal drug ChEBI antidiarrheal drugs ChEBI antidiarrheals ChEBI antidiarrhoeal ChEBI antidiarrhoeal agent ChEBI antidiarrhoeal agents ChEBI antidiarrhoeal drugs ChEBI antidiarrhoeals ChEBI antiperistaltic ChEBI antiperistaltic agent ChEBI antiperistaltic agents ChEBI antiperistaltic drug ChEBI antiperistaltic drugs ChEBI antiperistaltics ChEBI A drug used for its effects on the gastrointestinal system, e.g. controlling gastric acidity, regulating gastrointestinal motility and water flow, and improving digestion. chebi_ontology gastrointestinal agent gastrointestinal agents gastrointestinal drugs CHEBI:55324 gastrointestinal drug gastrointestinal agent ChEBI gastrointestinal agents ChEBI gastrointestinal drugs ChEBI A cyclic compound having as ring members atoms of at least two different elements. Heterocyclic compound chebi_ontology compuesto heterociclico compuestos heterociclicos heterocycle heterocyclic compounds CHEBI:5686 heterocyclic compound Heterocyclic compound KEGG_COMPOUND compuesto heterociclico IUPAC compuestos heterociclicos IUPAC heterocycle ChEBI heterocyclic compounds ChEBI An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of glycine. 0 C2H5NO2 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N 75.06660 75.03203 [NH3+]CC([O-])=O Gmelin:1807 MetaCyc:GLY 2-azaniumylacetate chebi_ontology glycine CHEBI:57305 glycine zwitterion Gmelin:1807 Gmelin 2-azaniumylacetate IUPAC glycine UniProt A fatty acid anion with a chain length of C13 to C22. -1 CO2R 44.010 43.98983 [O-]C([*])=O CHEBI:13652 chebi_ontology a long-chain carboxylate a long-chain fatty acid long-chain fatty acid anions CHEBI:57560 long-chain fatty acid anion a long-chain carboxylate ChEBI a long-chain fatty acid UniProt long-chain fatty acid anions ChEBI Zwitterionic form of gamma-amino-beta-hydroxybutyric acid having an anionic carboxy group and a protonated amino group. 0 C4H9NO3 InChI=1S/C4H9NO3/c5-2-3(6)1-4(7)8/h3,6H,1-2,5H2,(H,7,8) YQGDEPYYFWUPGO-UHFFFAOYSA-N 119.11920 119.05824 [NH3+]CC(O)CC([O-])=O 4-azaniumyl-3-hydroxybutanoate chebi_ontology 4-amino-3-hydroxybutanoate 4-ammonio-3-hydroxybutanoate CHEBI:57630 gamma-amino-beta-hydroxybutyric acid zwitterion 4-azaniumyl-3-hydroxybutanoate IUPAC 4-amino-3-hydroxybutanoate UniProt 4-ammonio-3-hydroxybutanoate ChEBI Zwitterionic form of L-methionine having a anionic carboxy group and a cationic amino group; major species at pH 7.3. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1 FFEARJCKVFRZRR-BYPYZUCNSA-N 149.21100 149.05105 CSCC[C@H]([NH3+])C([O-])=O Gmelin:560248 MetaCyc:MET (2S)-2-azaniumyl-4-(methylsulfanyl)butanoate chebi_ontology (2S)-2-ammonio-4-(methylsulfanyl)butanoate L-methionine CHEBI:57844 L-methionine zwitterion Gmelin:560248 Gmelin (2S)-2-azaniumyl-4-(methylsulfanyl)butanoate IUPAC (2S)-2-ammonio-4-(methylsulfanyl)butanoate ChEBI L-methionine UniProt Zwitterionic form of 6-aminopenicillanic acid arising from migration of a proton from the carboxy group to the 6-amino group; major species at pH 7.3. 0 C8H12N2O3S InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/t3-,4+,6-/m1/s1 NGHVIOIJCVXTGV-ALEPSDHESA-N 216.25700 216.05686 [H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2[NH3+])C([O-])=O 6-azaniumyl-2,2-dimethylpenam-3alpha-carboxylate chebi_ontology (2S,5R,6R)-6-azaniumyl-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate 6-aminopenicillanate CHEBI:57869 6-aminopenicillanic acid zwitterion 6-azaniumyl-2,2-dimethylpenam-3alpha-carboxylate IUPAC (2S,5R,6R)-6-azaniumyl-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate ChEBI 6-aminopenicillanate UniProt Zwitterionic form of D-methionine arising from transfer of a proton from the carboxy to the amino group; major species at pH 7.3. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1 FFEARJCKVFRZRR-SCSAIBSYSA-N 149.21100 149.05105 CSCC[C@@H]([NH3+])C([O-])=O MetaCyc:CPD-218 (2R)-2-azaniumyl-4-(methylsulfanyl)butanoate chebi_ontology (2R)-2-ammonio-4-(methylsulfanyl)butanoate D-methionine CHEBI:57932 D-methionine zwitterion (2R)-2-azaniumyl-4-(methylsulfanyl)butanoate IUPAC (2R)-2-ammonio-4-(methylsulfanyl)butanoate IUPAC D-methionine UniProt Zwitterionic form of creatine arising from transfer of a proton from the carboxy to the guanidino group; major species at pH 7.3. 0 C4H9N3O2 InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9) CVSVTCORWBXHQV-UHFFFAOYSA-N 131.13320 131.06948 CN(CC([O-])=O)C(N)=[NH2+] MetaCyc:CREATINE {[amino(iminio)methyl](methyl)amino}acetate chebi_ontology creatine CHEBI:57947 creatine zwitterion {[amino(iminio)methyl](methyl)amino}acetate IUPAC creatine UniProt The anion resulting from removal of a proton from the nitrogen at the 3 position (between the two carbonyl gropus) of riboflavin. -1 C17H19N4O6 InChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/p-1/t11-,12+,14-/m0/s1 AUNGANRZJHBGPY-SCRDCRAPSA-M 375.35600 375.13101 Cc1cc2nc3c(nc(=O)[n-]c3=O)n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C Beilstein:4924198 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-2H-benzo[g]pteridin-3-id-10(4H)-yl)-D-ribitol chebi_ontology 7,8-dimethyl-2,4-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-2H,3H,4H,10H-benzo[g]pteridin-3-ide riboflavin CHEBI:57986 riboflavin(1-) Beilstein:4924198 Beilstein 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-2H-benzo[g]pteridin-3-id-10(4H)-yl)-D-ribitol IUPAC 7,8-dimethyl-2,4-dioxo-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-2H,3H,4H,10H-benzo[g]pteridin-3-ide ChEBI riboflavin UniProt The conjugate acid of a primary aliphatic amine. +1 CH5NR 31.05710 31.04220 [NH3+]C[*] chebi_ontology an aliphatic amine primary aliphatic ammonium cation primary aliphatic ammonium cations primary aliphatic ammonium ions CHEBI:58001 primary aliphatic ammonium ion an aliphatic amine UniProt primary aliphatic ammonium cation ChEBI primary aliphatic ammonium cations ChEBI primary aliphatic ammonium ions ChEBI An ammonium ion that is the conjugate acid of trimethylamine, obtained via protonation of the nitrogen; major species at pH 7.3. +1 C3H10N InChI=1S/C3H9N/c1-4(2)3/h1-3H3/p+1 GETQZCLCWQTVFV-UHFFFAOYSA-O 60.11820 60.08078 C[NH+](C)C MetaCyc:TRIMETHYLAMINE Reaxys:16709444 N,N-dimethylmethanaminium chebi_ontology trimethylamine trimethylammonium cation trimethylazanium trimethylazanium cation CHEBI:58389 trimethylammonium Reaxys:16709444 Reaxys N,N-dimethylmethanaminium IUPAC trimethylamine UniProt trimethylammonium cation ChEBI trimethylazanium ChEBI trimethylazanium cation ChEBI The conjugate base of an N-acetyl-D-amino acid. -1 C4H5NO3R 115.08740 115.02694 CC(=O)N[C@H]([*])C([O-])=O chebi_ontology N-acetyl-D-amino acetate(1-) N-acetyl-D-amino acid anions N-acetyl-D-amino carboxylate anions an N-acetyl-D-amino acid CHEBI:58496 N-acetyl-D-amino acid anion N-acetyl-D-amino acetate(1-) ChEBI N-acetyl-D-amino acid anions ChEBI N-acetyl-D-amino carboxylate anions ChEBI an N-acetyl-D-amino acid UniProt Any fatty acid anion obtained by removal of a proton from the carboxy group of a short-chain fatty acid (chain length of less than C6). -1 CO2R 44.010 43.98983 [O-]C([*])=O chebi_ontology a short-chain fatty acid short-chain fatty acid anions CHEBI:58951 short-chain fatty acid anion a short-chain fatty acid UniProt short-chain fatty acid anions ChEBI Any fatty acid anion in which there is no C-C unsaturation. chebi_ontology saturated fatty acid anions CHEBI:58953 saturated fatty acid anion saturated fatty acid anions ChEBI Any saturated fatty acid anion lacking a carbon side-chain. chebi_ontology straight-chain saturated fatty acid anions CHEBI:58954 straight-chain saturated fatty acid anion straight-chain saturated fatty acid anions ChEBI Any fatty acid anion with a carbon side-chain or isopropyl termination. chebi_ontology branched-chain fatty acid anions CHEBI:58955 branched-chain fatty acid anion branched-chain fatty acid anions ChEBI Any saturated fatty acid anion with a carbon side-chain or isopropyl termination. chebi_ontology branched-chain saturated fatty acid anions CHEBI:58956 branched-chain saturated fatty acid anion branched-chain saturated fatty acid anions ChEBI Any substance capable of eliciting an immune response only when attached to a large carrier such as a protein. Examples include dinitrophenols; oligosaccharides; peptides; and heavy metals. PMID:17875790 PMID:17986299 PMID:19101624 PMID:291959 PMID:3782019 chebi_ontology haptens CHEBI:59174 hapten PMID:17875790 Europe PMC PMID:17986299 Europe PMC PMID:19101624 Europe PMC PMID:291959 Europe PMC PMID:3782019 Europe PMC haptens ChEBI Any fatty acid whose skeletal carbon atoms form an unbranched open chain. chebi_ontology straight-chain fatty acids CHEBI:59202 straight-chain fatty acid straight-chain fatty acids ChEBI A fatty acid anion formed by deprotonation of the carboxylic acid functional group of a straight-chain fatty acid. chebi_ontology straight-chain FA anion straight-chain FA anions straight-chain fatty acid anions CHEBI:59203 straight-chain fatty acid anion straight-chain FA anion ChEBI straight-chain FA anions ChEBI straight-chain fatty acid anions ChEBI Any member of the sub-set of polyunsaturated fatty acid for which there is an absolute dietary requirement. PMID:1745654 PMID:19034351 PMID:7609665 chebi_ontology EFA EFAs EFS acides gras indispensables acidos grasos esenciales essential fatty acids essentielle Fettsaeuren CHEBI:59549 essential fatty acid PMID:1745654 Europe PMC PMID:19034351 Europe PMC PMID:7609665 Europe PMC EFA ChEBI EFAs ChEBI EFS ChEBI acides gras indispensables ChEBI acidos grasos esenciales ChEBI essential fatty acids ChEBI essentielle Fettsaeuren ChEBI Any fatty acid with a chain length of between C6 and C12. 0 CHO2R 45.01740 44.99765 OC([*])=O chebi_ontology MCFA MCFAs medium-chain fatty acids CHEBI:59554 medium-chain fatty acid MCFA ChEBI MCFAs ChEBI medium-chain fatty acids ChEBI A fatty acid anion resulting from the deprotonation of the carboxylic acid moiety of a medium-chain fatty acid. -1 CO2R 44.010 43.98983 [O-]C([*])=O chebi_ontology MCFA anion MCFA anions a medium chain fatty acid medium-chain FA anion medium-chain FA anions medium-chain fatty acid anions CHEBI:59558 medium-chain fatty acid anion MCFA anion ChEBI MCFA anions ChEBI a medium chain fatty acid UniProt medium-chain FA anion ChEBI medium-chain FA anions ChEBI medium-chain fatty acid anions ChEBI An organic anion that is the conjugate base of diamino acid. chebi_ontology diamino acid anions CHEBI:59561 diamino acid anion diamino acid anions ChEBI Compounds containing one or more phosphoric acid units. chebi_ontology CHEBI:59698 phosphoric acids A reagent that forms a bond to its reaction partner (the electrophile) by donating both bonding electrons. chebi_ontology nucleophile nucleophiles nucleophilic reagents CHEBI:59740 nucleophilic reagent nucleophile ChEBI nucleophiles ChEBI nucleophilic reagents ChEBI A zwitterionic tautomer of S-adenosyl-L-methionine arising from shift of the proton from the carboxy group to the amino group. +1 C15H23N6O5S InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8+,10+,11+,14+,27?/m0/s1 MEFKEPWMEQBLKI-AIRLBKTGSA-O 399.44500 399.14452 C[S+](CC[C@H]([NH3+])C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 [(3S)-3-azaniumyl-3-carboxylatopropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium chebi_ontology S-adenosyl-L-methionine CHEBI:59789 S-adenosyl-L-methionine zwitterion [(3S)-3-azaniumyl-3-carboxylatopropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium IUPAC S-adenosyl-L-methionine SUBMITTER S-adenosyl-L-methionine UniProt Conjugate base of an L-alpha-amino acid arising from deprotonation of the C-1 carboxy group. -1 C2H3NO2R 73.051 73.01638 [C@H](C(=O)[O-])(N)* chebi_ontology L-alpha-amino carboxylate CHEBI:59814 L-alpha-amino acid anion L-alpha-amino carboxylate ChEBI Zwitterionic form of an L-alpha-amino acid having an anionic carboxy group and a protonated amino group. 0 C2H4NO2R 74.059 74.02420 [NH3+][C@@H]([*])C([O-])=O chebi_ontology L-alpha-amino acid zwitterions an L-alpha-amino acid CHEBI:59869 L-alpha-amino acid zwitterion L-alpha-amino acid zwitterions ChEBI an L-alpha-amino acid UniProt Zwitterionic form of a D-alpha-amino acid having an anionic carboxy group and a protonated amino group. 0 C2H4NO2R 74.059 74.02420 [NH3+][C@H]([*])C([O-])=O chebi_ontology D-alpha-amino acid zwitterions a D-alpha-amino acid CHEBI:59871 D-alpha-amino acid zwitterion D-alpha-amino acid zwitterions ChEBI a D-alpha-amino acid UniProt A carboxylic acid anion that is the conjugate base of an N-acyl-L-alpha-amino acid arising from deprotonation of the C-1 carboxy group. -1 C3H2NO3R2 100.05290 100.00347 [O-]C(=O)[C@H]([*])NC([*])=O chebi_ontology N-acyl-L-alpha-amino acid(1-) an N-acyl-L-amino acid CHEBI:59874 N-acyl-L-alpha-amino acid anion N-acyl-L-alpha-amino acid(1-) ChEBI an N-acyl-L-amino acid UniProt The conjugate base of an N-acyl-D-alpha-amino acid arising from deprotonation of the C-1 carboxy group. -1 C3H2NO3R2 100.05290 100.00347 [O-]C(=O)[C@@H]([*])NC([*])=O chebi_ontology N-acyl-D-alpha-amino acid(1-) an N-acyl-D-amino acid CHEBI:59876 N-acyl-D-alpha-amino acid anion N-acyl-D-alpha-amino acid(1-) ChEBI an N-acyl-D-amino acid UniProt A drug which interferes with the binding, fusion and entry of an HIV virion to a human cell. By blocking this step in HIV's replication cycle, such agents slow the progression from HIV infection to AIDS. PMID:22470838 Wikipedia:Entry_inhibitor chebi_ontology HIV entry inhibitor HIV entry inhibitors HIV fusion inhibitors CHEBI:59886 HIV fusion inhibitor PMID:22470838 Europe PMC HIV entry inhibitor ChEBI HIV entry inhibitors ChEBI HIV fusion inhibitors ChEBI A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. chebi_ontology Chemische Substanz CHEBI:59999 chemical substance Chemische Substanz ChEBI A mixture is a chemical substance composed of multiple molecules, at least two of which are of a different kind. chebi_ontology Mischung CHEBI:60004 mixture Mischung ChEBI A metal cation with a valence of two. chebi_ontology a divalent metal cation CHEBI:60240 divalent metal cation a divalent metal cation UniProt An atom or small molecule with a positive charge that does not contain carbon in covalent linkage, with a valency of one. chebi_ontology a monovalent cation CHEBI:60242 monovalent inorganic cation a monovalent cation UniProt A hydrolase inhibitor that interferes with the action of any hydrolase acting on peptide bonds (peptidase), EC 3.4.*.*). CHEBI:76763 chebi_ontology EC 3.4.* (hydrolase acting on peptide bond) inhibitor EC 3.4.* (hydrolase acting on peptide bonds) inhibitors EC 3.4.* (hydrolases acting on peptide bond) inhibitors EC 3.4.* (peptidase) inhibitor EC 3.4.* (peptidase) inhibitors EC 3.4.* inhibitor EC 3.4.* inhibitors inhibitor of hydrolases acting on peptide bond (EC 3.4.*) inhibitors of hydrolases acting on peptide bond (EC 3.4.*) peptidase inhibitors protease inhibitor protease inhibitors CHEBI:60258 EC 3.4.* (hydrolases acting on peptide bond) inhibitor EC 3.4.* (hydrolase acting on peptide bond) inhibitor ChEBI EC 3.4.* (hydrolase acting on peptide bonds) inhibitors ChEBI EC 3.4.* (hydrolases acting on peptide bond) inhibitors ChEBI EC 3.4.* (peptidase) inhibitor ChEBI EC 3.4.* (peptidase) inhibitors ChEBI EC 3.4.* inhibitor ChEBI EC 3.4.* inhibitors ChEBI inhibitor of hydrolases acting on peptide bond (EC 3.4.*) ChEBI inhibitors of hydrolases acting on peptide bond (EC 3.4.*) ChEBI peptidase inhibitors ChEBI protease inhibitor ChEBI protease inhibitors ChEBI Flavin protonated to pH 7.3 -1 C12H8N4O2R 240.21750 240.06473 Cc1cc2nc3c(nc(=O)[n-]c3=O)n([*])c2cc1C chebi_ontology an oxidized flavin CHEBI:60531 flavin(1-) an oxidized flavin UniProt Any substance that inhibits the action of N-methyl-D-aspartate (NMDA) receptors. They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs. CHEBI:60797 chebi_ontology N-methyl-D-aspartate receptor antagonist N-methyl-D-aspartate receptor antagonists NMDA receptor antagonists NMDAR antagonist NMDAR antagonists CHEBI:60643 NMDA receptor antagonist N-methyl-D-aspartate receptor antagonist ChEBI N-methyl-D-aspartate receptor antagonists ChEBI NMDA receptor antagonists ChEBI NMDAR antagonist ChEBI NMDAR antagonists ChEBI Any substance which inhibits the action of receptors for excitatory amino acids. chebi_ontology EAA receptor antagonist EAA receptor antagonists excitatory amino acid antagonists excitatory amino acid receptor antagonist excitatory amino acid receptor antagonists CHEBI:60798 excitatory amino acid antagonist EAA receptor antagonist ChEBI EAA receptor antagonists ChEBI excitatory amino acid antagonists ChEBI excitatory amino acid receptor antagonist ChEBI excitatory amino acid receptor antagonists ChEBI Any pharmacological or immunological agent that modifies the effect of other agents such as drugs or vaccines while having few if any direct effects when given by itself. chebi_ontology adjuvants CHEBI:60809 adjuvant adjuvants ChEBI Any alpha-amino acid anion in which the parent amino acid has D-configuration. -1 C2H3NO2R 73.051 73.01638 [C@@H](C(=O)[O-])(N)* chebi_ontology D-alpha-amino acid anions D-alpha-amino carboxylate CHEBI:60895 D-alpha-amino acid anion D-alpha-amino acid anions ChEBI D-alpha-amino carboxylate ChEBI A hormone antagonist that blocks angiotensin receptors. chebi_ontology angiotensin receptor antagonists CHEBI:61016 angiotensin receptor antagonist angiotensin receptor antagonists ChEBI An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the function of histone deacetylase (EC 3.5.1.98). Wikipedia:Histone_deacetylase_inhibitor chebi_ontology EC 3.5.1.98 (histone deacetylase) inhibitors EC 3.5.1.98 inhibitor EC 3.5.1.98 inhibitors HDAC inhibitor HDAC inhibitors HDACi HDACis HDI HDIs histone amidohydrolase inhibitor histone amidohydrolase inhibitors histone deacetylase (EC 3.5.1.98) inhibitor histone deacetylase (EC 3.5.1.98) inhibitors histone deacetylase inhibitor histone deacetylase inhibitors CHEBI:61115 EC 3.5.1.98 (histone deacetylase) inhibitor EC 3.5.1.98 (histone deacetylase) inhibitors ChEBI EC 3.5.1.98 inhibitor ChEBI EC 3.5.1.98 inhibitors ChEBI HDAC inhibitor ChEBI HDAC inhibitors ChEBI HDACi ChEBI HDACis ChEBI HDI ChEBI HDIs ChEBI histone amidohydrolase inhibitor ChEBI histone amidohydrolase inhibitors ChEBI histone deacetylase (EC 3.5.1.98) inhibitor ChEBI histone deacetylase (EC 3.5.1.98) inhibitors ChEBI histone deacetylase inhibitor ChEBI histone deacetylase inhibitors ChEBI Any compound that has a nucleobase as a part. chebi_ontology nucleobase-containing compound nucleobase-containing compounds nucleobase-containing molecular entities CHEBI:61120 nucleobase-containing molecular entity nucleobase-containing compound SUBMITTER nucleobase-containing compounds ChEBI nucleobase-containing molecular entities ChEBI Any hydroxy carboxylic acid which contains a hydroxy group located beta- to the carboxylic acid group. chebi_ontology 3-hydroxy carboxylic acids 3-hydroxycarboxylic acid 3-hydroxycarboxylic acids beta-hydroxy carboxylic acid beta-hydroxy carboxylic acids beta-hydroxycarboxylic acid beta-hydroxycarboxylic acids CHEBI:61355 3-hydroxy carboxylic acid 3-hydroxy carboxylic acids ChEBI 3-hydroxycarboxylic acid ChEBI 3-hydroxycarboxylic acids ChEBI beta-hydroxy carboxylic acid ChEBI beta-hydroxy carboxylic acids ChEBI beta-hydroxycarboxylic acid ChEBI beta-hydroxycarboxylic acids ChEBI A lipid-rich mixture containing glycerol, fatty acids, phosphoric acid and other components. lecithins http://langual.org Codex::322 Europe::322 PMID:12545497 PMID:17288433 http://www.langual.org/langual_thesaurus.asp?termid=B3130 chebi_ontology CHEBI:61995 LanguaL curation note: See "food additive" comments. LanguaL term definition: Food additive. lecithin PMID:12545497 Europe PMC PMID:17288433 Europe PMC Zwitterionic form of a polar amino acid having an anionic carboxy group and a protonated amino group. 0 C2H4NO2R 74.059 74.02420 C(C([O-])=O)(*)[NH3+] MetaCyc:Polar-amino-acids chebi_ontology a polar amino acid CHEBI:62031 polar amino acid zwitterion MetaCyc:Polar-amino-acids SUBMITTER a polar amino acid UniProt Any branched-chain fatty acid containing methyl branches only. PMID:17030019 PMID:19747846 PMID:19933331 chebi_ontology methyl-branched fatty acids CHEBI:62499 methyl-branched fatty acid PMID:17030019 Europe PMC PMID:19747846 Europe PMC PMID:19933331 SUBMITTER methyl-branched fatty acids ChEBI The dicarboxylic acid dianion formed from folic acid by loss of a proton from each of the two carboxy groups in the glutamic acid moiety. -2 C19H17N7O6 InChI=1S/C19H19N7O6/c20-19-25-15-14(17(30)26-19)23-11(8-22-15)7-21-10-3-1-9(2-4-10)16(29)24-12(18(31)32)5-6-13(27)28/h1-4,8,12,21H,5-7H2,(H,24,29)(H,27,28)(H,31,32)(H3,20,22,25,26,30)/p-2/t12-/m0/s1 OVBPIULPVIDEAO-LBPRGKRZSA-L 439.38160 439.12513 Nc1nc2ncc(CNc3ccc(cc3)C(=O)N[C@@H](CCC([O-])=O)C([O-])=O)nc2c(=O)[nH]1 MetaCyc:CPD-12826 N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamate(2-) chebi_ontology folate CHEBI:62501 folate(2-) MetaCyc:CPD-12826 SUBMITTER N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}benzoyl)-L-glutamate(2-) IUPAC folate UniProt Any additive that enhances the efficiency of fuel. chebi_ontology fuel additives fuel enhancer CHEBI:62803 fuel additive fuel additives ChEBI fuel enhancer ChEBI Any compound that is able to prevent damage to the liver. chebi_ontology antihepatotoxic agent hepatoprotective agents CHEBI:62868 hepatoprotective agent antihepatotoxic agent ChEBI hepatoprotective agents ChEBI The chemical role played by a substance that stabilizes an emulsion by increasing its kinetic stability. chebi_ontology emulgent emulgents emulsifiers CHEBI:63046 emulsifier emulgent ChEBI emulgents ChEBI emulsifiers ChEBI A carbohydrate derivative arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to an oxygen, carbon, nitrogen or sulfur atom of a separate entity. chebi_ontology glycosyl compounds CHEBI:63161 glycosyl compound glycosyl compounds ChEBI Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds. chebi_ontology carbohydrate derivatives derivatised carbohydrate derivatised carbohydrates derivatized carbohydrate derivatized carbohydrates CHEBI:63299 carbohydrate derivative carbohydrate derivatives ChEBI derivatised carbohydrate ChEBI derivatised carbohydrates ChEBI derivatized carbohydrate ChEBI derivatized carbohydrates ChEBI A sulfur-containing amino acid whose alpha-carboxylic acid group is ionized (not protonated). chebi_ontology sulfur-containing amino-acid anions CHEBI:63470 sulfur-containing amino-acid anion sulfur-containing amino-acid anions ChEBI A branched-chain amino acid whose alpha-carboxylic acid group is ionized (not protonated). chebi_ontology branched-chain amino-acid anions CHEBI:63471 branched-chain amino-acid anion branched-chain amino-acid anions ChEBI An aromatic amino acid whose alpha-carboxylic acid group is ionized (non-protonated). chebi_ontology aromatic amino-acid anions CHEBI:63473 aromatic amino-acid anion aromatic amino-acid anions ChEBI Any compound that can be used for the treatment of neurodegenerative disorders. chebi_ontology neuroprotectant neuroprotectants neuroprotective agents CHEBI:63726 neuroprotective agent neuroprotectant ChEBI neuroprotectants ChEBI neuroprotective agents ChEBI Any lactone in which the cyclic carboxylic ester group forms a part of a cyclic macromolecule. CHEBI:50333 chebi_ontology macrocyclic lactones CHEBI:63944 macrocyclic lactone macrocyclic lactones ChEBI An antagonist at the metabotropic glutamate receptor. chebi_ontology mGluR antagonist mGluR antagonists metabotropic glutamate receptor antagonists CHEBI:63963 metabotropic glutamate receptor antagonist mGluR antagonist ChEBI mGluR antagonists ChEBI metabotropic glutamate receptor antagonists ChEBI Any substance which is added to food to preserve or enhance its flavour and/or appearance. Wikipedia:Food_additive chebi_ontology food additives CHEBI:64047 food additive food additives ChEBI A food additive that is used to change or otherwise control the acidity or alkalinity of foods. They may be acids, bases, neutralising agents or buffering agents. Wikipedia:Acidity_regulator chebi_ontology acidity regulator acidity regulators food acidity regulators pH control agent pH control agents CHEBI:64049 food acidity regulator acidity regulator ChEBI acidity regulators ChEBI food acidity regulators ChEBI pH control agent ChEBI pH control agents ChEBI An agonist that selectively binds to and activates AMPA receptors. Wikipedia:AMPA_receptor chebi_ontology AMPA receptor agonists AMPAR agonist alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor agonist quisqualate receptor agonist CHEBI:64102 AMPA receptor agonist AMPA receptor agonists ChEBI AMPAR agonist ChEBI alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor agonist ChEBI quisqualate receptor agonist ChEBI An amino acid zwitterion arising from transfer of a proton from the carboxy to the amino group of methionine; major species at pH 7.3. 0 C5H11NO2S InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8) FFEARJCKVFRZRR-UHFFFAOYSA-N 149.21100 149.05105 CSCCC([NH3+])C([O-])=O 2-azaniumyl-4-(methylsulfanyl)butanoate chebi_ontology 2-ammonio-4-(methylsulfanyl)butanoate methionine CHEBI:64558 methionine zwitterion 2-azaniumyl-4-(methylsulfanyl)butanoate IUPAC 2-ammonio-4-(methylsulfanyl)butanoate IUPAC methionine UniProt An EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor that interferes with the action of glycine hydroxymethyltransferase (EC 2.1.2.1). Wikipedia:Glycine_hydroxymethyltransferase chebi_ontology 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitor 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitors EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitors EC 2.1.2.1 inhibitor EC 2.1.2.1 inhibitors L-serine hydroxymethyltransferase inhibitor L-serine hydroxymethyltransferase inhibitors L-threonine aldolase inhibitor L-threonine aldolase inhibitors allothreonine aldolase inhibitor allothreonine aldolase inhibitors glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitor glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitors glycine hydroxymethyltransferase inhibitor glycine hydroxymethyltransferase inhibitors serine aldolase inhibitor serine aldolase inhibitors serine hydroxymethylase inhibitor serine hydroxymethylase inhibitors serine hydroxymethyltransferase inhibitor serine hydroxymethyltransferase inhibitors serine transhydroxymethylase inhibitor serine transhydroxymethylase inhibitors threonine aldolase inhibitor threonine aldolase inhibitors CHEBI:64570 EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitor 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitor ChEBI 5,10-methylenetetrahydrofolate:glycine hydroxymethyltransferase inhibitors ChEBI EC 2.1.2.1 (glycine hydroxymethyltransferase) inhibitors ChEBI EC 2.1.2.1 inhibitor ChEBI EC 2.1.2.1 inhibitors ChEBI L-serine hydroxymethyltransferase inhibitor ChEBI L-serine hydroxymethyltransferase inhibitors ChEBI L-threonine aldolase inhibitor ChEBI L-threonine aldolase inhibitors ChEBI allothreonine aldolase inhibitor ChEBI allothreonine aldolase inhibitors ChEBI glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitor ChEBI glycine hydroxymethyltransferase (EC 2.1.2.1) inhibitors ChEBI glycine hydroxymethyltransferase inhibitor ChEBI glycine hydroxymethyltransferase inhibitors ChEBI serine aldolase inhibitor ChEBI serine aldolase inhibitors ChEBI serine hydroxymethylase inhibitor ChEBI serine hydroxymethylase inhibitors ChEBI serine hydroxymethyltransferase inhibitor ChEBI serine hydroxymethyltransferase inhibitors ChEBI serine transhydroxymethylase inhibitor ChEBI serine transhydroxymethylase inhibitors ChEBI threonine aldolase inhibitor ChEBI threonine aldolase inhibitors ChEBI An excitatory amino acid agonist which binds to NMDA receptors and triggers a response. chebi_ontology N-methyl-D-aspartate receptor agonist N-methyl-D-aspartate receptor agonists NMDA receptor agonists NMDAR agonist NMDAR agonists CHEBI:64571 NMDA receptor agonist N-methyl-D-aspartate receptor agonist ChEBI N-methyl-D-aspartate receptor agonists ChEBI NMDA receptor agonists ChEBI NMDAR agonist ChEBI NMDAR agonists ChEBI A food additive which is added to flour or dough to improve baking quality and/or colour. Wikipedia:Flour_treatment_agent flour treatment agent chebi_ontology dough improver dough improvers improving agent improving agents CHEBI:64577 flour treatment agent flour treatment agent ChEBI dough improver ChEBI dough improvers ChEBI improving agent ChEBI improving agents ChEBI An inorganic cation with a valency of two. chebi_ontology CHEBI:64641 divalent inorganic cation An organic molecular entity containing a single carbon atom (C1). chebi_ontology one-carbon compounds CHEBI:64708 one-carbon compound one-carbon compounds ChEBI Any organic molecular entity that is acidic and contains carbon in covalent linkage. chebi_ontology organic acids CHEBI:64709 organic acid organic acids ChEBI cosmetic role The role played by a substance in enhancing the appearance or odour of the human body; a name given to the substance itself or to a component of it. cosmetic Any substance that causes disturbance to organisms by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by the organism. Wikipedia:Poison chebi_ontology poisonous agent poisonous agents poisonous substance poisonous substances poisons toxic agent toxic agents toxic substance toxic substances CHEBI:64909 poison poisonous agent ChEBI poisonous agents ChEBI poisonous substance ChEBI poisonous substances ChEBI poisons ChEBI toxic agent ChEBI toxic agents ChEBI toxic substance ChEBI toxic substances ChEBI A drug used to treat or prevent infections caused by Mycobacteria, a genus of actinobacteria. Aerobic and nonmotile, members of the genus include the pathogens responsible for causing tuberculosis and leprosy. chebi_ontology antimycobacterial agent antimycobacterial agents antimycobacterial drugs antimycobacterials antimycobacterium CHEBI:64912 antimycobacterial drug antimycobacterial agent ChEBI antimycobacterial agents ChEBI antimycobacterial drugs ChEBI antimycobacterials ChEBI antimycobacterium ChEBI An antiviral agent that destroys or inhibits the replication of the human immunodeficiency virus. chebi_ontology anti-AIDS agent anti-AIDS agents anti-HIV agents CHEBI:64946 anti-HIV agent anti-AIDS agent ChEBI anti-AIDS agents ChEBI anti-HIV agents ChEBI An antiviral agent that destroys or inhibits the replication of the herpes simplex virus (also known as the human herpes virus). Wikipedia:Herpes_simplex_virus chebi_ontology anti-HHV agent anti-HHV agents anti-HSV agents anti-herpes simplex virus agent anti-herpes simplex virus agents anti-human herpes virus agent anti-human herpes virus agents CHEBI:64952 anti-HSV agent anti-HHV agent ChEBI anti-HHV agents ChEBI anti-HSV agents ChEBI anti-herpes simplex virus agent ChEBI anti-herpes simplex virus agents ChEBI anti-human herpes virus agent ChEBI anti-human herpes virus agents ChEBI An anti-HSV agent agent that destroys or inhibits the replication of herpes simplex virus-1. chebi_ontology anti-HHV-1 agent anti-HHV-1 agents anti-HHV-I agent anti-HHV-I agents anti-HSV-1 agents anti-HSV-I agent anti-HSV-I agents anti-human herpes virus-1 agent anti-human herpes virus-1 agents anti-human herpes virus-I agent anti-human herpes virus-I agents CHEBI:64953 anti-HSV-1 agent anti-HHV-1 agent ChEBI anti-HHV-1 agents ChEBI anti-HHV-I agent ChEBI anti-HHV-I agents ChEBI anti-HSV-1 agents ChEBI anti-HSV-I agent ChEBI anti-HSV-I agents ChEBI anti-human herpes virus-1 agent ChEBI anti-human herpes virus-1 agents ChEBI anti-human herpes virus-I agent ChEBI anti-human herpes virus-I agents ChEBI An anti-HSV agent agent that destroys or inhibits the replication of herpes simplex virus-2. chebi_ontology anti-HHV-2 agent anti-HHV-2 agents anti-HHV-II agent anti-HHV-II agents anti-HSV-2 agents anti-HSV-II agent anti-HSV-II agents anti-human herpes virus-2 agent anti-human herpes virus-2 agents anti-human herpes virus-II agent anti-human herpes virus-II agents CHEBI:64954 anti-HSV-2 agent anti-HHV-2 agent ChEBI anti-HHV-2 agents ChEBI anti-HHV-II agent ChEBI anti-HHV-II agents ChEBI anti-HSV-2 agents ChEBI anti-HSV-II agent ChEBI anti-HSV-II agents ChEBI anti-human herpes virus-2 agent ChEBI anti-human herpes virus-2 agents ChEBI anti-human herpes virus-II agent ChEBI anti-human herpes virus-II agents ChEBI Any compound that has anti-asthmatic effects. chebi_ontology anti-asthmatic agents antiasthmatic agent antiasthmatic agents CHEBI:65023 anti-asthmatic agent anti-asthmatic agents ChEBI antiasthmatic agent ChEBI antiasthmatic agents ChEBI Antipsychotic drugs which can have different modes of action but which tend to be more likely than second generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements; such body movements can become permanent even after treatment has ceased. Wikipedia:Typical_antipsychotic chebi_ontology first generation antipsychotic agent first generation antipsychotic agents first generation antipsychotic drug first generation antipsychotic drugs first generation antipsychotics typical antipsychotic typical antipsychotic agent typical antipsychotic agents typical antipsychotic drug typical antipsychotic drugs typical antipsychotics CHEBI:65190 first generation antipsychotic first generation antipsychotic agent ChEBI first generation antipsychotic agents ChEBI first generation antipsychotic drug ChEBI first generation antipsychotic drugs ChEBI first generation antipsychotics ChEBI typical antipsychotic ChEBI typical antipsychotic agent ChEBI typical antipsychotic agents ChEBI typical antipsychotic drug ChEBI typical antipsychotic drugs ChEBI typical antipsychotics ChEBI Antipsychotic drugs which can have different modes of action but which tend to be less likely than first generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements. chebi_ontology atypical antipsychotic atypical antipsychotic agent atypical antipsychotic agents atypical antipsychotic drug atypical antipsychotic drugs atypical antipsychotics second generation antipsychotic agent second generation antipsychotic agents second generation antipsychotic drug second generation antipsychotic drugs second generation antipsychotics CHEBI:65191 second generation antipsychotic atypical antipsychotic ChEBI atypical antipsychotic agent ChEBI atypical antipsychotic agents ChEBI atypical antipsychotic drug ChEBI atypical antipsychotic drugs ChEBI atypical antipsychotics ChEBI second generation antipsychotic agent ChEBI second generation antipsychotic agents ChEBI second generation antipsychotic drug ChEBI second generation antipsychotic drugs ChEBI second generation antipsychotics ChEBI Substances which are added to food in order to prevent decomposition caused by microbial growth or by undesirable chemical changes. chebi_ontology food preservatives CHEBI:65255 food preservative food preservatives ChEBI A food preservative which prevents decomposition of food by preventing the growth of fungi or bacteria. In European countries, E-numbers for permitted food preservatives are from E200 to E299, divided into sorbates (E200-209), benzoates (E210-219), sulfites (E220-229), phenols and formates (E230-239), nitrates (E240-259), acetates (E260-269), lactates (E270-279), propionates (E280-289) and others (E290-299). chebi_ontology antimicrobial food preservatives antimicrobial preservative antimicrobial preservatives CHEBI:65256 antimicrobial food preservative antimicrobial food preservatives ChEBI antimicrobial preservative ChEBI antimicrobial preservatives ChEBI Any substance which is used to neutralise stomach acidity. Wikipedia:Antacid chebi_ontology antacids CHEBI:65265 antacid antacids ChEBI An ammonium ion derivative resulting from the protonation of the nitrogen atom of a primary amino compound. Major species at pH 7.3. +1 H3NR 17.031 17.02655 [NH3+][*] chebi_ontology a primary amine substituted ammonium CHEBI:65296 primary ammonium ion a primary amine UniProt substituted ammonium ChEBI An alpha-amino acid anion that is the conjugate base of citrulline, obtained by deprotonation of the carboxy group. -1 C6H12N3O3 InChI=1S/C6H13N3O3/c7-4(5(10)11)2-1-3-9-6(8)12/h4H,1-3,7H2,(H,10,11)(H3,8,9,12)/p-1 RHGKLRLOHDJJDR-UHFFFAOYSA-M 174.17780 174.08841 NC(CCCNC(N)=O)C([O-])=O 2-amino-5-(carbamoylamino)pentanoate chebi_ontology CHEBI:66922 citrullinate 2-amino-5-(carbamoylamino)pentanoate IUPAC A monocarboxylic acid anion that is the conjugate base of creatine, obtained by deprotonation of the carboxy group. -1 C4H8N3O2 InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H3,5,6)(H,8,9)/p-1 CVSVTCORWBXHQV-UHFFFAOYSA-M 130.12520 130.06220 CN(CC([O-])=O)C(N)=N {[imino(amino)methyl](methyl)amino}acetate chebi_ontology (N-methylcarbamimidamido)acetate N-[amino(imino)methyl]-N-methylglycinate CHEBI:66924 creatinate {[imino(amino)methyl](methyl)amino}acetate IUPAC (N-methylcarbamimidamido)acetate ChEBI N-[amino(imino)methyl]-N-methylglycinate ChEBI Any compound which can be used to treat or alleviate the symptoms of dyskinesia. chebi_ontology antidyskinesia agents antidyskinesia drug antidyskinesia drugs antidyskinetic agent antidyskinetic agents antidyskinetic drug antidyskinetic drugs CHEBI:66956 antidyskinesia agent antidyskinesia agents ChEBI antidyskinesia drug ChEBI antidyskinesia drugs ChEBI antidyskinetic agent ChEBI antidyskinetic agents ChEBI antidyskinetic drug ChEBI antidyskinetic drugs ChEBI Any compound used for the treatment of eye conditions or eye diseases. chebi_ontology ophthalmic ophthalmic agent ophthalmic agents ophthalmics ophthalmological ophthalmologicals ophthalmology agent ophthalmology agents ophthalmology drugs CHEBI:66981 ophthalmology drug ophthalmic ChEBI ophthalmic agent ChEBI ophthalmic agents ChEBI ophthalmics ChEBI ophthalmological ChEBI ophthalmologicals ChEBI ophthalmology agent ChEBI ophthalmology agents ChEBI ophthalmology drugs ChEBI An N-acyl-L-alpha-amino acid anion obtained by deprotonation of any folic acid. chebi_ontology folate folate anion folate anions CHEBI:67011 folates folate ChEBI folate anion ChEBI folate anions ChEBI Any branched-chain fatty acid anion containing methyl branches only. chebi_ontology methyl-branched fatty acid anions CHEBI:67013 methyl-branched fatty acid anion methyl-branched fatty acid anions ChEBI A sulfonium betaine that is a conjugate base of S-adenosyl-L-methionine obtained by the deprotonation of the carboxy group. 0 C15H22N6O5S InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27?/m0/s1 MEFKEPWMEQBLKI-AIRLBKTGSA-N 398.43700 398.13724 C[S+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 CAS:29908-03-0 Drug_Central:2414 KEGG:C00019 KNApSAcK:C00007347 PDBeChem:SAM PMID:25628954 [(3S)-3-amino-3-carboxylatopropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonioacetate chebi_ontology AdoMet S-Adenosylmethionine SAM CHEBI:67040 S-adenosyl-L-methioninate CAS:29908-03-0 KEGG COMPOUND Drug_Central:2414 DrugCentral PMID:25628954 Europe PMC [(3S)-3-amino-3-carboxylatopropyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonioacetate IUPAC AdoMet KEGG_COMPOUND S-Adenosylmethionine KEGG_COMPOUND SAM KEGG_COMPOUND Any compound that has anti-inflammatory effects. chebi_ontology anti-inflammatory agents antiinflammatory agent antiinflammatory agents CHEBI:67079 anti-inflammatory agent anti-inflammatory agents ChEBI antiinflammatory agent ChEBI antiinflammatory agents ChEBI A provitamin that can be converted into vitamin A by enzymes from animal tissues. chebi_ontology provitamin As CHEBI:67200 provitamin A provitamin As ChEBI Any 1,4-benzoquinone carrying a single hydroxy substituent. 0 C6HO3R3 121.07030 120.99257 OC1=C([*])C(=O)C([*])=C([*])C1=O chebi_ontology 2-hydroxy-1,4-benzoquinones hydroxy-1,4-benzoquinone hydroxy-1,4-benzoquinones hydroxybenzoquinone hydroxybenzoquinones monohydroxybenzoquinones CHEBI:67273 monohydroxy-1,4-benzoquinones 2-hydroxy-1,4-benzoquinones ChEBI hydroxy-1,4-benzoquinone ChEBI hydroxy-1,4-benzoquinones ChEBI hydroxybenzoquinone ChEBI hydroxybenzoquinones ChEBI monohydroxybenzoquinones ChEBI Any monocyclic heteroarene consisting of a five-membered ring containing nitrogen. Azoles can also contain one or more other non-carbon atoms, such as nitrogen, sulfur or oxygen. Wikipedia:Azole chebi_ontology azoles CHEBI:68452 azole azoles ChEBI An antagonist at the AMPA receptor. Wikipedia:AMPA_receptor chebi_ontology AMPA receptor antagonists alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antagonist alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antagonists CHEBI:71014 AMPA receptor antagonist AMPA receptor antagonists ChEBI alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antagonist ChEBI alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antagonists ChEBI An enzyme inhibitor that inhibits the action of a transferase (EC 2.*) Wikipedia:Transferase chebi_ontology EC 2 inhibitor EC 2 inhibitors EC 2.* (transferase) inhibitors EC 2.* inhibitor EC 2.* inhibitors transferase inhibitor transferase inhibitors CHEBI:71300 EC 2.* (transferase) inhibitor EC 2 inhibitor ChEBI EC 2 inhibitors ChEBI EC 2.* (transferase) inhibitors ChEBI EC 2.* inhibitor ChEBI EC 2.* inhibitors ChEBI transferase inhibitor ChEBI transferase inhibitors ChEBI An organic anion that is the conjugate base of tetracycline obtained by deprotonation of the two enolic hydroxy groups and protonation of the tertiary amino group. -1 C22H23N2O8 InChI=1S/C22H24N2O8/c1-21(31)8-5-4-6-11(25)12(8)16(26)13-9(21)7-10-15(24(2)3)17(27)14(20(23)30)19(29)22(10,32)18(13)28/h4-6,9-10,15,25,27-28,31-32H,7H2,1-3H3,(H2,23,30)/p-1/t9-,10-,15-,21+,22-/m0/s1 OFVLGDICTFRJMM-WESIUVDSSA-M 443.42660 443.14599 [H][C@@]12C[C@@]3([H])C(C(=O)c4c(O)cccc4[C@@]3(C)O)=C([O-])[C@]1(O)C(=O)C(C(N)=O)=C([O-])[C@H]2[NH+](C)C (1S,4aS,11S,11aS,12aS)-3-carbamoyl-1-(dimethylazaniumyl)-4a,7,11-trihydroxy-11-methyl-4,6-dioxo-1,4,4a,6,11,11a,12,12a-octahydrotetracene-2,5-diolate chebi_ontology tetracycline anion CHEBI:71392 tetracycline(1-) (1S,4aS,11S,11aS,12aS)-3-carbamoyl-1-(dimethylazaniumyl)-4a,7,11-trihydroxy-11-methyl-4,6-dioxo-1,4,4a,6,11,11a,12,12a-octahydrotetracene-2,5-diolate IUPAC tetracycline anion ChEBI Benzoquinones with at least one hydroxy substituent. chebi_ontology hydroxybenzoquinones CHEBI:71648 hydroxybenzoquinone hydroxybenzoquinones ChEBI An amino-acid anion in which the amino group is situated gamma- to the carboxylate group. chebi_ontology gamma-amino acid anions CHEBI:71666 gamma-amino acid anion gamma-amino acid anions ChEBI Any compound that promotes the growth of new blood vessels from pre-existing vessels. chebi_ontology pro-angiogenic agents proangiogenic agent proangiogenic agents CHEBI:72571 pro-angiogenic agent pro-angiogenic agents ChEBI proangiogenic agent ChEBI proangiogenic agents ChEBI Any molecule that consists of at least one carbon atom as part of the electrically neutral entity. chebi_ontology organic compound organic compounds organic molecules CHEBI:72695 organic molecule organic compound ChEBI organic compounds ChEBI organic molecules ChEBI A drug used in treating and healing of wounds. Wikipedia:Wound_healing chebi_ontology vulneraries wound-healing agent wound-healing agents wound-healing drug wound-healing drugs CHEBI:73336 vulnerary vulneraries ChEBI wound-healing agent ChEBI wound-healing agents ChEBI wound-healing drug ChEBI wound-healing drugs ChEBI A role borne by a molecule that acts to counteract or neutralize the deleterious effects of paracetamol (acetaminophen). PMID:16354242 PMID:16573399 PMID:16575097 PMID:22348679 PMID:22352734 PMID:22353666 PMID:22835053 PMID:22998987 PMID:7112203 chebi_ontology Tylenol poisoning antidote Tylenol poisoning antidotes acetaminophen poisoning antidote acetaminophen poisoning antidotes antidote to Tylenol poisoning antidote to acetaminophen poisoning antidotes to Tylenol poisoning antidotes to acetaminophen poisoning antidotes to paracetamol poisoning paracetamol poisoning antidote paracetamol poisoning antidotes CHEBI:74529 antidote to paracetamol poisoning PMID:16354242 Europe PMC PMID:16573399 Europe PMC PMID:16575097 Europe PMC PMID:22348679 Europe PMC PMID:22352734 Europe PMC PMID:22353666 Europe PMC PMID:22835053 Europe PMC PMID:22998987 Europe PMC PMID:7112203 Europe PMC Tylenol poisoning antidote ChEBI Tylenol poisoning antidotes ChEBI acetaminophen poisoning antidote ChEBI acetaminophen poisoning antidotes ChEBI antidote to Tylenol poisoning ChEBI antidote to acetaminophen poisoning ChEBI antidotes to Tylenol poisoning ChEBI antidotes to acetaminophen poisoning ChEBI antidotes to paracetamol poisoning ChEBI paracetamol poisoning antidote ChEBI paracetamol poisoning antidotes ChEBI Any organic aromatic compound having one or more hydroxy groups attached to a heteroarene ring. chebi_ontology hetaryl hydroxy compound hetaryl hydroxy compounds heteroaromatic hydroxy compound heteroaromatic hydroxy compounds heteroaryl hydroxy compounds CHEBI:74818 heteroaryl hydroxy compound hetaryl hydroxy compound ChEBI hetaryl hydroxy compounds ChEBI heteroaromatic hydroxy compound ChEBI heteroaromatic hydroxy compounds ChEBI heteroaryl hydroxy compounds ChEBI A ligase inhibitor that interferes with the action of a C-N bond-forming ligase (EC 6.3.*.*). chebi_ontology C--N bond-forming ligase inhibitor C--N bond-forming ligase inhibitors C-N bond-forming ligase (EC 6.3.*) inhibitor C-N bond-forming ligase (EC 6.3.*) inhibitors C-N bond-forming ligase inhibitor C-N bond-forming ligase inhibitors EC 6.3.* (C-N bond-forming ligase) inhibitorS EC 6.3.* inhibitor EC 6.3.* inhibitors EC 6.3.*.* inhibitor EC 6.3.*.* inhibitors CHEBI:75600 EC 6.3.* (C-N bond-forming ligase) inhibitor C--N bond-forming ligase inhibitor ChEBI C--N bond-forming ligase inhibitors ChEBI C-N bond-forming ligase (EC 6.3.*) inhibitor ChEBI C-N bond-forming ligase (EC 6.3.*) inhibitors ChEBI C-N bond-forming ligase inhibitor ChEBI C-N bond-forming ligase inhibitors ChEBI EC 6.3.* (C-N bond-forming ligase) inhibitorS ChEBI EC 6.3.* inhibitor ChEBI EC 6.3.* inhibitors ChEBI EC 6.3.*.* inhibitor ChEBI EC 6.3.*.* inhibitors ChEBI Any enzyme inhibitor that interferes with the action of a ligase (EC 6.*.*.*). Ligases are enzymes that catalyse the joining of two molecules with concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. Wikipedia:Ligase chebi_ontology EC 6.* (ligase) inhibitors EC 6.* inhibitor EC 6.* inhibitors EC 6.*.*.* inhibitor EC 6.*.*.* inhibitors ligase inhibitor ligase inhibitors CHEBI:75603 EC 6.* (ligase) inhibitor EC 6.* (ligase) inhibitors ChEBI EC 6.* inhibitor ChEBI EC 6.* inhibitors ChEBI EC 6.*.*.* inhibitor ChEBI EC 6.*.*.* inhibitors ChEBI ligase inhibitor ChEBI ligase inhibitors ChEBI Any metabolite produced during a metabolic reaction in eukaryotes, the taxon that include members of the fungi, plantae and animalia kingdoms. chebi_ontology eukaryotic metabolites CHEBI:75763 eukaryotic metabolite eukaryotic metabolites ChEBI Any eukaryotic metabolite produced during a metabolic reaction in animals that include diverse creatures from sponges, insects to mammals. CHEBI:77721 CHEBI:77743 chebi_ontology animal metabolites CHEBI:75767 animal metabolite animal metabolites ChEBI Any animal metabolite produced during a metabolic reaction in mammals. CHEBI:77464 CHEBI:77744 chebi_ontology mammalian metabolites CHEBI:75768 mammalian metabolite mammalian metabolites ChEBI A role played by any of the group of eight water-soluble vitamins originally thought to be a single compound (vitamin B). The group comprises of vitamin B1, B2, B3, B5, B6, B7, B9, and B12 (Around 20 other compounds were once thought to be B vitamins but are no longer classified as such). B vitamins play important roles in cell metabolism. PMID:22743781 PMID:23093174 PMID:23238962 PMID:23449527 PMID:23462586 PMID:23690582 Wikipedia:B_vitamin chebi_ontology B vitamins B-group vitamin B-group vitamins vitamin B CHEBI:75769 B vitamin PMID:22743781 Europe PMC PMID:23093174 Europe PMC PMID:23238962 Europe PMC PMID:23449527 Europe PMC PMID:23462586 Europe PMC PMID:23690582 Europe PMC B vitamins ChEBI B-group vitamin ChEBI B-group vitamins ChEBI vitamin B ChEBI Any mammalian metabolite produced during a metabolic reaction in a mouse (Mus musculus). chebi_ontology Mus musculus metabolite Mus musculus metabolites mouse metabolites CHEBI:75771 mouse metabolite Mus musculus metabolite ChEBI Mus musculus metabolites ChEBI mouse metabolites ChEBI Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae). CHEBI:76949 CHEBI:76951 chebi_ontology S. cerevisiae metabolite S. cerevisiae metabolites S. cerevisiae secondary metabolite S. cerevisiae secondary metabolites Saccharomyces cerevisiae metabolites Saccharomyces cerevisiae secondary metabolites baker's yeast metabolite baker's yeast metabolites baker's yeast secondary metabolite baker's yeast secondary metabolites CHEBI:75772 Saccharomyces cerevisiae metabolite S. cerevisiae metabolite ChEBI S. cerevisiae metabolites ChEBI S. cerevisiae secondary metabolite ChEBI S. cerevisiae secondary metabolites ChEBI Saccharomyces cerevisiae metabolites ChEBI Saccharomyces cerevisiae secondary metabolites ChEBI baker's yeast metabolite ChEBI baker's yeast metabolites ChEBI baker's yeast secondary metabolite ChEBI baker's yeast secondary metabolites ChEBI Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. chebi_ontology prokaryotic metabolites CHEBI:75787 prokaryotic metabolite prokaryotic metabolites ChEBI An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any aromatic amino-acid. 0 C2H4NO2R 74.059 74.02420 [NH3+]C([*])C([O-])=O MetaCyc:Aromatic-Amino-Acids chebi_ontology an aromatic amino-acid aromatic amino-acid zwitterions CHEBI:76042 aromatic amino-acid zwitterion MetaCyc:Aromatic-Amino-Acids SUBMITTER an aromatic amino-acid UniProt aromatic amino-acid zwitterions ChEBI Any metabolite produced by metabolism of a xenobiotic compound. chebi_ontology xenobiotic metabolites CHEBI:76206 xenobiotic metabolite xenobiotic metabolites ChEBI A compressed gas or liquid with a boiling point lower than room temperature which to used to propel and dispense liquids such as deodorants, insecticides, paints, etc. from aerosol cans. PMID:22519407 PMID:24001847 chebi_ontology propellants CHEBI:76414 propellant PMID:22519407 Europe PMC PMID:24001847 Europe PMC propellants ChEBI Any metabolite produced during a metabolic reaction in marine macro- and microorganisms. CHEBI:77078 chebi_ontology marine metabolites CHEBI:76507 marine metabolite marine metabolites ChEBI Any unsaturated fatty acid anion containing more than one C-C unsaturated bond. Major species at pH 7.3. chebi_ontology PUFA polyunsaturated fatty acid anions CHEBI:76567 polyunsaturated fatty acid anion PUFA SUBMITTER polyunsaturated fatty acid anions ChEBI A fatty acid anion obtained by deprotonation of the carboxy group of any omega-methyl fatty acid; major species at pH 7.3. -1 C2H3O2R 59.044 59.01330 C[*]C([O-])=O chebi_ontology an omega-methyl fatty acid CHEBI:76619 omega-methyl fatty acid anion an omega-methyl fatty acid UniProt A transferase inhibitor inhibiting the action of transferase of a one-carbon-containing group (EC 2.1.*.*). chebi_ontology C1-transferase (EC 2.1.*) inhibitor C1-transferase (EC 2.1.*) inhibitors C1-transferase inhibitor C1-transferase inhibitors EC 2.1.* (C1-transferase) inhibitors EC 2.1.* inhibitor EC 2.1.* inhibitors one-carbon-containing group transferase inhibitor one-carbon-containing group transferase inhibitors CHEBI:76655 EC 2.1.* (C1-transferase) inhibitor C1-transferase (EC 2.1.*) inhibitor ChEBI C1-transferase (EC 2.1.*) inhibitors ChEBI C1-transferase inhibitor ChEBI C1-transferase inhibitors ChEBI EC 2.1.* (C1-transferase) inhibitors ChEBI EC 2.1.* inhibitor ChEBI EC 2.1.* inhibitors ChEBI one-carbon-containing group transferase inhibitor ChEBI one-carbon-containing group transferase inhibitors ChEBI An enzyme inhibitor which interferes with the action of a lyase (EC 4.*.*.*). Lyases are enzymes cleaving C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation. Wikipedia:Lyase chebi_ontology EC 4.* (lyase) inhibitors EC 4.* inhibitor EC 4.* inhibitors EC 4.*.*.* inhibitor EC 4.*.*.* inhibitors lyase (EC 4.*) inhibitor lyase (EC 4.*) inhibitorS lyase inhibitor lyase inhibitors CHEBI:76710 EC 4.* (lyase) inhibitor EC 4.* (lyase) inhibitors ChEBI EC 4.* inhibitor ChEBI EC 4.* inhibitors ChEBI EC 4.*.*.* inhibitor ChEBI EC 4.*.*.* inhibitors ChEBI lyase (EC 4.*) inhibitor ChEBI lyase (EC 4.*) inhibitorS ChEBI lyase inhibitor ChEBI lyase inhibitors ChEBI A lyase inhibitor which inhibits the action of a C-N lyase (EC 4.3.*.*). chebi_ontology C-N lyase (EC 4.3.*) inhibitor C-N lyase (EC 4.3.*) inhibitors C-N lyase inhibitor C-N lyase inhibitors EC 4.3.* (C-N lyase) inhibitors EC 4.3.* inhibitor EC 4.3.* inhibitors CHEBI:76713 EC 4.3.* (C-N lyase) inhibitor C-N lyase (EC 4.3.*) inhibitor ChEBI C-N lyase (EC 4.3.*) inhibitors ChEBI C-N lyase inhibitor ChEBI C-N lyase inhibitors ChEBI EC 4.3.* (C-N lyase) inhibitors ChEBI EC 4.3.* inhibitor ChEBI EC 4.3.* inhibitors ChEBI An enzyme inhibitor which interferes with the action of an oxidoreductase (EC 1.*.*.*). Wikipedia:Oxidoreductase chebi_ontology EC 1.* (oxidoreductase) inhibitors EC 1.* inhibitor EC 1.* inhibitors oxidoreductase (EC 1.*) inhibitor oxidoreductase (EC 1.*) inhibitors oxidoreductase inhibitor oxidoreductase inhibitors CHEBI:76725 EC 1.* (oxidoreductase) inhibitor EC 1.* (oxidoreductase) inhibitors ChEBI EC 1.* inhibitor ChEBI EC 1.* inhibitors ChEBI oxidoreductase (EC 1.*) inhibitor ChEBI oxidoreductase (EC 1.*) inhibitors ChEBI oxidoreductase inhibitor ChEBI oxidoreductase inhibitors ChEBI An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on the CH-OH group of donors (EC 1.1.*.*). chebi_ontology EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitors EC 1.1.* inhibitor EC 1.1.* inhibitors inhibitor of oxidoreductase acting on CH-OH group of donor inhibitor of oxidoreductase acting on CH-OH group of donors inhibitors of oxidoreductase acting on CH-OH group of donor inhibitors of oxidoreductase acting on CH-OH group of donors oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitor oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitors oxidoreductase acting on donor CH-OH group inhibitor oxidoreductase acting on donor CH-OH group inhibitors CHEBI:76726 EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitor EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitors ChEBI EC 1.1.* inhibitor ChEBI EC 1.1.* inhibitors ChEBI inhibitor of oxidoreductase acting on CH-OH group of donor ChEBI inhibitor of oxidoreductase acting on CH-OH group of donors ChEBI inhibitors of oxidoreductase acting on CH-OH group of donor ChEBI inhibitors of oxidoreductase acting on CH-OH group of donors ChEBI oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitor ChEBI oxidoreductase acting on donor CH-OH group (EC 1.1.*) inhibitors ChEBI oxidoreductase acting on donor CH-OH group inhibitor ChEBI oxidoreductase acting on donor CH-OH group inhibitors ChEBI An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on the CH-NH2 group of donors (EC 1.4.*.*). EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor chebi_ontology EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitors EC 1.4.* inhibitor EC 1.4.* inhibitors inhibitor of oxidoreductase acting on CH-NH2 group of donor inhibitor of oxidoreductase acting on CH-NH2 group of donors inhibitors of oxidoreductase acting on CH-NH2 group of donor inhibitors of oxidoreductase acting on CH-NH2 group of donors oxidoreductase acting on CH-NH2 group of donor inhibitor oxidoreductase acting on CH-NH2 group of donor inhibitors oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitor oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitors CHEBI:76730 EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor ChEBI EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitors ChEBI EC 1.4.* inhibitor ChEBI EC 1.4.* inhibitors ChEBI inhibitor of oxidoreductase acting on CH-NH2 group of donor ChEBI inhibitor of oxidoreductase acting on CH-NH2 group of donors ChEBI inhibitors of oxidoreductase acting on CH-NH2 group of donor ChEBI inhibitors of oxidoreductase acting on CH-NH2 group of donors ChEBI oxidoreductase acting on CH-NH2 group of donor inhibitor ChEBI oxidoreductase acting on CH-NH2 group of donor inhibitors ChEBI oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitor ChEBI oxidoreductase acting on CH-NH2 group of donors (EC 1.4.*) inhibitors ChEBI An oxidoreductase inhibitor which interferes with the action of an oxidoreductase acting on hydrogen as donors (EC 1.14.*.*). chebi_ontology EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitors EC 1.14.* inhibitor EC 1.14.* inhibitors inhibitor of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitor of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitor oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitor oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitors CHEBI:76741 EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitors ChEBI EC 1.14.* inhibitor ChEBI EC 1.14.* inhibitors ChEBI inhibitor of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) ChEBI inhibitor of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) ChEBI inhibitors of oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) ChEBI inhibitors of oxidoreductases acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) ChEBI oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitor ChEBI oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen (EC 1.14.*) inhibitors ChEBI oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitor ChEBI oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen inhibitors ChEBI Any enzyme inhibitor that interferes with the action of a hydrolase (EC 3.*.*.*). Wikipedia:Hydrolase chebi_ontology EC 3.* (hydrolase) inhibitors EC 3.* inhibitor EC 3.* inhibitors EC 3.*.*.* inhibitor EC 3.*.*.* inhibitors hydrolase (EC 3.*) inhibitor hydrolase (EC 3.*) inhibitors hydrolase inhibitor hydrolase inhibitors CHEBI:76759 EC 3.* (hydrolase) inhibitor EC 3.* (hydrolase) inhibitors ChEBI EC 3.* inhibitor ChEBI EC 3.* inhibitors ChEBI EC 3.*.*.* inhibitor ChEBI EC 3.*.*.* inhibitors ChEBI hydrolase (EC 3.*) inhibitor ChEBI hydrolase (EC 3.*) inhibitors ChEBI hydrolase inhibitor ChEBI hydrolase inhibitors ChEBI A hydrolase inhibitor that interferes with the action of any ester hydrolase (EC 3.1.*.*). chebi_ontology EC 3.1.* (ester hydrolase) inhibitors EC 3.1.* inhibitor EC 3.1.* inhibitors ester hydrolase (EC 3.1.*) inhibitor ester hydrolase (EC 3.1.*) inhibitors ester hydrolase inhibitor ester hydrolase inhibitors CHEBI:76760 EC 3.1.* (ester hydrolase) inhibitor EC 3.1.* (ester hydrolase) inhibitors ChEBI EC 3.1.* inhibitor ChEBI EC 3.1.* inhibitors ChEBI ester hydrolase (EC 3.1.*) inhibitor ChEBI ester hydrolase (EC 3.1.*) inhibitors ChEBI ester hydrolase inhibitor ChEBI ester hydrolase inhibitors ChEBI Any hydrolase inhibitor that interferes with the action of a hydrolase acting on C-N bonds, other than peptide bonds (EC 3.5.*.*). chebi_ontology EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors EC 3.5.* inhibitor EC 3.5.* inhibitors CHEBI:76764 EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitor ChEBI EC 3.5.* (hydrolase acting on non-peptide C-N bond) inhibitors ChEBI EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitor ChEBI EC 3.5.* (hydrolases acting on C-N bonds, other than peptide bonds) inhibitors ChEBI EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitors ChEBI EC 3.5.* inhibitor ChEBI EC 3.5.* inhibitors ChEBI An EC 3.1.* (ester hydrolase) inhibitor that interferes with the action of a carboxylic ester hydrolase (EC 3.1.1.*). chebi_ontology EC 3.1.1.* (carboxylic ester hydrolase) inhibitors EC 3.1.1.* inhibitor EC 3.1.1.* inhibitors carboxylic ester hydrolase (EC 3.1.1.*) inhibitor carboxylic ester hydrolase (EC 3.1.1.*) inhibitors CHEBI:76773 EC 3.1.1.* (carboxylic ester hydrolase) inhibitor EC 3.1.1.* (carboxylic ester hydrolase) inhibitors ChEBI EC 3.1.1.* inhibitor ChEBI EC 3.1.1.* inhibitors ChEBI carboxylic ester hydrolase (EC 3.1.1.*) inhibitor ChEBI carboxylic ester hydrolase (EC 3.1.1.*) inhibitors ChEBI Any EC 3.4.* (hydrolases acting on peptide bond) inhibitor that interferes with the activity of a peptidyl dipeptidase (EC 3.4.15.*). chebi_ontology EC 3.4.15.* (peptidyl-dipeptidase) inhibitors EC 3.4.15.* inhibitor EC 3.4.15.* inhibitors inhibitor of peptidyl-dipeptidases inhibitor of peptidyl-dipeptidases (EC 3.4.15.*) inhibitors of peptidyl-dipeptidases inhibitors of peptidyl-dipeptidases (EC 3.4.15.*) peptidyl-dipeptidase (EC 3.4.15.*) inhibitor peptidyl-dipeptidase (EC 3.4.15.*) inhibitors peptidyl-dipeptidase inhibitor peptidyl-dipeptidase inhibitors CHEBI:76782 EC 3.4.15.* (peptidyl-dipeptidase) inhibitor EC 3.4.15.* (peptidyl-dipeptidase) inhibitors ChEBI EC 3.4.15.* inhibitor ChEBI EC 3.4.15.* inhibitors ChEBI inhibitor of peptidyl-dipeptidases ChEBI inhibitor of peptidyl-dipeptidases (EC 3.4.15.*) ChEBI inhibitors of peptidyl-dipeptidases ChEBI inhibitors of peptidyl-dipeptidases (EC 3.4.15.*) ChEBI peptidyl-dipeptidase (EC 3.4.15.*) inhibitor ChEBI peptidyl-dipeptidase (EC 3.4.15.*) inhibitors ChEBI peptidyl-dipeptidase inhibitor ChEBI peptidyl-dipeptidase inhibitors ChEBI An EC 3.5.* (hydrolases acting on non-peptide C-N bonds) inhibitor that interferes with the action of any non-peptide linear amide C-N hydrolase (EC 3.5.1.*). chebi_ontology EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors EC 3.5.1.* inhibitor EC 3.5.1.* inhibitors non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors CHEBI:76807 EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitors ChEBI EC 3.5.1.* inhibitor ChEBI EC 3.5.1.* inhibitors ChEBI non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitor ChEBI non-peptide linear amide C-N hydrolase (EC 3.5.1.*) inhibitors ChEBI An EC 6.3.* (C-N bond-forming ligase) inhibitor that interferes with the action of any acid-ammonia (or amine) ligase (EC 6.3.1.*). chebi_ontology EC 6.3.1.* (acid-ammonia/amine ligase) inhibitors EC 6.3.1.* inhibitor EC 6.3.1.* inhibitors acid-ammonia (or amine) ligase inhibitor acid-ammonia (or amine) ligase inhibitors CHEBI:76823 EC 6.3.1.* (acid-ammonia/amine ligase) inhibitor EC 6.3.1.* (acid-ammonia/amine ligase) inhibitors ChEBI EC 6.3.1.* inhibitor ChEBI EC 6.3.1.* inhibitors ChEBI acid-ammonia (or amine) ligase inhibitor ChEBI acid-ammonia (or amine) ligase inhibitors ChEBI An EC 4.3.* (C-N lyase) inhibitor that interferes with the action of any ammonia-lyase (EC 4.3.1.*). chebi_ontology EC 4.3.1.* (ammonia-lyase) inhibitors EC 4.3.1.* (ammonia-lyases) inhibitor EC 4.3.1.* (ammonia-lyases) inhibitors EC 4.3.1.* inhibitor EC 4.3.1.* inhibitors ammonia-lyase (EC 4.3.1.*) inhibitor ammonia-lyase (EC 4.3.1.*) inhibitors ammonia-lyase inhibitor ammonia-lyase inhibitors CHEBI:76832 EC 4.3.1.* (ammonia-lyase) inhibitor EC 4.3.1.* (ammonia-lyase) inhibitors ChEBI EC 4.3.1.* (ammonia-lyases) inhibitor ChEBI EC 4.3.1.* (ammonia-lyases) inhibitors ChEBI EC 4.3.1.* inhibitor ChEBI EC 4.3.1.* inhibitors ChEBI ammonia-lyase (EC 4.3.1.*) inhibitor ChEBI ammonia-lyase (EC 4.3.1.*) inhibitors ChEBI ammonia-lyase inhibitor ChEBI ammonia-lyase inhibitors ChEBI An EC 1.1.* (oxidoreductase acting on donor CH-OH group) inhibitor that uses NAD(+) or NADP(+) as acceptor (EC 1.1.1.*). chebi_ontology EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+)acceptor) inhibitors EC 1.1.1.* inhibitor EC 1.1.1.* inhibitors oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitor oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitors CHEBI:76835 EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+)acceptor) inhibitors ChEBI EC 1.1.1.* inhibitor ChEBI EC 1.1.1.* inhibitors ChEBI oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitor ChEBI oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor (EC 1.1.1.*) inhibitors ChEBI An EC 1.14.* (oxidoreductase acting on paired donors, with incorporation or reduction of molecular oxygen) inhibitor that interferes with the action of any such enzyme incorporating one atom of oxygen and using reduced flavin or flavoprotein as donor (EC 1.14.14.*). chebi_ontology EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors EC 1.14.14.* inhibitor EC 1.14.14.* inhibitors oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitor oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitors CHEBI:76838 EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors ChEBI EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor ChEBI EC 1.14.14.* (oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitors ChEBI EC 1.14.14.* inhibitor ChEBI EC 1.14.14.* inhibitors ChEBI oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitor ChEBI oxidoreductase acting on paired donors, with incorporation of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor (EC 1.14.14.*) inhibitors ChEBI An EC 1.4.* (oxidoreductase acting on donor CH-NH2 group) inhibitor that interferes with the action of any such enzyme using oxygen as acceptor (EC 1.4.3.*). chebi_ontology EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitors EC 1.4.3.* inhibitor EC 1.4.3.* inhibitors oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitor oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitors CHEBI:76861 EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitor EC 1.4.3.* (oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor) inhibitors ChEBI EC 1.4.3.* inhibitor ChEBI EC 1.4.3.* inhibitors ChEBI oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitor ChEBI oxidoreductase acting on donor CH-NH2 group, oxygen as acceptor (EC 1.4.3.*) inhibitors ChEBI An EC 2.1.* (C1-transferase) inhibitor that interferes with the action of any hydroxymethyl-, formyl- and related transferase (EC 2.1.2.*). chebi_ontology EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitors EC 2.1.2.* inhibitor EC 2.1.2.* inhibitors hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitor hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitors CHEBI:76874 EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitor EC 2.1.2.* (hydroxymethyl-, formyl- and related transferases) inhibitors ChEBI EC 2.1.2.* inhibitor ChEBI EC 2.1.2.* inhibitors ChEBI hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitor ChEBI hydroxymethyl-, formyl- and related transferases (EC 2.1.2.*) inhibitors ChEBI A drug which increases the blood glucose level. chebi_ontology diabetes inducer hyperglycemic agents CHEBI:76916 hyperglycemic agent diabetes inducer ChEBI hyperglycemic agents ChEBI Any eukaryotic metabolite produced during a metabolic reaction in plants, the kingdom that include flowering plants, conifers and other gymnosperms. CHEBI:75766 CHEBI:76925 chebi_ontology plant metabolites plant secondary metabolites CHEBI:76924 plant metabolite plant metabolites ChEBI plant secondary metabolites ChEBI An enzyme inhibitor that interferes with one or more steps in a metabolic pathway. chebi_ontology metabolic pathway inhibitor metabolic pathway inhibitors pathway inhibitors CHEBI:76932 pathway inhibitor metabolic pathway inhibitor ChEBI metabolic pathway inhibitors ChEBI pathway inhibitors ChEBI Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds. CHEBI:75765 CHEBI:76947 chebi_ontology fungal metabolites CHEBI:76946 fungal metabolite fungal metabolites ChEBI Any human metabolite produced by metabolism of a xenobiotic compound in humans. chebi_ontology human xenobiotic metabolites CHEBI:76967 human xenobiotic metabolite human xenobiotic metabolites ChEBI Any prokaryotic metabolite produced during a metabolic reaction in bacteria. CHEBI:75760 CHEBI:76970 chebi_ontology CHEBI:76969 bacterial metabolite Any bacterial metabolite produced during a metabolic reaction in Escherichia coli. chebi_ontology E.coli metabolite E.coli metabolites Escherichia coli metabolites CHEBI:76971 Escherichia coli metabolite E.coli metabolite ChEBI E.coli metabolites ChEBI Escherichia coli metabolites ChEBI A compound that alters the structure of mucus so as to decrease its viscosity and thereby facilitate its removal by ciliary action and expectoration. Compare with antitussives, which suppress the cough reflex, and expectorants, which are considered to increase the volume of secretions in the respiratory tract, so facilitating their removal by ciliary action and coughing. PMID:17419975 PMID:17594730 PMID:20031934 PMID:2117172 PMID:22895919 chebi_ontology mucolytics CHEBI:77034 mucolytic PMID:17419975 Europe PMC PMID:17594730 Europe PMC PMID:20031934 Europe PMC PMID:2117172 Europe PMC PMID:22895919 Europe PMC mucolytics ChEBI An EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that interferes with the action of prostaglandin-E2 9-reductase (EC 1.1.1.189). Wikipedia:Prostaglandin-E2_9-reductase chebi_ontology (5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitor (5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitors 9-keto-prostaglandin E2 reductase inhibitor 9-keto-prostaglandin E2 reductase inhibitors 9-ketoprostaglandin reductase inhibitor 9-ketoprostaglandin reductase inhibitors EC 1.1.1.189 (prostaglandin-E2 9-reductase) inhibitors EC 1.1.1.189 inhibitor EC 1.1.1.189 inhibitors PGE-9-ketoreductase inhibitor PGE-9-ketoreductase inhibitors PGE2 9-oxoreductase inhibitor PGE2 9-oxoreductase inhibitors PGE2-9-OR inhibitor PGE2-9-OR inhibitors PGE2-9-ketoreductase inhibitor PGE2-9-ketoreductase inhibitors prostaglandin 9-ketoreductase inhibitor prostaglandin 9-ketoreductase inhibitors prostaglandin E 9-ketoreductase inhibitor prostaglandin E 9-ketoreductase inhibitors prostaglandin E2-9-oxoreductase inhibitor prostaglandin E2-9-oxoreductase inhibitors prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitor prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitors reductase, 15-hydroxy-9-oxoprostaglandin inhibitor reductase, 15-hydroxy-9-oxoprostaglandin inhibitors CHEBI:77119 EC 1.1.1.189 (prostaglandin-E2 9-reductase) inhibitor (5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitor ChEBI (5Z,13E)-(15S)-9alpha,11alpha,15-trihydroxyprosta-5,13-dienoate:NADP(+) 9-oxidoreductase inhibitors ChEBI 9-keto-prostaglandin E2 reductase inhibitor ChEBI 9-keto-prostaglandin E2 reductase inhibitors ChEBI 9-ketoprostaglandin reductase inhibitor ChEBI 9-ketoprostaglandin reductase inhibitors ChEBI EC 1.1.1.189 (prostaglandin-E2 9-reductase) inhibitors ChEBI EC 1.1.1.189 inhibitor ChEBI EC 1.1.1.189 inhibitors ChEBI PGE-9-ketoreductase inhibitor ChEBI PGE-9-ketoreductase inhibitors ChEBI PGE2 9-oxoreductase inhibitor ChEBI PGE2 9-oxoreductase inhibitors ChEBI PGE2-9-OR inhibitor ChEBI PGE2-9-OR inhibitors ChEBI PGE2-9-ketoreductase inhibitor ChEBI PGE2-9-ketoreductase inhibitors ChEBI prostaglandin 9-ketoreductase inhibitor ChEBI prostaglandin 9-ketoreductase inhibitors ChEBI prostaglandin E 9-ketoreductase inhibitor ChEBI prostaglandin E 9-ketoreductase inhibitors ChEBI prostaglandin E2-9-oxoreductase inhibitor ChEBI prostaglandin E2-9-oxoreductase inhibitors ChEBI prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitor ChEBI prostaglandin-E2 9-reductase (EC 1.1.1.189) inhibitors ChEBI reductase, 15-hydroxy-9-oxoprostaglandin inhibitor ChEBI reductase, 15-hydroxy-9-oxoprostaglandin inhibitors ChEBI A food additive that imparts colour to food. In European countries, E-numbers for permitted food colours are from E 100 to E 199, divided into yellows (E 100-109), oranges (E 110-119), reds (E 120-129), blues and violets (E 130-139), greens (E 140-149), browns and blacks (E 150-159), and others (E 160-199). Wikipedia:Food_coloring chebi_ontology food coloring food colorings food colourings CHEBI:77182 food colouring food coloring ChEBI food colorings ChEBI food colourings ChEBI A diuretic that acts on the ascending loop of Henle in the kidney. Wikipedia:Loop_diuretic chebi_ontology loop diuretics CHEBI:77608 loop diuretic loop diuretics ChEBI An EC 4.3.1.* (ammonia-lyase) inhibitor that interferes with the action of histidine ammonia-lyase (EC 4.3.1.3). Wikipedia:Histidine_ammonia-lyase chebi_ontology EC 4.3.1.3 (histidine ammonia-lyase) inhibitors EC 4.3.1.3 inhibitor EC 4.3.1.3 inhibitors L-histidine ammonia-lyase (urocanate-forming) inhibitor L-histidine ammonia-lyase (urocanate-forming) inhibitors L-histidine ammonia-lyase inhibitor L-histidine ammonia-lyase inhibitors histidase inhibitor histidase inhibitors histidinase inhibitor histidinase inhibitors histidine alpha-deaminase inhibitor histidine alpha-deaminase inhibitors histidine ammonia-lyase (EC 4.3.1.3) inhibitor histidine ammonia-lyase (EC 4.3.1.3) inhibitors histidine ammonia-lyase inhibitor histidine ammonia-lyase inhibitors CHEBI:77703 EC 4.3.1.3 (histidine ammonia-lyase) inhibitor EC 4.3.1.3 (histidine ammonia-lyase) inhibitors ChEBI EC 4.3.1.3 inhibitor ChEBI EC 4.3.1.3 inhibitors ChEBI L-histidine ammonia-lyase (urocanate-forming) inhibitor ChEBI L-histidine ammonia-lyase (urocanate-forming) inhibitors ChEBI L-histidine ammonia-lyase inhibitor ChEBI L-histidine ammonia-lyase inhibitors ChEBI histidase inhibitor ChEBI histidase inhibitors ChEBI histidinase inhibitor ChEBI histidinase inhibitors ChEBI histidine alpha-deaminase inhibitor ChEBI histidine alpha-deaminase inhibitors ChEBI histidine ammonia-lyase (EC 4.3.1.3) inhibitor ChEBI histidine ammonia-lyase (EC 4.3.1.3) inhibitors ChEBI histidine ammonia-lyase inhibitor ChEBI histidine ammonia-lyase inhibitors ChEBI Any mammalian metabolite produced during a metabolic reaction in humans (Homo sapiens). CHEBI:75770 CHEBI:77123 chebi_ontology H. sapiens metabolite H. sapiens metabolites Homo sapiens metabolite Homo sapiens metabolites CHEBI:77746 human metabolite H. sapiens metabolite ChEBI H. sapiens metabolites ChEBI Homo sapiens metabolite ChEBI Homo sapiens metabolites ChEBI A zwitterion obtained by transfer of a proton from the 2-hydroxy group to the 1-amino group of tetracycline. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.). 0 C22H24N2O8 InChI=1S/C22H24N2O8/c1-21(31)8-5-4-6-11(25)12(8)16(26)13-9(21)7-10-15(24(2)3)17(27)14(20(23)30)19(29)22(10,32)18(13)28/h4-6,9-10,15,25,27-28,31-32H,7H2,1-3H3,(H2,23,30)/t9-,10-,15-,21+,22-/m0/s1 OFVLGDICTFRJMM-WESIUVDSSA-N 444.43460 444.15327 C[NH+](C)[C@H]1[C@@H]2C[C@H]3C(=C(O)[C@]2(O)C(=O)C(C(N)=O)=C1[O-])C(=O)c1c(O)cccc1[C@@]3(C)O (1S,4aS,11S,11aS,12aS)-3-carbamoyl-1-(dimethylazaniumyl)-4a,5,7,11-tetrahydroxy-11-methyl-4,6-dioxo-1,4,4a,6,11,11a,12,12a-octahydrotetracen-2-olate chebi_ontology tetracycline CHEBI:77932 tetracycline zwitterion (1S,4aS,11S,11aS,12aS)-3-carbamoyl-1-(dimethylazaniumyl)-4a,5,7,11-tetrahydroxy-11-methyl-4,6-dioxo-1,4,4a,6,11,11a,12,12a-octahydrotetracen-2-olate IUPAC tetracycline UniProt An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of amidase (EC 3.5.1.4). Wikipedia:Amidase chebi_ontology EC 3.5.1.4 (amidase) inhibitors EC 3.5.1.4 inhibitor EC 3.5.1.4 inhibitors N-acetylaminohydrolase inhibitor N-acetylaminohydrolase inhibitors acylamidase inhibitor acylamidase inhibitors acylamide amidohydrolase inhibitor acylamide amidohydrolase inhibitors amidase (EC 3.5.1.4) inhibitor amidase (EC 3.5.1.4) inhibitors amidase inhibitor amidase inhibitors amidohydrolase inhibitor amidohydrolase inhibitors deaminase inhibitor deaminase inhibitors fatty acylamidase inhibitor fatty acylamidase inhibitors CHEBI:77941 EC 3.5.1.4 (amidase) inhibitor EC 3.5.1.4 (amidase) inhibitors ChEBI EC 3.5.1.4 inhibitor ChEBI EC 3.5.1.4 inhibitors ChEBI N-acetylaminohydrolase inhibitor ChEBI N-acetylaminohydrolase inhibitors ChEBI acylamidase inhibitor ChEBI acylamidase inhibitors ChEBI acylamide amidohydrolase inhibitor ChEBI acylamide amidohydrolase inhibitors ChEBI amidase (EC 3.5.1.4) inhibitor ChEBI amidase (EC 3.5.1.4) inhibitors ChEBI amidase inhibitor ChEBI amidase inhibitors ChEBI amidohydrolase inhibitor ChEBI amidohydrolase inhibitors ChEBI deaminase inhibitor ChEBI deaminase inhibitors ChEBI fatty acylamidase inhibitor ChEBI fatty acylamidase inhibitors ChEBI A food additive that is used to make or keep fruit or vegetable tissues firm and crisp. or which interacts with gelling agents such as pectin to produce or strengthen a gel. Wikipedia:Firming_agent chebi_ontology firming agent firming agents food firming agents CHEBI:77960 food firming agent firming agent ChEBI firming agents ChEBI food firming agents ChEBI An antioxidant that used as a food additives to help guard against food deterioration. chebi_ontology food antioxidants CHEBI:77962 food antioxidant food antioxidants ChEBI A propellant that is used to expel foods from an aerosol container. chebi_ontology food propellants CHEBI:78017 food propellant food propellants ChEBI A polyunsaturated fatty acid anion that is the conjugate base of docosahexaenoic acid, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C22H31O2 327.4803 327.23241 [O-]C([*])=O chebi_ontology CHEBI:78060 docosahexaenoate Any saturated fatty acid anion containing 3 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3. -1 C3H5O2 73.07060 73.02895 [O-]C([*])=O chebi_ontology fatty acid 3:0 CHEBI:78113 fatty acid anion 3:0 fatty acid 3:0 UniProt Any saturated fatty acid anion containing 4 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3. -1 C4H7O2 87.09718 87.04460 [O-]C([*])=O chebi_ontology fatty acid 4:0 CHEBI:78115 fatty acid anion 4:0 fatty acid 4:0 UniProt Any saturated fatty acid anion containing 6 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3. -1 C6H11O2 115.15034 115.07590 [O-]C([*])=O chebi_ontology fatty acid 6:0 CHEBI:78116 fatty acid anion 6:0 fatty acid 6:0 UniProt Any saturated fatty acid anion containing 16 carbons. Formed by deprotonation of the carboxylic acid moiety. Major species at pH 7.3. -1 C16H31O2 255.41610 255.23241 [O-]C([*])=O chebi_ontology fatty acid 16:0 CHEBI:78123 fatty acid anion 16:0 fatty acid 16:0 UniProt A monocarboxylic acid anion that is the conjugate base of N-acetyl-L-cysteine, obtained by deprotonation of the carboxy group; major species at pH 7.3. -1 C5H8NO3S InChI=1S/C5H9NO3S/c1-3(7)6-4(2-10)5(8)9/h4,10H,2H2,1H3,(H,6,7)(H,8,9)/p-1/t4-/m0/s1 PWKSKIMOESPYIA-BYPYZUCNSA-M 162.18700 162.02304 CC(=O)N[C@@H](CS)C([O-])=O MetaCyc:CPD-9175 PMID:19268377 Reaxys:6327823 (2R)-2-acetamido-3-sulfanylpropanoate chebi_ontology N-acetyl-L-cysteine CHEBI:78236 N-acetyl-L-cysteinate MetaCyc:CPD-9175 SUBMITTER PMID:19268377 SUBMITTER Reaxys:6327823 Reaxys (2R)-2-acetamido-3-sulfanylpropanoate IUPAC N-acetyl-L-cysteine UniProt food component role A physiological role played by any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. Any substance that is distributed in foodstuffs. It includes materials derived from plants or animals, such as vitamins or minerals, as well as environmental contaminants. chebi_ontology dietary component dietary components food components CHEBI:78295 food component dietary component ChEBI dietary components ChEBI food components ChEBI Any minor or unwanted substance introduced into the environment that can have undesired effects. chebi_ontology environmental contaminants CHEBI:78298 environmental contaminant environmental contaminants ChEBI A substance used in a thermodynamic heat pump cycle or refrigeration cycle that undergoes a phase change from a gas to a liquid and back. Refrigerants are used in air-conditioning systems and freezers or refrigerators and are assigned a "R" number (by ASHRAE - formerly the American Society of Heating, Refrigerating and Air Conditioning Engineers), which is determined systematically according to their molecular structure. Wikipedia:Refrigerant chebi_ontology refrigerants CHEBI:78433 refrigerant refrigerants ChEBI An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3. 0 C2H4NO2R 74.059 74.02420 [NH3+]C([*])C([O-])=O CHEBI:83409 MetaCyc:Alpha-Amino-Acids chebi_ontology an alpha-amino acid CHEBI:78608 alpha-amino acid zwitterion MetaCyc:Alpha-Amino-Acids SUBMITTER an alpha-amino acid UniProt Any organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation. chebi_ontology carbohydrates and derivatives carbohydrates and their derivatives CHEBI:78616 carbohydrates and carbohydrate derivatives carbohydrates and derivatives ChEBI carbohydrates and their derivatives ChEBI Any metabolite produced by all living cells. chebi_ontology essential metabolite essential metabolites fundamental metabolites CHEBI:78675 fundamental metabolite essential metabolite ChEBI essential metabolites ChEBI fundamental metabolites ChEBI Any organic molecular entity that contains at least one C=C bond. chebi_ontology olefinic compounds CHEBI:78840 olefinic compound olefinic compounds ChEBI A long-chain fatty acid anion that is the conjugate base of hexadecanoic acid (palmitic acid); major species at pH 7.3. -1 C16H31O2 InChI=1S/C16H32O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h2-15H2,1H3,(H,17,18)/p-1 IPCSVZSSVZVIGE-UHFFFAOYSA-M 255.41610 255.23295 CCCCCCCCCCCCCCCC([O-])=O CHEBI:231736 Beilstein:3589907 CAS:143-20-4 Gmelin:344266 HMDB:HMDB0000220 MetaCyc:PALMITATE Reaxys:3589907 hexadecanoate chebi_ontology (16:0) 1-hexyldecanoate 1-pentadecanecarboxylate CH3-[CH2]14-COO(-) Hexadecanoic acid, ion(1-) n-hexadecanoate n-hexadecoate palmitate pentadecanecarboxylate CHEBI:7896 hexadecanoate Beilstein:3589907 Beilstein CAS:143-20-4 ChemIDplus Gmelin:344266 Gmelin Reaxys:3589907 Reaxys hexadecanoate IUPAC hexadecanoate UniProt (16:0) ChEBI 1-hexyldecanoate HMDB 1-pentadecanecarboxylate ChEBI CH3-[CH2]14-COO(-) ChEBI Hexadecanoic acid, ion(1-) ChemIDplus n-hexadecanoate ChEBI n-hexadecoate ChEBI palmitate ChEBI pentadecanecarboxylate ChEBI Any inorganic anion with a valency of three. chebi_ontology trivalent inorganic anions CHEBI:79387 trivalent inorganic anion trivalent inorganic anions ChEBI Any inorganic anion with a valency of two. chebi_ontology divalent inorganic anions CHEBI:79388 divalent inorganic anion divalent inorganic anions ChEBI Any inorganic anion with a valency of one. chebi_ontology monovalent inorganic anions CHEBI:79389 monovalent inorganic anion monovalent inorganic anions ChEBI A member of the class of monohydroxy-1,4-benzoquinones that is 2-hydroxy-1,4-benzoquinone carrying an additional methyl substituent at position 5. 0 C7H6O3 InChI=1S/C7H6O3/c1-4-2-6(9)7(10)3-5(4)8/h2-3,10H,1H3 BMBZVGUSOUAIMK-UHFFFAOYSA-N 138.121 138.03169 C=1C(C(=CC(C1C)=O)O)=O CAS:615-91-8 KEGG:C18316 MetaCyc:CPD-9135 Reaxys:1861302 2-hydroxy-5-methylcyclohexa-2,5-diene-1,4-dione chebi_ontology 2-Hydroxy-5-methyl-1,4-benzoquinone 2-Hydroxy-5-methyl-p-benzoquinone CHEBI:81667 2-hydroxy-5-methylquinone CAS:615-91-8 ChemIDplus CAS:615-91-8 KEGG COMPOUND Reaxys:1861302 Reaxys 2-hydroxy-5-methylcyclohexa-2,5-diene-1,4-dione IUPAC 2-Hydroxy-5-methyl-1,4-benzoquinone KEGG_COMPOUND 2-Hydroxy-5-methyl-p-benzoquinone ChemIDplus An elemental molecular entity in which all of the atoms have atomic number 26. chebi_ontology CHEBI:82663 elemental iron A Daphnia metabolite produced by the species Daphnia galeata. chebi_ontology Daphnia galeata metabolites CHEBI:83038 Daphnia galeata metabolite Daphnia galeata metabolites ChEBI An animal metabolite produced by arthropods such as crabs, lobsters, crayfish, shrimps and krill. chebi_ontology crustacean metabolites CHEBI:83039 crustacean metabolite crustacean metabolites ChEBI A Daphnia metabolite produced by the species Daphnia magna. chebi_ontology Daphnia magna metabolites CHEBI:83056 Daphnia magna metabolite Daphnia magna metabolites ChEBI A crustacean metabolite produced by the genus of small planktonic arthropods, Daphnia Wikipedia:Daphnia chebi_ontology Daphnia metabolites CHEBI:83057 Daphnia metabolite Daphnia metabolites ChEBI Any derivative of a proteinogenic amino acid resulting from reaction at an amino group, carboxy group, or a side-chain functional group, or from the replacement of any hydrogen by a heteroatom. chebi_ontology canonical amino acid derivative canonical amino acid derivatives canonical amino-acid derivative canonical amino-acid derivatives proteinogenic amino acid derivatives proteinogenic amino-acid derivative proteinogenic amino-acid derivatives CHEBI:83811 proteinogenic amino acid derivative canonical amino acid derivative ChEBI canonical amino acid derivatives ChEBI canonical amino-acid derivative ChEBI canonical amino-acid derivatives ChEBI proteinogenic amino acid derivatives ChEBI proteinogenic amino-acid derivative ChEBI proteinogenic amino-acid derivatives ChEBI Any derivative of a non-proteinogenic amino acid resulting from reaction at an amino group or carboxy group, or from the replacement of any hydrogen by a heteroatom. chebi_ontology non-canonical amino acid derivative non-canonical amino-acid derivatives non-proteinogenic amino-acid derivatives CHEBI:83812 non-proteinogenic amino acid derivative non-canonical amino acid derivative ChEBI non-canonical amino-acid derivatives ChEBI non-proteinogenic amino-acid derivatives ChEBI Any of the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. Apart from glycine, which is non-chiral, all have L configuration. Wikipedia:Proteinogenic_amino_acid chebi_ontology canonical amino acid canonical amino acids proteinogenic amino acids CHEBI:83813 proteinogenic amino acid canonical amino acid ChEBI canonical amino acids ChEBI proteinogenic amino acids ChEBI Any amino-acid that is not naturally encoded in the genetic code of any organism. Wikipedia:Non-proteinogenic_amino_acids chebi_ontology non-canonical amino acid non-canonical amino acids non-canonical amino-acid non-canonical amino-acids non-coded amino acid non-coded amino acids non-coded amino-acid non-coded amino-acids non-proteinogenic amino acids non-proteinogenic amino-acid non-proteinogenic amino-acids CHEBI:83820 non-proteinogenic amino acid non-canonical amino acid ChEBI non-canonical amino acids ChEBI non-canonical amino-acid ChEBI non-canonical amino-acids ChEBI non-coded amino acid ChEBI non-coded amino acids ChEBI non-coded amino-acid ChEBI non-coded amino-acids ChEBI non-proteinogenic amino acids ChEBI non-proteinogenic amino-acid ChEBI non-proteinogenic amino-acids ChEBI Any derivative of an amino acid resulting from reaction at an amino group, carboxy group, side-chain functional group, or from the replacement of any hydrogen by a heteroatom. The definition normally excludes peptides containing amino acid residues. CHEBI:25359 chebi_ontology amino acid derivatives modified amino acids CHEBI:83821 amino acid derivative amino acid derivatives ChEBI modified amino acids ChEBI A proteinogenic amino acid derivative resulting from the formal reaction of L-cysteine at the amino group, carboxy group, or thiol group, or from the replacement of any hydrogen of L-cysteine by a heteroatom. chebi_ontology L-cysteine derivatives CHEBI:83824 L-cysteine derivative L-cysteine derivatives ChEBI Any alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids. chebi_ontology non-proteinogenic alpha-amino acids non-proteinogenic alpha-amino-acid non-proteinogenic alpha-amino-acids CHEBI:83925 non-proteinogenic alpha-amino acid non-proteinogenic alpha-amino acids ChEBI non-proteinogenic alpha-amino-acid ChEBI non-proteinogenic alpha-amino-acids ChEBI A fatty acid anion obtained by deprotonation of the carboxy group of any 2-saturated fatty acid. -1 C2H2O2R 58.036 58.00548 [O-]C(=O)C[*] chebi_ontology 1,2-saturated fatty acid anion a 1,2-saturated fatty acid CHEBI:83955 2-saturated fatty acid anion 1,2-saturated fatty acid anion ChEBI a 1,2-saturated fatty acid UniProt A methyl-branched fatty acid anion obtained by deprotonation of the carboxy group of any 3-methyl fatty acid; major species at pH 7.3. -1 C4H6O2R 86.089 86.03678 CC([*])CC([O-])=O chebi_ontology 3-methyl fatty acid 3-methyl-branched fatty acid anion 3-methyl-branched fatty acid(1-) CHEBI:83972 3-methyl fatty acid anion 3-methyl fatty acid UniProt 3-methyl-branched fatty acid anion ChEBI 3-methyl-branched fatty acid(1-) SUBMITTER A proteinogenic amino acid derivative resulting from reaction of L-glutamic acid at the amino group or either of the carboxy groups, or from the replacement of any hydrogen of L-glutamic acid by a heteroatom. chebi_ontology L-glutamic acid derivatives CHEBI:83982 L-glutamic acid derivative L-glutamic acid derivatives ChEBI Any metabolite (endogenous or exogenous) found in human urine samples. chebi_ontology human urinary metabolites CHEBI:84087 human urinary metabolite human urinary metabolites ChEBI An EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor that interferes with the action of nicotinamidase (EC 3.5.1.19). Wikipedia:Nicotinamidase chebi_ontology EC 3.5.1.19 (nicotinamidase) inhibitors EC 3.5.1.19 inhibitor EC 3.5.1.19 inhibitors YNDase inhibitor YNDase inhibitors nicotinamidase (EC 3.5.1.19) inhibitor nicotinamidase (EC 3.5.1.19) inhibitors nicotinamidase inhibitor nicotinamidase inhibitors nicotinamide amidase inhibitor nicotinamide amidase inhibitors nicotinamide amidohydrolase inhibitor nicotinamide amidohydrolase inhibitors nicotinamide deaminase inhibitor nicotinamide deaminase inhibitors CHEBI:84264 EC 3.5.1.19 (nicotinamidase) inhibitor EC 3.5.1.19 (nicotinamidase) inhibitors ChEBI EC 3.5.1.19 inhibitor ChEBI EC 3.5.1.19 inhibitors ChEBI YNDase inhibitor ChEBI YNDase inhibitors ChEBI nicotinamidase (EC 3.5.1.19) inhibitor ChEBI nicotinamidase (EC 3.5.1.19) inhibitors ChEBI nicotinamidase inhibitor ChEBI nicotinamidase inhibitors ChEBI nicotinamide amidase inhibitor ChEBI nicotinamide amidase inhibitors ChEBI nicotinamide amidohydrolase inhibitor ChEBI nicotinamide amidohydrolase inhibitors ChEBI nicotinamide deaminase inhibitor ChEBI nicotinamide deaminase inhibitors ChEBI Any eukaryotic metabolite produced during a metabolic reaction in algae including unicellular organisms like chlorella and diatoms to multicellular organisms like giant kelps and brown algae. chebi_ontology algal metabolites CHEBI:84735 algal metabolite algal metabolites ChEBI skin lightening agent role Any cosmetic used to lighten the colour of skin by reducing the concentration of melanin. skin lightening agent Any member of the class of cholanic acids carrying two hydroxy substituents at unspecified positions. chebi_ontology dihydroxycholanic acids CHEBI:85184 dihydroxycholanic acid dihydroxycholanic acids ChEBI An organonitrogen heterocyclic antibiotic whose structure contains a quinolone or quinolone-related skeleton. chebi_ontology quinolone antibiotics CHEBI:86324 quinolone antibiotic quinolone antibiotics ChEBI Any antifungal agent used to prevent or treat fungal infections in humans or animals. Wikipedia:Antifungal chebi_ontology anti-fungal drug anti-fungal drugs anti-fungal medication anti-fungal medications antifungal drugs antifungal medication antifungal medications pharmaceutical fungicide pharmaceutical fungicides CHEBI:86327 antifungal drug anti-fungal drug ChEBI anti-fungal drugs ChEBI anti-fungal medication ChEBI anti-fungal medications ChEBI antifungal drugs ChEBI antifungal medication ChEBI antifungal medications ChEBI pharmaceutical fungicide ChEBI pharmaceutical fungicides ChEBI A class of sulfonamides whose members generally have bacteriostatic antibiotic properties. PMID:24443047 PMID:24928456 PMID:25064257 PMID:25796473 PMID:26177406 Wikipedia:Sulfonamide_(medicine) chebi_ontology sulfonamide antibiotics sulfonamide antimicrobial agent sulfonamide antimicrobial agents sulphonamide antibiotic sulphonamide antibiotics CHEBI:87228 sulfonamide antibiotic PMID:24443047 Europe PMC PMID:24928456 Europe PMC PMID:25064257 Europe PMC PMID:25796473 Europe PMC PMID:26177406 Europe PMC sulfonamide antibiotics ChEBI sulfonamide antimicrobial agent ChEBI sulfonamide antimicrobial agents ChEBI sulphonamide antibiotic ChEBI sulphonamide antibiotics ChEBI Any metal which causes the onset of an allergic reaction. chebi_ontology allergenic metal allergenic metals metal allergens CHEBI:88184 metal allergen allergenic metal ChEBI allergenic metals ChEBI metal allergens ChEBI Any drug which causes the onset of an allergic reaction. chebi_ontology allergenic drug CHEBI:88188 drug allergen allergenic drug ChEBI An organic anion obtained by deprotonation of the hydroxy group of 2-hydroxy-5-methylquinone. It is the major microspecies at pH 7.3 (according to Marvin v 6.2.0.). -1 C7H5O3 InChI=1S/C7H6O3/c1-4-2-6(9)7(10)3-5(4)8/h2-3,10H,1H3/p-1 BMBZVGUSOUAIMK-UHFFFAOYSA-M 137.113 137.02442 C1(C=C(C(C=C1C)=O)[O-])=O MetaCyc:CPD-9135 4-methyl-3,6-dioxocyclohexa-1,4-dien-1-olate chebi_ontology 2-hydroxy-5-methylquinone 2-hydroxy-5-methylquinone(1-) CHEBI:88190 2-oxido-5-methylquinone MetaCyc:CPD-9135 SUBMITTER 4-methyl-3,6-dioxocyclohexa-1,4-dien-1-olate IUPAC 2-hydroxy-5-methylquinone UniProt 2-hydroxy-5-methylquinone(1-) ChEBI A drug that acts as an antagonist, agonist, reverse agonist, or in some other fashion when interacting with cellular receptors. chebi_ontology receptor modulators CHEBI:90710 receptor modulator receptor modulators ChEBI A carboxylic acic anion obtained by deprotonation of the carboxy group of any aromatic carboxylic acid. Major species at pH 7.3. -1 CO2R 44.010 43.98983 *C([O-])=O chebi_ontology an aromatic carboxylate CHEBI:91007 aromatic carboxylate an aromatic carboxylate UniProt Any inhibitor of erythropoietin, a glycoprotein hormone that controls erythropoiesis (red blood cell production). chebi_ontology EPO inhibitor EPO inhibitors erythropoietin inhibitors CHEBI:91025 erythropoietin inhibitor EPO inhibitor ChEBI EPO inhibitors ChEBI erythropoietin inhibitors ChEBI A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 cell CL:0000000 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CARO:mah A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:0000013 cell in vivo cell To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). native cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:mah A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. BTO:0000414 CALOHA:TS-2026 CARO:0000077 FBbt:00000124 FMA:66768 WBbt:0003672 epitheliocyte cell epithelial cell A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. FB:ma GOC:tfm MESH:A11.436 An epithelial cell that is part of a duct. cell duct epithelial cell An epithelial cell that is part of a duct. https://orcid.org/0000-0001-5208-3432 cell branched duct epithelial cell An endothelial cell that lines the vasculature. cuboidal endothelial cell of vascular tree cell blood vessel endothelial cell true An endothelial cell that lines the vasculature. GOC:tfm CALOHA:TS-1249 cell squamous epithelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. FMA:66773 mesotheliocyte cell mesothelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. GOC:tfm ISBN:0721662544 A cell which moves among different tissues of the body, via blood, lymph, or other medium. cell circulating cell A cell which moves among different tissues of the body, via blood, lymph, or other medium. GOC:add An epithelial cell of the lung. BTO:0004299 lung epithelial cell cell epithelial cell of lung An epithelial cell of the lung. https://orcid.org/0000-0001-5208-3432 An epithelial cell of the pancreas. BTO:0000028 pancreas epithelial cell pancreatic epithelial cell cell epithelial cell of pancreas true An epithelial cell of the pancreas. GOC:tfm An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 CALOHA:TS-0278 FMA:66772 endotheliocyte cell From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. GOC:tfm MESH:D042783 PMID:21275341 http://en.wikipedia.org/wiki/Endothelial_cell https://sourceforge.net/tracker/?func=detail&atid=440764&aid=3364936&group_id=36855 A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. CALOHA:TS-2085 FMA:86494 cell glandular epithelial cell A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. GOC:tfm A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 cell secretory cell A cell that specializes in controlled release of one or more substances. GOC:tfm ISBN:0721662544 A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 cell exocrine cell A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. ISBN:0198547684 cell protein secreting cell A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. FMA:83809 endocrinocyte cell endocrine cell A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. MESH:A06.407 cell steroid hormone secreting cell A somatic cell located in skeletal muscle. BTO:0004392 CALOHA:TS-2158 FMA:9727 skeletal muscle cell cell cell of skeletal muscle A somatic cell located in skeletal muscle. GOC:tfm A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. boundary cell cell lining cell A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. JB:jb A cell whose primary function is to prevent the transport of stuff across compartments. cell barrier cell A cell whose primary function is to prevent the transport of stuff across compartments. JB:jb A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier. BTO:0001238 CALOHA:TS-0922 FMA:72298 VHOG:0001348 cell Sertoli cell true A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier. MESH:A05.360.444.849.789 A cell of the outer of the three germ layers of the embryo. FMA:72549 ectoderm cell cell ectodermal cell A cell of the outer of the three germ layers of the embryo. MESH:A16.254.425.273 A cell of the middle germ layer of the embryo. FMA:72554 mesoblast mesoderm cell cell mesodermal cell A cell of the middle germ layer of the embryo. MESH:A16.254.425.660 A cell of the inner of the three germ layers of the embryo. FMA:72555 endoderm cell cell endodermal cell A cell of the inner of the three germ layers of the embryo. MESH:A16.254.425.407 A cell that lacks a nucleus. FMA:68647 non-nucleated cell cell anucleate cell A cell that lacks a nucleus. FB:ma A cell with a single nucleus. cell single nucleate cell A cell with a single nucleus. FB:ma GOC:tfm cell binucleate cell A cell with more than one nucleus. AEO:0000203 WBbt:0008074 syncitium syncytial cell syncytium cell multinucleate cell A cell with more than one nucleus. FB:ma cell eukaryotic cell An epithelial cell found in the trachea. CL:1000474 FMA:74793 tracheocyte cell This class is for the vertebrate tracheal structure. For the analagous insect cell type, see 'respiratory tube epithelial cell' tracheal epithelial cell true An epithelial cell found in the trachea. GOC:tfm A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris. sebocyte cell sebum secreting cell A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris. MESH:A12.200.702 cell extraembryonic cell An epithelial cell of the integument (the outer layer of an organism). CL:1000396 BTO:0001470 CALOHA:TS-0283 FMA:62411 cell of epidermis epithelial cell of skin cell epidermal cell An epithelial cell of the integument (the outer layer of an organism). Flybase:dsj MA:ma cell of epidermis FMA:62411 epithelial cell of skin FMA:62411 cell tracheoblast A peptide hormone secreting cell that secretes androgen binding protein. cell androgen binding protein secreting cell A peptide hormone secreting cell that secretes androgen binding protein. GO:tfm cell animal cell An epithelial cell of the cornea. CL:1000431 BTO:0004298 CALOHA:TS-0173 FMA:70551 epithelial cell of cornea cell corneal epithelial cell true An epithelial cell of the cornea. GOC:tfm epithelial cell of cornea FMA:70551 A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). FMA:83625 acinic cell acinous cell cell acinar cell A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). GOC:tfm http://www.copewithcytokines.de A cell whose primary function is to support other cell types. BTO:0002315 cell supportive cell A cell whose primary function is to support other cell types. FB:ma GOC:tfm A connective tissue cell found in bone. adiehl 2011-11-16T04:28:16Z cell bone cell true A connective tissue cell found in bone. GOC:add GO_REF:0000034 A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. 2017-01-30T18:53:32Z https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 cell https://github.com/obophenotype/cell-ontology/issues/448 abnormal cell A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. GOC:add GOC:cg GOC:wdd A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. tmeehan 2010-06-24T03:16:29Z BTO:0000028 CALOHA:TS-0737 FMA:63032 acinar cell of pancreas cell pancreatic acinar cell true A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. GOC:tfm ISBN:0517223651 PMID:20395539 http://www.copewithcytokines.de/cope.cgi?key=pancreatic%20acinar%20cells An epithelial cell derived from endoderm. tmeehan 2010-06-29T03:38:14Z FMA:69075 cell endo-epithelial cell An epithelial cell derived from endoderm. FMA:69075 GOC:tfm An epithelial cell derived from ectoderm. tmeehan 2010-06-29T03:38:22Z FMA:69074 cell ecto-epithelial cell An epithelial cell derived from ectoderm. FMA:69074 GOC:tfm Epithelial cell derived from mesoderm or mesenchyme. tmeehan 2010-06-29T03:49:14Z FMA:69076 epithelial mesenchymal cell cell meso-epithelial cell Epithelial cell derived from mesoderm or mesenchyme. FMA:69076 GOC:tfm A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. tmeehan 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 cell MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell true A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. GOC:tfm ISBN:0618947256 A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol. tmeehan 2010-08-24T01:37:44Z FMA:69545 adrenal cortex cell adrenocortical cell cell cortical cell of adrenal gland true A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol. GOC:tfm An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. tmeehan 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 vascular endothelial cell cubodial endothelial cell of vascular tree cell These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. GOC:dsd GOC:tfm PMID:12768659 A sebum secreting cell of the skin that secretes sebum into the hair follicles. tmeehan 2010-08-24T09:27:52Z CL:0002587 sebocyte BTO:0004613 FMA:70953 cell acinar cell of sebaceous gland true A sebum secreting cell of the skin that secretes sebum into the hair follicles. GOC:tfm An endothelial cell found in capillaries. tmeehan 2010-08-24T10:15:00Z BTO:0004956 CALOHA:TS-0112 FMA:67756 cell capillary endothelial cell true An endothelial cell found in capillaries. GOC:tfm An epithelial cell of the uterus. tmeehan 2010-08-24T10:45:54Z CL:1000294 FMA:256161 cell epithelial cell of uterus true An epithelial cell of the uterus. GOC:tfm Epithelial cells derived from general body ectoderm and ectoderm placodes. tmeehan 2010-08-26T08:31:08Z FMA:70556 cell general ecto-epithelial cell Epithelial cells derived from general body ectoderm and ectoderm placodes. GOC:tfm An epithelial cell found in the lining of the stomach. tmeehan 2010-08-25T03:22:08Z CL:1000399 FMA:62948 cell epithelial cell of stomach true An epithelial cell found in the lining of the stomach. GOC:tfm A mucous cell in the epithelium of the stomach. tmeehan 2010-08-25T03:38:51Z CL:1000404 FMA:63464 cell mucous cell of stomach A mucous cell in the epithelium of the stomach. GOC:tfm An epithelial cell of the tracheobronchial tree. tmeehan 2010-09-02T02:09:14Z CL:1000407 FMA:66816 cell epithelial cell of tracheobronchial tree An epithelial cell of the tracheobronchial tree. GOC:tfm An epithelial cell of the prostate. tmeehan 2010-09-07T01:49:29Z CL:1000295 CL:1000408 FMA:256163 FMA:66817 prostate epithelial cell cell epithelial cell of prostate true An epithelial cell of the prostate. GOC:tfm A cell containing at least one nucleus. tmeehan 2010-09-07T03:32:33Z FMA:67513 cell nucleate cell A cell containing at least one nucleus. GOC:tfm An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. tmeehan 2010-09-08T09:26:53Z cell epithelial cell of alimentary canal An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. GOC:tfm ISBN:0721662544 An epithelial cell of the esophagus. tmeehan 2010-09-08T09:28:20Z CL:1000402 FMA:63071 cell epithelial cell of esophagus true An epithelial cell of the esophagus. GOC:tfm An epithelial cell of the large intestine. tmeehan 2010-09-08T09:28:22Z CL:1000292 BTO:0004297 FMA:256157 cell epithelial cell of colon epithelial cell of large intestine true An epithelial cell of the large intestine. GOC:tfm An epithelial cell of the small intestine. tmeehan 2010-09-08T09:41:46Z CL:1000293 FMA:256159 cell epithelial cell of small intestine true An epithelial cell of the small intestine. GOC:tfm An epithelial cell of thyroid gland. tmeehan 2010-09-08T01:46:51Z CL:1000297 FMA:256167 cell epithelial cell of thyroid gland true An epithelial cell of thyroid gland. GOC:tfm An epithelial cell of the parathyroid gland. tmeehan 2010-09-08T02:29:38Z CL:1000429 FMA:70547 cell epithelial cell of parathyroid gland true An epithelial cell of the parathyroid gland. GOC:tfm An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. tmeehan 2010-09-14T10:57:26Z CL:1000403 FMA:63134 cell endothelial cell of sinusoid An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. GOC:tfm ISBN:0618947256 An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies. tmeehan 2010-09-13T02:34:22Z CL:1000459 CALOHA:TS-1040 FMA:72208 epithelial cell of thymus gland epithelial reticular cell epithelial reticular cell of thymus thymic epithelial cell cell epithelial cell of thymus true An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies. FMA:72208 GOC:tfm An epithelial cell of a skin gland. tmeehan 2010-09-14T12:00:07Z FMA:70657 epithelial cell of gland of skin cell epithelial cell of skin gland An epithelial cell of a skin gland. GOC:tfm An ecto-epithelial cell of the prostate gland that secretes hormones. tmeehan 2010-09-14T03:01:58Z CALOHA:TS-1280 FMA:74390 FMA:86774 glandular cell of prostate neuro-epithelial cell of prostate gland cell endocrine-paracrine cell of prostate gland An ecto-epithelial cell of the prostate gland that secretes hormones. GOC:tfm A cell that is part of the nervous system. tmeehan 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 cell neural cell A cell that is part of the nervous system. GOC:tfm ISBN:0618947256 A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. tmeehan 2010-09-15T03:01:54Z CL:1000406 CALOHA:TS-2096 FMA:63875 cell connective tissue cell true A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. GOC:tfm ISBN:0618947256 A cell of the embryo. tmeehan 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 FMA:82841 WBbt:0007028 cell embryonic cell A cell of the embryo. FMA:0618947256 An epithelial cell of the bronchus. tmeehan 2010-09-20T02:00:00Z BTO:0002922 cell bronchial epithelial cell An epithelial cell of the bronchus. GOC:tfm An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. tmeehan 2010-09-21T04:33:05Z CL:1000475 FMA:75621 endocardial endothelial cell endothelial cell of endocardium cell endocardial cell An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. GOC:tfm ISSN:0452-3458 endothelial cell of endocardium FMA:75621 An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. tmeehan 2010-09-23T03:17:12Z BTO:0004562 cTEC cell cortical thymic epithelial cell An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. GOC:tfm PMID:18403190 An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. tmeehan 2010-09-23T03:17:14Z BTO:0004563 mTEC cell medullary thymic epithelial cell An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. GOC:tfm PMID:18180458 A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure. tmeehan 2010-09-23T04:18:50Z trabeculocyte cell trabecular meshwork cell true A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure. GOC:tfm PMID:14500801 An endo-epithelial cell of the respiratory tract. tmeehan 2010-09-23T04:38:49Z BTO:0004533 airway epithelial cell cell respiratory epithelial cell true An endo-epithelial cell of the respiratory tract. GOC:tfm A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). tmeehan 2010-09-24T09:44:42Z BTO:0001268 FMA:72300 WBbt:0008378 cell somatic cell A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). GOC:tfm ISBN:0721662544 A cell located in the heart, including both muscle and non muscle cells. tmeehan 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 FMA:84791 heart cell cell From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte true A cell located in the heart, including both muscle and non muscle cells. GOC:tfm A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc tmeehan 2010-12-07T04:03:56Z BTO:0002441 FMA:84639 cell adventitial cell A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc GOC:tfm An epithelial cell of the kidney. tmeehan 2011-02-08T10:46:34Z KUPO:0001019 cell kidney epithelial cell true An epithelial cell of the kidney. GOC:tfm KUPO:SJ An epithelial cell of the cervix. tmeehan 2011-02-24T08:20:08Z cervical canal epithelial cell cervical canal of uterus epithelial cell cervix epithelial cell cervix of uterus epithelial cell epithelial cell of cervical canal epithelial cell of cervical canal of uterus epithelial cell of cervix of uterus epithelial cell of neck of uterus epithelial cell of uterine cervix neck of uterus epithelial cell uterine cervix epithelial cell cell epithelial cell of cervix true An epithelial cell of the cervix. GOC:tfm cervical canal epithelial cell GOC:tfm cervical canal of uterus epithelial cell GOC:tfm cervix epithelial cell GOC:tfm cervix of uterus epithelial cell GOC:tfm epithelial cell of cervical canal GOC:tfm epithelial cell of cervical canal of uterus GOC:tfm epithelial cell of cervix of uterus GOC:tfm epithelial cell of neck of uterus GOC:tfm epithelial cell of uterine cervix GOC:tfm neck of uterus epithelial cell GOC:tfm uterine cervix epithelial cell GOC:tfm An epithelial cell of the intrahepatic portion of the bile duct. tmeehan 2011-02-28T01:20:20Z cell intrahepatic bile duct epithelial cell true An epithelial cell of the intrahepatic portion of the bile duct. GOC:tfm An endothelial cell that is part of the vein. tmeehan 2011-02-28T03:48:11Z CL:1000393 FMA:62104 KUPO:0001099 endothelial cell of vein venous endothelial cell cell vein endothelial cell true An endothelial cell that is part of the vein. GOC:tfm An endothelial progenitor cell that participates in angiogenesis during development. tmeehan 2011-02-28T04:20:39Z cell See CL:0002619. embryonic blood vessel endothelial progenitor cell An endothelial progenitor cell that participates in angiogenesis during development. GOC:tfm An animal cell that is part of a hair follicle. tmeehan 2011-03-01T04:11:01Z cell hair follicle cell true An animal cell that is part of a hair follicle. GOC:tfm An epithelial cell of the intestine. tmeehan 2011-03-01T05:18:31Z cell intestinal epithelial cell true An epithelial cell of the intestine. GOC:tfm A connective tissue cell of the nucleus pulposus cell of intervertebral disc. tmeehan 2011-03-02T02:12:23Z cell nucleus pulposus cell of intervertebral disc A connective tissue cell of the nucleus pulposus cell of intervertebral disc. GOC:tfm An epithelial cell of the placenta. tmeehan 2011-03-02T03:21:30Z cell placental epithelial cell true An epithelial cell of the placenta. GOC:tfm An epithelial cell of the kidney cortex. KUPO:0001016 cell renal cortical epithelial cell true true An epithelial cell of the kidney cortex. GOC:tfm A blood vessel endothelial cell that is part of the retina. tmeehan 2011-03-06T03:28:27Z cell retinal blood vessel endothelial cell true A blood vessel endothelial cell that is part of the retina. GOC:tfm An acinar cell of salivary gland. tmeehan 2011-03-14T02:22:22Z cell acinar cell of salivary gland true An acinar cell of salivary gland. GOC:tfm A cell of the seminiferous tubule epithelium. tmeehan 2011-03-15T11:59:23Z cell seminiferous tubule epithelial cell true A cell of the seminiferous tubule epithelium. GOC:tfm tmeehan 2011-06-21T12:28:55Z cell epithelial cell of upper respiratory tract true tmeehan 2011-06-21T12:29:31Z cell epithelial cell of lower respiratory tract true A glandular epithelial cell of the endometrium. tmeehan 2011-07-08T03:54:08Z FMA:86489 cell glandular cell of endometrium A glandular epithelial cell of the endometrium. GOC:tfm A glandular epithelial cell of the esophagus. tmeehan 2011-07-08T03:55:57Z FMA:86548 cell glandular cell of esophagus true true A glandular epithelial cell of the esophagus. GOC:tfm A glandular epithelial cell of the large intestine. tmeehan 2011-07-08T04:03:01Z FMA:87194 cell glandular cell of the large intestine true A glandular epithelial cell of the large intestine. GOC:tfm A glandular epithelial cell that is part of the stomach. tmeehan 2011-07-11T01:20:35Z CALOHA:TS-1284 FMA:86554 cell glandular cell of stomach true A glandular epithelial cell that is part of the stomach. GOC:tfm terryh 2011-10-25T03:49:41Z cell kidney cortical cell true An endocrine cell that is part of the pancreas. cell pancreatic endocrine cell An endocrine cell that is part of the pancreas. GOC:dos Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 cell retinal cell Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. GOC:pr An epithelial cell that is part_of a umbilical artery. GOC:cjm umbilical artery epithelial cell epithelial cell of umbilical artery cardiac blood vessel endothelial cell cardiac endothelial cell A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites. paraxial mesoderm cell somitic mesoderm cell presomitic mesoderm cell paraxial cell A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites. GOC:NV PMID:11687492 A mesothelial cell that is part of the epicardium. mesothelial cell of epicardium Epithelial cell that is part of the colon epithelium. colonic epithelial cell colon epithelial cell Epithelial cell that is part of the colon epithelium. GOC:NV pronephric nephron tubule epithelial cell metanephric nephron tubule epithelial cell lung secretory cell An epithelial cell that is part of the urethra. FMA:256165 cell epithelial cell of urethra true An epithelial cell that is part of the urethra. GOC:tfm A mesothelial cell that is part of the dura mater. FMA:256516 squamous mesothelial cell of dura mater cell mesothelial cell of dura mater true A mesothelial cell that is part of the dura mater. GOC:tfm squamous mesothelial cell of dura mater FMA:256516 An endothelial cell that is part of the hepatic sinusoid. BTO:000125 FMA:62911 LSEC endotheliocyte of hepatic sinusoid liver senusoidal endothelial cell cell endothelial cell of hepatic sinusoid An endothelial cell that is part of the hepatic sinusoid. GOC:tfm LSEC PMID:30348985 endotheliocyte of hepatic sinusoid FMA:62911 liver senusoidal endothelial cell PMID:30348985 An endothelial cell that is part of the arteriole. FMA:67760 KUPO:0001097 cell endothelial cell of arteriole true An endothelial cell that is part of the arteriole. GOC:tfm A blood vessel endothelial cell that is part of an arterial endothelium. CL:0002542 BTO:0004758 FMA:67761 KUPO:0001095 arterial endothelial cell cell endothelial cell of artery A blood vessel endothelial cell that is part of an arterial endothelium. GOC:tfm An endothelial cell that is part of the venule. FMA:67762 cell endothelial cell of venule true An endothelial cell that is part of the venule. GOC:tfm An epithelial cell that is part of the gallbladder. FMA:67780 cell epithelial cell of gall bladder true An epithelial cell that is part of the gallbladder. GOC:tfm An epithelial cell that is part of the external acoustic meatus. FMA:70555 cell epithelial cell of external acoustic meatus true An epithelial cell that is part of the external acoustic meatus. GOC:tfm An epithelial cell that is part of the lacrimal sac. FMA:70560 cell epithelial cell of lacrimal sac An epithelial cell that is part of the lacrimal sac. GOC:tfm A mesothelial cell that is part of the anterior chamber of eyeball. FMA:70615 cell mesothelial cell of anterior chamber of eye true A mesothelial cell that is part of the anterior chamber of eyeball. GOC:tfm An epithelial cell that is part of the sweat gland. FMA:70952 cell epithelial cell of sweat gland An epithelial cell that is part of the sweat gland. GOC:tfm An epithelial cell that is part of the nephron. FMA:70965 cell epithelial cell of nephron An epithelial cell that is part of the nephron. GOC:tfm A mesothelial cell that is part of the parietal peritoneum. FMA:72142 cell mesothelial cell of parietal peritoneum A mesothelial cell that is part of the parietal peritoneum. GOC:tfm A mesothelial cell that is part of the visceral peritoneum. FMA:72143 cell mesothelial cell of visceral peritoneum A mesothelial cell that is part of the visceral peritoneum. GOC:tfm A mesothelial cell that is part of the peritoneum. FMA:86736 peritoneal mesothelial cell cell mesothelial cell of peritoneum true A mesothelial cell that is part of the peritoneum. GOC:tfm peritoneal mesothelial cell FMA:86736 A mesothelial cell that is part of the pleura. FMA:86737 pleural mesothelial cell cell mesothelial cell of pleura true A mesothelial cell that is part of the pleura. GOC:tfm pleural mesothelial cell FMA:86737 A mesothelial cell that is part of the parietal pleura. FMA:86738 cell mesothelial cell of parietal pleura A mesothelial cell that is part of the parietal pleura. GOC:tfm A mesothelial cell that is part of the visceral pleura. FMA:86739 cell mesothelial cell of visceral pleura A mesothelial cell that is part of the visceral pleura. GOC:tfm An epithelial cell that is part of a nephron tubule. FMA:86785 KUPO:0001022 kidney tubule epithelial cell cell This needs to be further defined as a juxtamedullary nephron. Will request the juxtamedullary nephron tubule class from UBERON. nephron tubule epithelial cell An epithelial cell that is part of a nephron tubule. GOC:tfm KUPO:0001010 cell kidney cell true KUPO:0001017 cell kidney medulla cell true KUPO:0001018 cell kidney pelvis cell true KUPO:0001020 cell kidney tubule cell KUPO:0001060 cell kidney medulla collecting duct epithelial cell KUPO:0001063 cell kidney cortex collecting duct epithelial cell KUPO:0001115 cell lower urinary tract cell true KUPO:0001116 cell ureteral cell true KUPO:0001119 cell ureter adventitial cell true KUPO:0001014 cell kidney blood vessel cell true KUPO:0001029 cell kidney arterial blood vessel cell true KUPO:0001030 cell kidney capillary endothelial cell KUPO:0001031 cell kidney venous blood vessel cell true KUPO:0001077 cell kidney cortex artery cell true KUPO:0001084 cell kidney cortex vein cell true KUPO:0001012 Wikipedia:Kidney_collecting_duct_cell cell kidney collecting duct cell KUPO:0001120 cell bladder cell KUPO:0001123 cell urethra cell An epithelial cell of the exocrine pancreas. FMA:70986 exocrine pancreas cell cell epithelial cell of exocrine pancreas An epithelial cell of the exocrine pancreas. GOC:tfm cl endothelial cell of lung pulmonary vessel endothelial cell lung endothelial cell BTO:0001141 cl PAEC cell pulmonary artery endothelial cell PAEC cell BTO:0001141 A vascular endothelial cell found in colon blood vessels. CALOHA:TS-2397 colon endothelial cells colonic endothelial cell colon endothelial cell A vascular endothelial cell found in colon blood vessels. NPX:PDR https://orcid.org/0000-0001-5208-3432 colon endothelial cells CALOHA:TS-2397 colonic endothelial cell CALOHA:TS-2397 Cell of the nasopharyngeal epithelium. CALOHA:TS-2398 nasopharynx respiratory epithelial cells nasopharyngeal epithelial cell Cell of the nasopharyngeal epithelium. NPX:PDR nasopharynx respiratory epithelial cells CALOHA:TS-2398 Squamous cell of uterine cervix epithelium. CALOHA:TS-1251 cervix squamous cell cervix squamous epithelial cell cervix, uterine squamous epithelial cells uterine cervix squamous epithelial cell uterine cervix squamous epithelial cells uterine cervix squamous cell Squamous cell of uterine cervix epithelium. NPX:PDR cervix squamous cell CALOHA:TS-1251 cervix squamous epithelial cell CALOHA:TS-1251 cervix, uterine squamous epithelial cells CALOHA:TS-1251 uterine cervix squamous epithelial cell CALOHA:TS-1251 uterine cervix squamous epithelial cells CALOHA:TS-1251 Squamous cell of oral epithelium. CALOHA:TS-1252 oral cavity mucosa squamous cell oral cavity mucosa squamous epithelial cell oral mucosa squamous epithelial cell oral mucosa squamous epithelial cells oral mucosa squamous cell Squamous cell of oral epithelium. NPX:PDR oral cavity mucosa squamous cell CALOHA:TS-1252 oral cavity mucosa squamous epithelial cell CALOHA:TS-1252 oral mucosa squamous epithelial cell CALOHA:TS-1252 oral mucosa squamous epithelial cells CALOHA:TS-1252 Squamous cell of tonsil epithelium. CALOHA:TS-1253 tonsil squamous epithelial cell tonsil squamous epithelial cells tonsillar squamous cell tonsillar squamous epithelial cell tonsil squamous cell Squamous cell of tonsil epithelium. NPX:PDR tonsil squamous epithelial cell CALOHA:TS-1253 tonsil squamous epithelial cells CALOHA:TS-1253 tonsillar squamous cell CALOHA:TS-1253 tonsillar squamous epithelial cell CALOHA:TS-1253 Squamous cell of vaginal epithelium. CALOHA:TS-1254 vagina squamous epithelial cell vagina squamous epithelial cells vaginal squamous cell vaginal squamous epithelial cell vagina squamous cell Squamous cell of vaginal epithelium. NPX:PDR vagina squamous epithelial cell CALOHA:TS-1254 vagina squamous epithelial cells CALOHA:TS-1254 vaginal squamous cell CALOHA:TS-1254 vaginal squamous epithelial cell CALOHA:TS-1254 Glandular cell of uterine cervix epithelium. CALOHA:TS-1273 cervix glandular cell cervix, uterine glandular cell cervix, uterine glandular cells uterine cervix glandular cell Glandular cell of uterine cervix epithelium. NPX:PDR cervix glandular cell CALOHA:TS-1273 cervix, uterine glandular cell CALOHA:TS-1273 cervix, uterine glandular cells CALOHA:TS-1273 Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1274 colon glandular cells colon glandular cell Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. NPX:PDR colon glandular cells CALOHA:TS-1274 Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell. CALOHA:TS-1275 duodenum glandular cells duodenum glandular cell Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell. NPX:PDR duodenum glandular cells CALOHA:TS-1275 Glandular cell of epididymal epithelium. CALOHA:TS-1276 epididymal glandular cell epididymis glandular cells epididymis glandular cell Glandular cell of epididymal epithelium. NPX:PDR epididymal glandular cell CALOHA:TS-1276 epididymis glandular cells CALOHA:TS-1276 Glandular cell of oviduct epithelium. Example: peg cells, ciliated cells. CALOHA:TS-1277 fallopian tube glandular cell fallopian tube glandular cells uterine tube glandular cell oviduct glandular cell Glandular cell of oviduct epithelium. Example: peg cells, ciliated cells. HPA:HPA NPX:PDR fallopian tube glandular cell CALOHA:TS-1277 fallopian tube glandular cells CALOHA:TS-1277 uterine tube glandular cell CALOHA:TS-1277 Glandular cell of gall bladder epithelium. CALOHA:TS-1278 gall bladder glandular cells gallbladder glandular cell gallbladder glandular cells gall bladder glandular cell Glandular cell of gall bladder epithelium. NPX:PDR gall bladder glandular cells CALOHA:TS-1278 gallbladder glandular cell CALOHA:TS-1278 gallbladder glandular cells CALOHA:TS-1278 Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells. CALOHA:TS-1279 parathyroid gland glandular cell parathyroid gland glandular cells parathyroid glandular cell Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells. HPA:HPA NPX:PDR parathyroid gland glandular cell CALOHA:TS-1279 parathyroid gland glandular cells CALOHA:TS-1279 Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1281 rectal glandular cell rectum glandular cells rectum glandular cell Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells. NPX:PDR rectal glandular cell CALOHA:TS-1281 rectum glandular cells CALOHA:TS-1281 Glandular cell of salivary gland. Example: Serous cells, mucous cells, cuboidal epithelial cells of the intercalated ducts, simple cuboidal epithelium of the striated ducts, epithelial cells of excretory ducts. CALOHA:TS-1282 salivary gland glandular cells salivary gland glandular cell Glandular cell of salivary gland. Example: Serous cells, mucous cells, cuboidal epithelial cells of the intercalated ducts, simple cuboidal epithelium of the striated ducts, epithelial cells of excretory ducts. HPA:HPA NPX:PDR salivary gland glandular cells CALOHA:TS-1282 Glandular cell of seminal vesicle epithelium. CALOHA:TS-1283 seminal vesicle glandular cells seminal vesicle glandular cell Glandular cell of seminal vesicle epithelium. NPX:PDR seminal vesicle glandular cells CALOHA:TS-1283 A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) . CALOHA:TS-1286 FMA:86928 small bowel glandular cell small intestinal glandular cell small intestine glandular cells small intestine glandular cell A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) . NCI_Thesaurus:Small_Intestinal_Glandular_Cell NPX:PDR small bowel glandular cell CALOHA:TS-1286 small intestinal glandular cell CALOHA:TS-1286 small intestine glandular cells CALOHA:TS-1286 Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts. BTO:0000028 CALOHA:TS-1242 exocrine pancreas glandular cell pancreas exocrine glandular cells pancreas exocrine glandular cell Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts. HPA:HPA NPX:PDR exocrine pancreas glandular cell CALOHA:TS-1242 pancreas exocrine glandular cells CALOHA:TS-1242 Hormone secreting cell located in the cortex of adrenal gland. Glandular cells in the adrenal cortex secrete mineralocorticoids, glucocorticoids and androgens. CALOHA:TS-2177 adrenal gland glandular cells adrenal glandular cell suprarenal gland glandular cell adrenal gland glandular cell Hormone secreting cell located in the cortex of adrenal gland. Glandular cells in the adrenal cortex secrete mineralocorticoids, glucocorticoids and androgens. NPX:PDR adrenal gland glandular cells CALOHA:TS-2177 adrenal glandular cell CALOHA:TS-2177 suprarenal gland glandular cell CALOHA:TS-2177 Endothelial cells forming the walls of the capillaries within the cerebral cortex. CALOHA:TS-2372 cerebral cortex endothelial cells endothelial cells of cerebral cortex cerebral cortex endothelial cell Endothelial cells forming the walls of the capillaries within the cerebral cortex. NPX:PDR cerebral cortex endothelial cells CALOHA:TS-2372 endothelial cells of cerebral cortex CALOHA:TS-2372 Any cell that is part of a pituitary gland. TermGenie 2014-03-26T22:14:56Z cell CL:2000004 pituitary gland cell Any cell that is part of a pituitary gland. GOC:TermGenie Any blood vessel endothelial cell that is part of a dermis. TermGenie 2014-06-04T15:12:06Z cell CL:2000010 dermis blood vessel endothelial cell Any blood vessel endothelial cell that is part of a dermis. GOC:TermGenie Any native cell that is part of a inner cell mass. TermGenie 2014-06-24T23:16:53Z cell CL:2000020 inner cell mass cell Any native cell that is part of a inner cell mass. GOC:TermGenie Any native cell that is part of a sebaceous gland. TermGenie 2014-06-24T23:17:00Z cell CL:2000021 sebaceous gland cell Any native cell that is part of a sebaceous gland. GOC:TermGenie Any native cell that is part of a cardiac septum. TermGenie 2014-06-24T23:17:07Z cell CL:2000022 cardiac septum cell Any native cell that is part of a cardiac septum. GOC:TermGenie Any native cell that is part of a hypothalamus. TermGenie 2014-06-25T01:17:50Z cell CL:2000030 hypothalamus cell Any native cell that is part of a hypothalamus. GOC:TermGenie Any endothelial cell of artery that is part of a umbilical cord. TermGenie 2014-10-06T19:01:48Z cell CL:2000052 http://www.sciencellonline.com/site/productInformation.php?keyword=8010 umbilical artery endothelial cell Any endothelial cell of artery that is part of a umbilical cord. GOC:TermGenie Any endothelial cell that is part of a spleen. TermGenie 2014-10-06T19:06:04Z cell CL:2000053 http://www.sciencellonline.com/site/productInformation.php?keyword=5500 splenic endothelial cell Any endothelial cell that is part of a spleen. GOC:TermGenie Any epithelial cell that is part of a female gonad. TermGenie 2014-10-07T17:59:13Z cell CL:2000064 http://www.sciencellonline.com/site/productInformation.php?keyword=7310 ovarian surface epithelial cell Any epithelial cell that is part of a female gonad. GOC:TermGenie Any vein endothelial cell that is part of a hindlimb stylopod. TermGenie 2014-12-02T18:40:47Z cell CL:2000076 hindlimb stylopod vein endothelial cell Any vein endothelial cell that is part of a hindlimb stylopod. GOC:TermGenie A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. tmeehan 2009-12-23T10:53:24Z cell increased nucleus size A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell. GOC:tfm A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system. environmental environmental material Food material for humans and animals which is processed with the intention that it be consumable as a whole or added to other food products. Damion Dooley Foodon product type https://en.wikipedia.org/wiki/Food The FoodOn "food product" class is provided as a branch under which new food product categories and food products themselves can be placed. Here classes are provided to differentiate a food product by its food composition, processing and/or consumption characteristics. This avoids brand name products but it may include generic food dish categories. It has a much greater depth and polyhierarchy than other agency product type schemes have in an effort to group related products together. The upper level basis of this tree originated in the environment ontology (ENVO) and from the US Code of Federal Regulations. food product A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. SUBSET_SIREN:F17332 meat food product A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals. http://en.wikipedia.org/wiki/Meat This class includes food products which are derived from or produced by a plant. plant food product chicken meat food product Meat from bovines, especially domestic cattle (cows). beef food product Meat from bovines, especially domestic cattle (cows). http://en.wikipedia.org/wiki/Beef A seafood product is a vertebrate or invertibrate organism from an aquatic environment. Some of the subclasses are currently freshwater organisms. Damion Dooley seafood product fermented dairy food product fermented fish or seafood food product sea water fish food product plant fruit food product fermented fruit food product sugar condiment A lipid material derived from plants. Physically, oils are liquid at room temperature. Damion Dooley vegetable oil food product A food product which is derived from or produced by an animal that has a vertibrae. Damion Dooley vertebrate animal food product cereal grain food product Damion Dooley http://langual.org 2019-06-11T07:25:19Z SUBSET_SIREN:F5644 alcoholic beverage subset_siren SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) fermented beverage A food product made from an avian egg. avian egg food product bovine dairy food product cattle dairy food product A food product made from domesticated bird meat. Damion Dooley poultry meat food product A relish, sauce, or seasoning added to food to impart a particular flavour or to complement the dish. Damion Dooley https://en.wikipedia.org/wiki/Condiment condiment food product bovine meat food product fruit juice food product A food product deriving primarily from corn (maize). Damion Dooley maize food product maize (corn) food product cruciferous food product The default nut product is a whole, raw nut - meaning that the kernel is whole, and moderately or significantly dried, but not baked. Minimal references to nuts often leave ambiguous whether the shell is on or off. "I ate a peanut" doesn't clarify whether I ate a shell-off nut or whether I did the shelling. Damion Dooley SUBSET_SIREN:F16972 nut food product plant seed food product plant lipid food product plant stem food product invertebrate animal food product barley food product A product of the dry seeds of plants of the genus Pisum. Damion Dooley http://en.wikipedia.org/wiki/Legume dry pea food product PULSES are annual leguminous crops yielding from one to 12 grains or seeds of variable size, shape and colour within a pod. They are used for both food and feed. The term "pulses" is limited to crops harvested solely for dry grain, thereby excludingcrops harvested green for food (green peas, green beans, etc.) which are classified as vegetable crops. Also excluded are those crops used mainly for oil extraction (e.g.soybeand and groundnuts) and leguminous crops (e.g. seeds of clover and alfalfa) that are used exclusively for sowing purposes. Damion Dooley http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef04e.htm#4.02 pulse pulses pulse food product https://en.wikipedia.org/wiki/Legume#Classification_of_pulses A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment. Damion Dooley http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef10e.htm#1.01 http://www.langual.org/langual_thesaurus.asp?termid=H0151 herb and spice herb or spice spice or herb animal lipid food product A fish food product includes products made from any fish species (aquatic vertebrate with gills and fins). Damion Dooley fish food product avian food product plant derived beverage plant derived fermented beverage nonfermented plant derived beverage product A dairy food product has mammilian milk or a milk component as an ingredient. Damion Dooley http://www.langual.org/langual_thesaurus.asp?termid=H0242 dairy product milk product dairy food product milk or milk based food product Are all fermented foods considered preserved to some extent? Damion Dooley food (fermented) Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food. vegetable food product Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. botanical fruit food product Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. http://eurovoc.europa.eu/drupal/?q=request&amp;uri=http://eurovoc.europa.eu/1115 http://oek1.fao.org/skosmos/agrovoc/en/page/c_3119 http://www.fao.org/pollination/resources/glossary/en/ https://en.wikipedia.org/wiki/Fruit A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995) http://www.fao.org/pollination/resources/glossary/en/ legume http://purl.obolibrary.org/obo/FOODON_03411254 http://purl.obolibrary.org/obo/FOODON_03411338 legume food product A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. Regarding American regulatory aspects of egg products, see this summary: https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-graphic-000077 egg food product A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. Wikipedia:Egg_%28food%29 A hen egg food product is any food product consisting mainly of hen eggs or derivatives. https://en.wikipedia.org/wiki/Egg_as_food SUBSET_SIREN:F1074 hen egg food product A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants. Damion Dooley poultry food product shellfish food product Damion Dooley A fermentation process in which either carbohydrates, proteins or fats are modified through microbial, enzymatic and/or other biological process. food fermentation Hoi-dong is fermented sea mussel http://orcid.org/0000-0002-1816-4260 hoi-dong Fermented meat product is any product made primarily of meat subjected to a fermentation process. Damion Dooley fermented meat product An alcoholic drink (or alcoholic beverage) is a drink that contains ethanol, a type of alcohol produced by fermentation of grains, fruits, or other sources of sugar. Damion Dooley https://en.m.wikipedia.org/wiki/Alcoholic_drink SUBSET_SIREN:F10770 alcoholic beverage animal based refined or partially-refined food product barley vegetable food product A bean vegetable food product is a human or animal food product - such as a snap, shell or dry bean product - derived from the fruit pod, seed, or leaf of one of several genera of the flowering plant family Fabaceae. Note, this was previously labelled "Bean (vegetable) food product". We have been listing both dry and freshly harvested moist beans here, so have broadened the name scope. Damion Dooley bean food product http://purl.obolibrary.org/obo/FOODON_00002428 http://www.fao.org/es/faodef/fdef04e.htm#4.02 https://oconto.extension.wisc.edu/files/2011/02/The-Importance-of-Dry-Beans-in-Your-Diet.pdf A broad bean food product is a product derived from the broad bean plant. Damion Dooley broad bean food product broccoli vegetable food product brussels sprout vegetable food product A cabbage vegetable food product is a food product derived from the head or leaf portion of a cabbage plant. Damion Dooley 2019-06-27T13:30:10Z https://upload.wikimedia.org/wikipedia/commons/thumb/6/6f/Cabbage_and_cross_section_on_white.jpg/640px-Cabbage_and_cross_section_on_white.jpg cabbage vegetable food product A food product that derives from a cauliflower plant. cauliflower vegetable food product cephalopod food product A food product which normally exists as an ingredient to another food product, rather than eaten on its own, and is more complex than a chemical food component. food product component cloves clove food product vegetable corn food product cow milk based food product crustacean food product Damion Dooley Damion Dooley's note: This category was created to organize SIREN inspired food products. It will probably get merged with the upper level 'dietary supplement' food product type items. dietary or therapeutic formulation food product fermented cereal beverage A product made from the North American term for maize (Zea mays) grown for livestock fodder (silage), ethanol, cereal and processed food products. The principal field corn varieties are dent corn, flint corn, flour corn (also known as soft corn) which includes blue corn (Zea mays amylacea), and waxy corn. Damion Dooley dry corn food product dry corn field corn food product field corn sweetener product fish refined food product food flavoring or seasoning product food supplement food product fruit based alcoholic beverage gluten refined food product grain based alcoholic beverage human milk based food product barley malt beverage mollusk food product mollusc food product mussel food product nonalcoholic beverage A food product having peanuts as an ingredient. Damion Dooley http://langual.org 2019-06-19T22:56:38Z SUBSET_SIREN:F1350 subset_siren SIREN DB annotation: * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) peanut food product plant based refined or partially-refined food product An edible plant fat or oil product with characteristics that consumers desire such as bland flavour and odour, clear appearance, light colour, stability to oxidation and suitability for frying, and which is the result of a refining process that removes free fatty acids. Damion Dooley plant fat or oil refined food product plant floret vegetable food product plant fruit vegetable food product plant head vegetable food product food product by consumer group plant seed vegetable food product plant stem or spear vegetable food product plant sweetener organ meat product pumpkin food product rape fat or oil refined food product rapeseed food product refined or partially-refined food product sesame food product soybean refined food product soybean seed (field) food product http://purl.obolibrary.org/obo/FOODON_00002266 A soybean food product is a product derived from the soybean plant. Damion Dooley soy product soybean food product http://purl.obolibrary.org/obo/FOODON_00002265 squash food product sugar based cacao food product sugar cane refined or partially-refined food product sunflower food product http://www.langual.org/langual_thesaurus.asp?termid=H0202 sweetener food product vitamin and mineral food supplement food product vitamin as food supplement food product A meal type is the name of an eating occasion that may have location, food type, or other customary contextual features. (Damion's 1st draft definition) Damion Dooley food product by meal type A food product consisting of food material derived primarily from a single organism. Damion Dooley food product by organism Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience food foodstuff nourishment sustenance food material A process involving the physical transformation of a food source or food product into some derived organic material or food product Damion Dooley food transformation process Familiar examples of invertebrates include arthropods (insects, arachnids, crustaceans, and myriapods), mollusks (chitons, snails, bivalves, squids, and octopuses), annelids (earthworms and leeches), and cnidarians (hydras, jellyfishes, sea anemones, and corals).[wikipedia] Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a backbone or spine), derived from the notochord. This includes all animals apart from the subphylum Vertebrata. Damion Dooley https://en.wikipedia.org/wiki/Invertebrate animal invertebrate animal A class which contains food product categories qualified by a quality such as granularity or temperature, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. Damion Dooley food product by quality food object quality A food product consisting of food material derived from ingredients sourced from multiple organisms. Damion Dooley 2019-01-23T22:40:32Z multi-ingredient The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57 Namely, how to characterize the threshold of ingredients that make for multi-component classification? Salt, pepper, spices wouldn't normally make a food multi-component? multi-component food product Dairy cattle are a type of cattle bred for the ability to produce large quantities of milk, from which dairy products are made. This class covers both male and female members of a dairy breed. Damion Dooley https://en.wikipedia.org/wiki/Dairy_cattle 2019-01-26T22:49:27Z dairy cattle https://en.wikipedia.org/wiki/List_of_dairy_cattle_breeds Taurine cattle (Bos taurus taurus), also called European cattle, are a subspecies of domesticated cattle originating in the Near East. Both taurine cattle and indicine cattle (zebus) are descended from the aurochs. Taurine cattle were originally considered a distinct species, but are now typically grouped with zebus and aurochs into one species, Bos taurus. Most modern breeds of cattle are taurine cattle. Damion Dooley https://en.wikipedia.org/wiki/Taurine_cattle 2019-01-28T02:41:04Z http://www.langual.org/langual_thesaurus.asp?termid=B5186 taurine cattle An aquatic invertebrate may live entirely beneath the water, or may live upon its surface or on the plants surrounding it. Some breathe air, others breathe water. To move, they may walk, swim, float, skate, fly or glide on their bellies—or they may not move much at all. Because snails are members of gastropod, a subclass of molluscs, ... leading to aquatic invertebrates, we can't make aquatic invertebrates disjoint with terrestrial invertebrates. Damion Dooley https://nature.mdc.mo.gov/discover-nature/general-species-information/aquatic-invertebrate-facts 2019-04-29T19:23:38Z aquatic invertebrate Damion Dooley 2019-05-21T22:37:06Z Aves avian bird avian animal A food product organized by the process which it results from. Damion Dooley 2019-05-23T23:02:07Z food product by process A lipid food product is a food product made primarily of plant or animal fat or oil Damion Dooley 2019-06-11T09:18:41Z fats and oils oils and fats lipid food product Damion Dooley 2019-06-27T20:39:45Z canola plant food product A whole bean is a bean having an intact seed shape and composition. Damion Dooley's note. This could be enhanced to explicitly state the anatomical parts of a seed - seed coat, cotyledons, embryo etc. Currently the Plant Ontology is not explicit about this yet. Damion Dooley 2019-06-29T15:02:04Z bean bean (whole) Damion Dooley 2019-07-12T17:18:31Z pea food product Damion Dooley 2019-07-16T15:15:04Z broad bean (whole, raw) A liver food product is a food product that derives from one or more liver organs. Damion Dooley 2019-08-02T18:22:37Z liver food product A kidney food product is a food product that derives from one or more kidney organs Damion Dooley 2019-08-02T18:27:53Z kidney food product The red cabbage (purple-leaved varieties of Brassica oleracea Capitata Group) is a kind of cabbage, also known as purple cabbage, red kraut, or blue kraut after preparation. Its leaves are coloured dark red/purple. 2019-08-09T21:59:31Z red cabbage A multicellular eukaryotic heterotrophic organism within the kingdom Animalia. 2019-08-14T18:02:36Z animal 2019-08-24T15:43:48Z saffron saffron food product A food product not including meat and animal tissue products (such as gelatin or animal-derived rennet). https://en.wikipedia.org/wiki/Vegetarian_cuisine 2019-09-11T21:12:43Z vegetarian food vegetarian food product A seed of a peanut plant (Arachis hypogaea). http://orcid.org/0000-0002-8844-9165 FoodOn peanut peanut (whole) 2019-11-15T20:12:48Z hen 2020-01-08T00:20:27Z echinoderm food product A genus of plants in the mustard family (Brassicaceae). The members of the genus are informally known as cruciferous vegetables, cabbages, or mustard plants. bok choy vegetable food product bomdong vegetable food product broccolini vegetable food product chinese cabbage vegetable food product choy sum vegetable food product collard greens vegetable food product gai lan vegetable food product komatsuna vegetable food product mizuna vegetable food product rutabaga vegetable food product savoy cabbage vegetable food product tatsoi vegetable food product cole crop vegetable food product cruciferous vegetable food product brassica vegetable food product Food contact materials are materials that are intended to be in contact with food. These can be things that are quite obvious like a glass or a can for soft drinks as well as machinery in a food factory or a coffee machine. 2020-07-31T17:07:09Z food contact material 2020-09-09T19:28:43Z Maize plant A whole raw shell-off hen egg is the egg yolk and egg white obtained from a cracked egg. Damion Dooley http://langual.org SUBSET_SIREN:F1075 subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'whole egg' (http://purl.obolibrary.org/obo/FOODON_03420274) hen egg (whole, shell off, raw) A seed of a broad bean plant (Vicia faba). http://orcid.org/0000-0002-8844-9165 FoodOn http://langual.org SUBSET_SIREN:F1227 Windsor bean broad bean broadbean faba bean fava bean Horse bean field bean tic bean tick bean subset_siren broad bean (whole) http://langual.org SUBSET_SIREN:F1305 subset_siren fructose food product A pod of a peanut plant. Damion Dooley http://langual.org SUBSET_SIREN:F1353 subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * derives from 'seed in shell or hull' (http://purl.obolibrary.org/obo/FOODON_03420227) peanut pod http://langual.org SUBSET_SIREN:F1403 fresh bean subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) bean (whole, raw) A seed of a soyabean plant (Glycine max). http://orcid.org/0000-0002-8844-9165 FoodOn http://langual.org SUBSET_SIREN:F1415 soy bean soya bean soybean subset_siren soybean (whole) http://langual.org SUBSET_SIREN:F1444 subset_siren SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) * derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) vegetable juice food product A bean substance is a substance made by processing seed from a bean plant. Damion Dooley's note: This class is intended to provide the most generic reference to bean, as it does not imply any more information about the state of a bean - whether it is whole or in fragments, or fragments of several beans, whether it is dry, raw, or cooked etc. Damion Dooley https://en.wikipedia.org/wiki/Bean http://langual.org SUBSET_SIREN:F1467 subset_siren SIREN DB annotation: * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) bean substance http://langual.org SUBSET_SIREN:F1619 subset_siren SIREN DB annotation: * has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) * derives from 'germinated or sprouted seed' (http://purl.obolibrary.org/obo/FOODON_03420102) * formed as a result of 'flavoring, spice or herb added, natural' (http://purl.obolibrary.org/obo/FOODON_03460229) * formed as a result of 'alcohol fermentation process' (http://purl.obolibrary.org/obo/FOODON_03460232) * formed as a result of 'carbonated by fermentation' (http://purl.obolibrary.org/obo/FOODON_03460246) * formed as a result of 'preservation by filtration' (http://purl.obolibrary.org/obo/FOODON_03470121) beer A liquid prepared for consumption, or a product that can be combined with water or milk to make one. Damion Dooley http://langual.org 2019-09-12T00:00:00 beverage food product Fruit which has not been subjected to heat treatment, but which may have other mechanical processes such as slicing applied to it. http://langual.org SUBSET_SIREN:F2007 subset_siren SIREN DB annotation: * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) fruit (raw) http://langual.org SUBSET_SIREN:F2008 subset_siren SIREN DB annotation: * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) vegetable (raw) http://langual.org milk SUBSET_SIREN:F2116 cow milk subset_siren SIREN DB annotation: * has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) * derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) cow milk (liquid) http://langual.org SUBSET_SIREN:F2389 soy beverage subset_siren SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) soybean beverage http://langual.org SUBSET_SIREN:F2578 subset_siren SIREN DB annotation: * has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) * derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) canola oil http://langual.org SUBSET_SIREN:F3588 subset_siren SIREN DB annotation: * has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) * has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) * derives from 'sucrose' (http://purl.obolibrary.org/obo/CHEBI_17992) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) * has substance added 'flavoring or spice extract or concentrate added' (http://purl.obolibrary.org/obo/FOODON_03460100) * has substance added 'chocolate or cocoa added' (http://purl.obolibrary.org/obo/FOODON_03460231) * has substance added 'vegetable fat or oil added' (http://purl.obolibrary.org/obo/FOODON_03460263) dark chocolate Breast milk is the milk produced by the breasts (or mammary glands) of a human female to feed a child. https://en.wikipedia.org/wiki/Breast_milk http://langual.org SUBSET_SIREN:F3918 subset_siren SIREN DB annotation: * has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) * derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) human milk (raw) http://langual.org SUBSET_SIREN:F4497 subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) edible seed food product http://langual.org SUBSET_SIREN:F4616 subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'shelled egg' (http://purl.obolibrary.org/obo/UBERON_0007379) hen egg (whole, shell on, raw) Note that this allows for several kinds of fruit in one sample, e.g. "some fruit (whole,raw)" allows "apple (whole, raw)" and "orange (whole, raw)". Damion Dooley http://langual.org SUBSET_SIREN:F4644 fruit fruits subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) fruit (whole, raw) http://langual.org SUBSET_SIREN:F4869 sunflower seed subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) sunflower seed (whole kernel, raw) http://langual.org SUBSET_SIREN:F4870 subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) pumpkin seed (shell off) http://langual.org SUBSET_SIREN:F4996 subset_siren SIREN DB annotation: * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) soybean substance http://langual.org SUBSET_SIREN:F5288 subset_siren SIREN DB annotation: * has quality 'liquid, high viscosity, with small particles' (http://purl.obolibrary.org/obo/FOODON_03430121) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'extract, concentrate or isolate of plant or animal' (http://purl.obolibrary.org/obo/FOODON_03420228) sugar cane juice (pure) http://langual.org SUBSET_SIREN:F6123 subset_siren SIREN DB annotation: * has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) * derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) fish oil http://langual.org SUBSET_SIREN:F6429 subset_siren SIREN DB annotation: * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) meat (raw) http://langual.org SUBSET_SIREN:F6812 subset_siren SIREN DB annotation: * surrounded by 'can, bottle or jar' (http://purl.obolibrary.org/obo/FOODON_03490194) * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) * formed as a result of 'rehydration process' (http://purl.obolibrary.org/obo/FOODON_03460259) * formed as a result of 'sterilization by heating' (http://purl.obolibrary.org/obo/FOODON_03470123) peas (whole, rehydrated, canned) http://langual.org raw milk SUBSET_SIREN:F7455 milk subset_siren SIREN DB annotation: * has quality 'liquid, low viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430123) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) * has consumer 'not pasteurized claim or use' (http://purl.obolibrary.org/obo/FOODON_03510121) cow milk (raw) A whole raw liver is a whole liver organ obtained from an animal during a butchery process. Damion Dooley http://langual.org SUBSET_SIREN:F9772 liver subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'liver' (http://purl.obolibrary.org/obo/UBERON_0002107) liver (whole, raw) http://langual.org SUBSET_SIREN:F10006 subset_siren SIREN DB annotation: * derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) * formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) * formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) fermented bean product http://langual.org SUBSET_SIREN:F10043 canola meal subset_siren SIREN DB annotation: * has quality 'medium ground' (http://purl.obolibrary.org/obo/FOODON_03430117) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) * formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) * formed as a result of 'fat removal process' (http://purl.obolibrary.org/obo/FOODON_03460161) * has consumer 'food animal as consumer' (http://purl.obolibrary.org/obo/FOODON_03510015) rapeseed meal Hominy is a food produced from dried maize (corn) kernels that have been treated with an alkali, in a process called nixtamalization (nextamalli is the Nahuatl word for "hominy"). https://en.wikipedia.org/wiki/Hominy http://langual.org SUBSET_SIREN:F10226 paatsami subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * derives from 'seed, skin removed, germ removed (endosperm)' (http://purl.obolibrary.org/obo/FOODON_03420208) * formed as a result of 'food alkalization process' (http://purl.obolibrary.org/obo/FOODON_03460206) hominy http://m.grandcanyonnews.com/news/2009/feb/17/hopi-recipes-promote-healthy-eating-habits/ http://langual.org SUBSET_SIREN:F10306 sesame subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) sesame seed http://langual.org SUBSET_SIREN:F10387 subset_siren SIREN DB annotation: * has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) * derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) oil http://langual.org SUBSET_SIREN:F10482 subset_siren SIREN DB annotation: * has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) * derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) * formed as a result of 'food bleaching process' (http://purl.obolibrary.org/obo/FOODON_03460197) rapeseed oil http://langual.org SUBSET_SIREN:F10664 subset_siren SIREN DB annotation: * has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) * has substance added 'nutrient or dietary substance added' (http://purl.obolibrary.org/obo/FOODON_03460194) * has consumer 'dietary claim or use' (http://purl.obolibrary.org/obo/FOODON_03510023) vitamin supplement, prenatal http://langual.org SUBSET_SIREN:F10791 subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) corn (on-the-cob, kernel or parts) A whole raw kidney is a kidney obtained from an animal during a butchery process. http://langual.org SUBSET_SIREN:F10898 kidney subset_siren SIREN DB annotation: * has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) * derives from 'kidney' (http://purl.obolibrary.org/obo/UBERON_0002113) kidney (whole, raw) http://langual.org SUBSET_SIREN:F11126 subset_siren SIREN DB annotation: * has quality 'not heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440003) food (raw) http://langual.org SUBSET_SIREN:F11737 subset_siren processed food product http://langual.org SUBSET_SIREN:F15149 subset_siren SIREN DB annotation: * has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) * derives from 'high fructose syrup' (http://purl.obolibrary.org/obo/FOODON_03420272) corn syrup (high fructose) http://langual.org SUBSET_SIREN:F15150 subset_siren SIREN DB annotation: * derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) mammalian milk product http://langual.org SUBSET_SIREN:F15169 subset_siren SIREN DB annotation: * has substance added 'mineral added' (http://purl.obolibrary.org/obo/FOODON_03460159) * has substance added http://purl.obolibrary.org/obo/FOODON_03460163 * has substance added 'nutrient or dietary substance added' (http://purl.obolibrary.org/obo/FOODON_03460194) vitamin and mineral dietary supplement http://langual.org SUBSET_SIREN:F15171 subset_siren SIREN DB annotation: * has substance added http://purl.obolibrary.org/obo/FOODON_03460163 * has substance added 'nutrient or dietary substance added' (http://purl.obolibrary.org/obo/FOODON_03460194) multivitamin preparation A fish product is a home-made or commercially produced or retail or wholesale product containing substantial amounts of freshwater or saltwater fish and/or shellfish flesh. Note that this category should avoid items that mention a particular species of fish or shellfish. Damion Dooley http://langual.org SUBSET_SIREN:F15173 subset_siren SIREN DB annotation: * derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) fish product (unspecified species) https://en.wikipedia.org/wiki/Fish_products vegetable (whole or parts) http://langual.org SUBSET_SIREN:F15552 juice subset_siren juice beverage http://langual.org SUBSET_SIREN:F15615 subset_siren SIREN DB annotation: * derives from 'fruit part' (http://purl.obolibrary.org/obo/FOODON_03420167) fruit food product An egg produced by a chicken hen. http://langual.org egg SUBSET_SIREN:F16061 chicken egg hen egg subset_siren SIREN DB annotation: * derives from 'whole egg' (http://purl.obolibrary.org/obo/FOODON_03420274) This term is ambiguous about whether shell remains on egg or not, i.e. this encompasses both an uncooked egg in shell, or a boiled peeled egg, or a fried egg. hen egg (whole) http://langual.org SUBSET_SIREN:F16694 subset_siren SIREN DB annotation: * derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) vegetable fat food product A commercial product which is monosaccharide fructose, dried, ground, and of high purity. http://langual.org SUBSET_SIREN:F16754 crystaline fructose subset_siren SIREN DB annotation: * has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) * derives from 'fructose' (http://purl.obolibrary.org/obo/CHEBI_28757) * formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) * formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) crystaline fructose A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean). http://langual.org SUBSET_SIREN:F17170 subset_siren SIREN DB annotation: * derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) meat (whole or parts) Liquid food prepared from fruit (21 CFR 146). Products prepared from fruit juice by thickening with pectin are indexed under *FRUIT JELLY*; those thickened with gelatin are under *FRUIT BUTTER, JELLY, PRESERVE OR RELATED PRODUCT*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0104 fruit juice or related product (us cfr) Seasoned product that contains multiple ingredients and that is used in limited amounts to accompany other foods; excludes flavors, spices and herbs. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0105 condiment, dressing, gravy or sauce gravy, condiment, dressing or sauce sauce, condiment, dressing or gravy dressing, condiment, gravy or sauce (us cfr) Beverage containing no more than 0.5% alcohol; it may be flavored, sweetened or carbonated; includes soft drinks and steeped beverages; excludes milk in all forms, fruit juices, diluted fruit juices and vegetable juices. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0112 malt beverage, nonalcoholic nonalcoholic beverage (us cfr) Aromatic or pungent plant product used whole or ground as a seasoning in food products. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0113 herb or spice spice or herb (us cfr) A substance having greater than 2% of the caloric value of sucrose per equivalent unit of sweetening capacity. For example, the amount of such subtance having the sweetening capacity of 1 teaspoon of sucrose would have more than 0.4 calories (21 CFR 170.3(o)(21)). http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0118 nutritive carbohydrate sweetener sweetener, nutritive nutritive sweetener (us cfr) Any form of whole or milled grain, prepared grain product or starch containing product derived from non-grain sources. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0125 grain or starch product (us cfr) The liquid extracted or expressed from mature fruit with or without the application of heat. Includes concentrated juice and single-strength juice. If the single-strength juice is prepared from concentrate, then *WATER ADDED* should be used. Carbonated fruit juices are indexed by *FRUIT JUICE* or *FRUIT JUICE, DILUTED* and *CARBONATED* or the appropriate narrower term. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0127 juice, fruit fruit juice (us cfr) Extract, concentrate or isolate derived from a food source through one or more refining steps (see *EXTRACT, CONCENTRATE OR ISOLATE OF PLANT OR ANIMAL*) and marketed as such. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0129 refined or partially-refined food product (us cfr) Product that imparts or helps to impart a taste or aroma in food (21 CFR.170.3(n)(26). [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0133 seasoning or flavoring flavoring or seasoning (us cfr) A multiple-component food product typically containing a protein source, a vegetable, and a potato, rice or cereal-based component packaged to be served after heating, either as separate items or courses or mixed as recipe components; see 21 CFR 102.26, 102.28 and 104.47 for nutritional quality guidelines. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0139 compartmentalized dinner dinner with components separated in serving containers dinner, compartmentalized food packs with separate components heat and serve dinner multiple-course dinner tv dinner multicomponent meal (us cfr) Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0143 pie filling, fruit fruit or fruit product (us cfr) Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0148 milk or milk product (us cfr) Food product prepared by milling a grain or by producing flour, meal or grits from a non-grain source such as beans, starchy roots or tubers. Refined starch is indexed under *REFINED OR PARTIALLY REFINED FOOD PRODUCT*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0149 milled grain or starch product (us cfr) Meat (flesh and organs including blood and bone marrow) from mammals. Used for meat in all forms including cured meat, sausage or luncheon meat and meat product analogs. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0150 meat or meat product (from mammal) (us cfr) Vegetables in all forms except where a use-related product type descriptior (such as *PREPARED FOOD PRODUCT* or *SNACK FOOD*) takes precedence. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0152 vegetable or vegetable product (us cfr) Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0164 dairy product (us cfr) Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. Prepared foods often undergo several of the processes listed in *F. EXTENT OF HEAT TREATMENT* and *H. TREATMENT APPLIED*; these factors should be carefully considered in indexing. The classification of prepared food products emphasizes consumption characteristics. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0172 prepared dish prepared food product (us cfr) Food product that is usually pungent, tart, salty, or spicy and is used to enhance the flavors of other foods; includes catsup, relish, prepared mustard, prepared horseradish, and condiment sauces. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0179 relish or condiment condiment or relish (us cfr) Alcoholic beverage prepared from water, malted grain and hops (humulus) by brewing. Examples are beer, ale and malt liquor (27 CFR 7.10). http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0195 malt beverage (us cfr) Products of the flesh of animals. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0217 meat, poultry, seafood or related product (us cfr) Alcoholic or nonalcoholic beverage; excludes milk and milk-based beverages, fruit juices and fruit juice drinks, and vegetable juices. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0229 beverage (us cfr) A product added to a food item to achieve some degree of sweet taste; it may be nutritive or nonnutritive. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0237 sweetener (us cfr) Fruits and vegetables in all forms. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0257 fruit or vegetable product (us cfr) Nuts in all forms, including nut butters and pastes. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0260 nut or nut product (us cfr) Fresh egg in shell, liquid, frozen, dried egg or egg component, or egg product analog. Includes boiled, poached, scrambled, and fried eggs. Excludes prepared egg dishes, such as omelettes. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0261 egg or egg product (us cfr) The liquid extracted or expressed from mature vegetables with or without optional ingredients such as seasoning or salt. Products prepared from vegetable juice by thickening with gelatin or pectin are indexed under the broader term *VEGETABLE OR VEGETABLE PRODUCT*. For part or portion, index the part or the plant from which the juice was extracted, rather than *PLANT EXTRACT, CONCENTRATE, OR ISOLATE*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0264 juice, vegetable vegetable juice (us cfr) Flesh from fish or shellfish. Includes seafood product analogs and seafood-based sausage or luncheon meat as well as such products as squid ink and clam juice. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0267 seafood or seafood product (us cfr) Any form of cacao, cacao product, chocolate, chocolate product or chocolate product analog except chocolate candy; includes such products as cacao beans, cacao nibs, chocolate liquor, sweet or milk chocolate, and chocolate syrup; excludes flavors and extracts derived from cacao beans and chocolate- or cacao-flavored foods (21 CFR 163). [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0272 chocolate or cacao product cacao or chocolate product (us cfr) Meat (flesh and organs including blood and bone marrow) from poultry. Used for poultry meat in all forms including poultry product analogs and poultry-based sausage or luncheon meat. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0273 poultry or poultry product (us cfr) Beverage containing more than 0.5% alcohol; includes distilled spirits, malt beverage, and wine. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0278 alcoholic beverage (us cfr) Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0289 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. USA agency food product type http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0305 seed or seed product (us cfr) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0306 nut or seed product (us cfr) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0308 supplemental formulation (us cfr) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0309 therapeutic formulation dietary or therapeutic formulation (us cfr) Renamed from *PRODUCT TYPE, CODEX ALIMENTARIUS* in LanguaL 2008. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0352 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. international agency food product type An agency food product type is a class of food product defined by an agency or consortium. Damion Dooley http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0361 This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible. agency food product type Codex Alimentarius, Volume 2 - 1993, Section 2: Pesticide Residues in Food. The Codex Classification of food and animal feed commodities moving in trade and the description of the various items and groups of food and animal feedstuffs included in the present document have been developed by the Codex Committee on Pesticide Residues. It was first adopted by the 18th Session of the Codex Alimentarius Commission, (1989). The Codex Classification includes food commodities and animal feedstuffs for which Codex maximum residue limits will not necessarily be established. The Classification is intended to be as complete a listing of food commodities in trade as possible, classified into groups on the basis of the commodity's similar potential for pesticide residues. The Classification may also be appropriate for other purposes such as setting maximum levels for other types of residues or for other contaminants in food. The Codex Classification should be consulted in order to obtain a precise description of the food or animal feed commodities and, especially, in cases where Codex maximum residue limits have been set for groups of food and groups of animal feedstuffs. The Codex Classification is intended to promote harmonization of the terms used to describe commodities which are subject to maximum residue limits and of the approach to grouping commodities with similar potential for residue for which a common group maximum residue limit can be set. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0643 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. Codex Alimentarius classification of food and feed commodities http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0644 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. a. primary food commodities of plant origin (ccpr) Vegetables are foods derived from many different kinds of plants mostly annual and usually cultivated, commonly known by custom and tradition as "vegetables". In several countries, some of these commodities grown on large areas are distinguished as "field crops" or arable crops e.g. sugar beet. For the sake of convenience in this guide such crops are classified under Type 2 Vegetables. Exposure to pesticides is dependent on the particular part of the plant used for food and the growing practices. Vegetables may be consumed in whole or in part and in the form of fresh, dried or processed foods. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0650 02 vegetables (ccpr) Brassica (cole or cabbage) vegetables and flowerhead brassicas are foods derived from the leafy heads, stems and immature inflorescences of plants belonging to the genus Brassica or the family Cruciferae. Although Kohlrabi does not comply fully with the description above, for convenience and because of the similarity in residue behaviour the commodity is classified in this group. Koblrabi is a tuber-like enlargement of the stem. The edible part of the crop is partly protected from pesticides applied during the growing season by outer leaves, or skin (Kohlrabi). The entire vegetable after discarding obviously decomposed or withered leaves may be consumed. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A0675 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A1270 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. U.S. code of federal regulations, title 21 food product type https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl Index dietary/food supplements according to legal and market definitions. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A1298 food supplement nutritional supplement LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. The United States defines dietary supplements in the Dietary Supplement Health and Education Act of 1994 (DSHEA). Pub L 103-417, 108 STAT. 4235, (Oct. 25, 1994): A dietary supplement is a product taken by mouth that contains a "dietary ingredient" intended to supplement the diet. The "dietary ingredients" in these products may include: vitamins, minerals, herbs or other botanicals, amino acids, and substances such as enzymes, organ tissues, glandulars, and metabolites. Dietary supplements can also be extracts or concentrates, and may be found in many forms such as tablets, capsules, softgels, gelcaps, liquids, or powders. In the European Union, food supplements are framed by two kinds of regulations: - the EU vertical regulation relating to food supplements, composed with the directive 2002/46/CE (essentially for the definition of food supplements) and the regulation 1170/2009 (which lists the vitamins and minerals, and the chemical forms of the substances allowed in food supplements); - the EU transversal regulation relating to foodstuffs and especially the 2006/1924 regulation concerning nutrition and health claims, and the EU labeling transversal regulations, 90/496/EC and 2008/100/EC. The EU regulation 2002/46/CE defines food supplements as "foodstuffs the purpose of which is to supplement the normal diet and which are concentrated sources of nutrients or other substances with a nutritional or physiological effect, alone or in combination, marketed in dose form, namely forms such as capsules, pastilles, tablets, pills and other similar forms, sachets of powder, ampoules of liquids, drop dispensing bottles, and other similar forms of liquids and powders designed to be taken in measured small unit quantities". [Directive 2002/46/EC] Codex Alimentarius also includes supplements containing vitamins or dietary minerals [http://www.codexalimentarius.net/download/standards/10206/cxg_055e.pdf] dietary supplement Fibre supplements (or fiber supplements) are considered to be a form of a subgroup of functional dietary fibre, and in the United States are defined by the Institute of Medicine (IOM). According to the IOM, functional fibre "consists of isolated, non-digestible carbohydrates that have beneficial physiological effects in humans". Fibre supplements are widely available, and can be found in forms such as powders, tablets and capsules. Consumption of fibre supplements may be for: improving dietary intake, lowering blood cholesterol, alleviating irritable bowel syndrome, reducing the risk of colon cancer, and increasing feelings of satiety. [http://en.wikipedia.org/wiki/Fibre_supplements] WIKIPEDIA:Fibre_supplements http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=A1328 fiber fiber supplement fibre fibre supplement dietary supplement, fibre http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1001 pea plant edible seed cultivars Examples of stem vegetables are kohlrabi, celery, fennel and rhubarb. Examples of shoot vegetables are asparagus, hop, bamboo shoots and taugé. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1005 shoot vegetable stem or spear vegetable http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1006 fruit used as vegetable http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1009 polysaccharide-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1012 sugar-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1013 plant used for producing extract or concentrate http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1016 starch-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1017 oil-producing plant An aquatic animal is an animal, either vertebrate or invertebrate, which lives in the water for most or all of its lifetime. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1021 This is equivalent to: 'fish (food source)' or 'shellfish (food source)' or 'crustacean (food source)' or 'echinoderm (food source)' or 'coelenterate (food source)' However, this disjunction appears to be a burden on reasoners, and so this is currently not implemented. fish or lower water animal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1036 floret used as vegetable Any chemical or chemical mixture that exists in a food material or was added to a food material. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1041 LanguaL curation note: A chemical food component is a food substance derived from a nonliving source (e.g., salt, water or synthesized compounds). chemical food component http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1047 grain or seed-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1048 carbohydrate-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1049 protein-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1057 vegetable-producing plant, above-ground parts Mammals (from Latin mamma "breast") are vertebrate animals constituting the class Mammalia, and characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. Damion Dooley https://en.wikipedia.org/wiki/Mammal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1134 mammal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1140 fruit-producing plant Aquatic animals other than fish and shellfish http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1142 aquatic invertebrate animal (excluding shellfish) A legume is a plant or its fruit or seed in the family *Fabaceae* (or *Leguminosae*). Legumes are grown agriculturally, primarily for their grain seed called pulse, for livestock forage and silage, and as soil-enhancing green manure. Well-known legumes include alfalfa, clover, peas, beans, chickpeas, lentils, lupin bean, mesquite, carob, soybeans, peanuts and tamarind. [https://en.wikipedia.org/wiki/Legume] http://langual.org http://eol.org/pages/4277 http://www.langual.org/langual_thesaurus.asp?termid=B1156 fabaceae pod or seed vegetable plant Cattle (colloquially cows) are the most common type of large domesticated ungulates. They are a prominent modern member of the subfamily *Bovinae*, are the most widespread species of the genus *Bos*, and are most commonly classified collectively as *Bos taurus*... with three subspecies: *Bos taurus primigenius, Bos taurus indicus, Bos taurus taurus*. WIKIPEDIA:Cattle http://langual.org ITIS:183838 MSW3:14200687 http://eol.org/pages/328699 http://www.langual.org/langual_thesaurus.asp?termid=B1161 Bos taurus Linnaeus, 1758 cow auroch bos spp. bos taurus domesticated cattle cattle https://en.wikipedia.org/wiki/List_of_cattle_breeds http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1174 edible seed producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1179 flavor-producing plant herb-producing plant spice or flavor-producing plant Winter squash is an annual fruit representing several squash species within the genus Cucurbita. It differs from summer squash in that it is harvested and eaten in the mature fruit stage when the seeds within have matured fully and the skin has hardened into a tough rind. At this stage, most varieties of this fruit can be stored for use during the winter. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1189 curcurbita winter squash Cucurbita moschata Cucurbita pepo cucurbita maxima winter squash plant Californiacondor http://langual.org GRIN:12606 MANSFELD:4153 http://www.langual.org/langual_thesaurus.asp?termid=B1190 Cucurbita pepo L. cucurbita pepo yellow crookneck squash yellow squash summer squash plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1194 head vegetable A dairy cow is an adult female member of a dairy cattle breed http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1201 cow domesticated cattle dairy cow http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1208 squash plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1213 nut producing plant Fish are the gill-bearing aquatic craniate animals that lack limbs with digits. Most fish are ectothermic ("cold-blooded"), allowing their body temperatures to vary as ambient temperatures change, though some of the large active swimmers like white shark and tuna can hold a higher core temperature. Damion Dooley http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1222 fish Mussel is the common name used for members of several families of bivalve molluscs, from saltwater and freshwater habitats. These groups have in common a shell whose outline is elongated and asymmetrical compared with other edible clams, which are often more or less rounded or oval. Damion Dooley https://en.wikipedia.org/wiki/Mussel http://langual.org https://upload.wikimedia.org/wikipedia/commons/thumb/4/45/CornishMussels.JPG/640px-CornishMussels.JPG palaeoheterodonta pteriomorphia http://eol.org/pages/2235 http://www.langual.org/langual_thesaurus.asp?termid=B1223 mytilidae mussel http://langual.org DPNL 2003:13063 GRIN:33749 ITIS:505186 MANSFELD:10138 PLANTS:SEOR4 http://eol.org/pages/4428 http://www.langual.org/langual_thesaurus.asp?termid=B1226 simsim Sesamum indicum L. Sesamum orientale L. sesamum indicum sesamum orientale sesame plant http://langual.org DPNL 2003:10323 GRIN:317403 ITIS:40874 MANSFELD:33890 PLANTS:HOVU http://eol.org/pages/1114455 http://www.langual.org/langual_thesaurus.asp?termid=B1230 Hordeum vulgare L. hordeum vulgare barley plant http://langual.org DPNL 2003:13973 GRIN:311987 ITIS:42269 MANSFELD:36372 PLANTS:ZEMA http://eol.org/pages/1115259 http://www.langual.org/langual_thesaurus.asp?termid=B1232 Zea mays L. Zea mays subsp. mays maize zea mays LanguaL curation note: Use 'field corn' for any breakfast cereals or snack foods having 'corn' as the main ingredient. Zia mays plant Rapeseed (*Brassica napus*), also known as rape, oilseed rape, charlock (and, in the case of one particular group of cultivars, canola), is a bright-yellow flowering member of the family *Brassicaceae* (mustard or cabbage family), cultivated mainly for its oil-rich seed. It is the third-largest source of vegetable oil in the world. [https://en.wikipedia.org/wiki/Rapeseed] http://langual.org GRIN:311781 MANSFELD:24078 http://www.langual.org/langual_thesaurus.asp?termid=B1248 brassica napus rape plant Brassica napus L. emend. Metzg. var. napus canola canola plant oilseed rape plant rapeseed plant http://langual.org GRIN:50069 MANSFELD:12338 http://www.langual.org/langual_thesaurus.asp?termid=B1255 Syzygium aromaticum (L.) Merr. & L.M. Perry caryophyllus eugenia aromatica syzygium aromaticum clove plant Kale (also called Borecole) is a form of cabbage (*Brassica oleracea* Acephala Group) in which the central leaves do not form a head. It is considered to be closer to wild cabbage than most domesticated forms. The species *Brassica oleracea* contains a wide array of vegetables, including broccoli, cauliflower, and Brussels sprouts. The Cultivar Group Acephala also includes spring greens and collard greens, which are extremely similar genetically. Kale can be classified by leaf type: Curly leaved (Scots kales), Plain leaved, Rape kale, Leaf and spear (a cross between curly leaved and plain leaved kale), Cavolo nero (also known as black cabbage, Tuscan kale, Lacinato and dinosaur kale) WIKIPEDIA:Kale) http://langual.org DPNL 2003:8115 GRIN:319629 ITIS:23062 MANSFELD:23870 http://eol.org/pages/583899 http://www.langual.org/langual_thesaurus.asp?termid=B1281 Brassica oleracea L. Brassica oleracea L. var. sabellica L. Brassica oleracea var. sabellica L. brassica oleracea cole kale plant A vertebrate animal is any species of organism within the subphylum Vertebrata (chordates with backbones). Vertebrates represent the overwhelming majority of the phylum Chordata, with currently about 69,276 species described. Damion Dooley http://langual.org animal http://www.langual.org/langual_thesaurus.asp?termid=B1297 LanguaL curation note: For a unicellular animal, use *ALGAE OR FUNGUS USED AS FOOD SOURCE*. vertebrate animal Any grass cultivated (grown) for the edible components of its grain. Damion Dooley http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1324 grain plant http://langual.org GRIN:300472 MANSFELD:30744 http://www.langual.org/langual_thesaurus.asp?termid=B1338 Pisum sativum L. green pea plant lathyrus l. pisum l. pea plant *Vicia faba*, the Broad Bean, is a species of bean (*Fabaceae*) native to north Africa and southwest Asia, and extensively cultivated elsewhere. A variety is provisionally recognized: Vicia faba var. equina Pers. - Horse Bean. Although usually classified in the same genus Vicia as the vetches, some botanists treat it in a separate monotypic genus *Faba*. The term fava bean (from the Italian fava, meaning "broad bean") is usually used in English speaking countries such as the US, however the term broad bean is the most common name in the UK. WIKIPEDIA:Vicia_faba http://langual.org vicia faba DPNL 2003:13823 GRIN:300661 ITIS:26339 MANSFELD:30416 PLANTS:VIFA http://eol.org/pages/4277 http://www.langual.org/langual_thesaurus.asp?termid=B1367 faba bean plant fava bean plant horse bean plant horsebean plant Vicia faba L. Vicia faba L. (varieties for human consumption) broad bean plant Crustaceans form a large, diverse arthropod taxon which includes such familiar animals as crabs, lobsters, crayfish, shrimp, krill, woodlice, and barnacles. [https://en.wikipedia.org/wiki/Crustacean] http://langual.org http://eol.org/pages/2598871 http://www.langual.org/langual_thesaurus.asp?termid=B1374 crustacea crustacean http://langual.org GRIN:32617 MANSFELD:35616 http://www.langual.org/langual_thesaurus.asp?termid=B1378 Saccharum officinarum L. saccharum officinarum sugar cane plant Field corn is maize of varieties that (in contrast with sweet corn and popcorn) are not, in the United States, grown primarily for consumption as human food in the form of fresh kernels. More than 98% of corn-growing land in the U.S. is in use for field-corn production. Principal field corn varieties are Dent corn, Flint corn, Flour corn (including blue corn (*Zea mays amylacea*), and Waxy corn. WIKIPEDIA:Field_corn http://langual.org GRIN:311987 PLANTS:ZEMAM2 http://eol.org/pages/8223 http://www.langual.org/langual_thesaurus.asp?termid=B1379 Zea mays L. ssp. mays Zea mays L. subsp. mays Zea mays ssp. mays L. corn, field dent corn flint corn maize podcorn zea mays var. indentata (not acc.) zea mays var. indurata (not acc.) Field corn is a general term used in North America for corn varieties other than sweet corn, popcorn, yellow food grade corn used for yellow corn meal or flour and corn starch, and white food-grade corn used for white meal or flour and corn starch. Source: https://en.wikipedia.org/wiki/Field_corn LanguaL curation note: Searching note--use 'field corn' for any breakfast cereal or snack food having 'corn' as the first ingredient. field corn plant Cabbage or headed cabbage (comprising several cultivars of Brassica oleracea) is a leafy blue, red (purple), or white (pale blue) biennial plant grown as an annual vegetable crop for its dense-leaved heads. https://en.wikipedia.org/wiki/Cabbage http://langual.org DPNL 2003:8101 GRIN:7668 ITIS:23062 ITIS:526963 PLANTS:BROL http://eol.org/pages/583899 http://www.langual.org/langual_thesaurus.asp?termid=B1406 Brassica oleracea L. Brassica oleracea var. oleracea L. brassica oleracea varieties cabbage plant The term shellfish is used both broadly and specifically. For regulatory purposes it is often narrowly defined as filter-feeding molluscs such as clams, mussels, and oyster to the exclusion of crustaceans and all else. Although their shells may differ, all shellfish are invertebrates. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1433 Covers both freshwater and saltwater organisms shellfish Broccoli is a plant in the cabbage family, whose large flower head is used as a vegetable. The word broccoli, from the Italian plural of broccolo, refers to "the flowering top of a cabbage". Broccoli is usually boiled or steamed, but may be eaten raw and has become popular as a raw vegetable in hors d'oeuvre trays. Broccoli is classified in the *Italica* cultivar group of the species *Brassica oleracea*. Broccoli has large flower heads, usually green in color, arranged in a tree-like fashion on branches sprouting from a thick, edible stalk. The mass of flower heads is surrounded by leaves. Broccoli most closely resembles cauliflower, which is a different cultivar group of the same species. WIKIPEDIA:Broccoli http://langual.org DPNL 2003:8104 GRIN:105447 ITIS:530957 MANSFELD:37506 PLANTS:BROLB http://eol.org/pages/4219 http://www.langual.org/langual_thesaurus.asp?termid=B1443 Brassica oleracea L. var. botrytis L. Brassica oleracea L. var. italica Plenck Brassica oleracea var. botrytis L. brassica oleracea l. convar. botrytis var. italica brassica oleracea var. botrytis brassica oleracea var. italica broccoli plant http://langual.org ITIS:176086 http://eol.org/pages/1049263 http://www.langual.org/langual_thesaurus.asp?termid=B1457 gallus domesticus gallus gallus domesticus Gallus gallus (Linnaeus, 1758) chicken https://www.usda.gov/media/blog/2011/11/17/poultry-classifications-get-21st-century-upgrade http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1563 fjerkrae gamebird fowl game birds poultry or game bird order= obolibrary:FOODON_03411297 # vertebrate obolibrary:FOODON_00002452 # invertebrate obolibrary:PO_0000003 # whole plant obolibrary:FOODON_03411301 # algae obolibrary:FOODON_03411261 # fungae obolibrary:FOODON_03412345 # lichen This is a hierarchy of organisms, grouped minimally in a combination of taxonomy and consumer-oriented food groups. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1564 This was LanguaL definition: Individual plant or animal from which the food product or its major ingredient is derived; also a chemical food source [FDA CFSAN 1995]. food product organismal source Leaf vegetables, also called leafy greens, salad greens, pot herbs, vegetable greens, or simply greens, are plant leaves eaten as a vegetable, sometimes accompanied by tender petioles and shoots. https://en.wikipedia.org/wiki/Leaf_vegetable http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1566 leafy green leafy vegetable A bean plant is one of several genera of the flowering plant family Fabaceae, which has seed pods, seeds, and/or leaf material used for human or animal food. https://en.wikipedia.org/wiki/Bean http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1567 bean plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1579 vegetable-producing plant http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1607 nut or edible seed producing plant http://langual.org DPNL 2003:8107 GRIN:7675 ITIS:530959 MANSFELD:23884 PLANTS:BROLG http://eol.org/pages/4219 http://www.langual.org/langual_thesaurus.asp?termid=B1611 Brassica oleracea L. var. gemmifera DC. Brassica oleracea L. var. gemmifera Zenker Brassica oleracea var. gemmifera (DC.) Zenker Brassica oleracea var. gemmifera DC. brassica oleracea var. gemmifera brussels sprout plant A mature female chicken (usually more than 10 months of age) with meat less tender than that of a roaster, and with a nonflexible breastbone tip. http://langual.org hen http://www.langual.org/langual_thesaurus.asp?termid=B1713 stewing chicken stewing hen chicken hen Cucurbita (Latin for gourd) is a genus of herbaceous vines in the gourd family, Cucurbitaceae, also known as cucurbits, native to the Andes and Mesoamerica. Five species are grown worldwide for their edible fruit, variously known as squash, pumpkin, or gourd depending on species, variety, and local parlance, and for their seeds. http://langual.org GRIN:12957 MANSFELD:4048 http://www.langual.org/langual_thesaurus.asp?termid=B2091 Cucurbita maxima L. (Duch.) pumpkin plant cucurbita spp. pumpkin, squash or gourd squash, gourd or pumpkin plant *Mollusca* is a large phylum of invertebrate animals whose members are known as molluscs or mollusks. Molluscs are the largest marine phylum, comprising about 23% of all the named marine organisms. Numerous molluscs also live in freshwater and terrestrial habitats. [https://en.wikipedia.org/wiki/Mollusca] http://langual.org EC:No 216/2009 MOL FAO ASFIS:MOL http://eol.org/pages/2195 http://www.langual.org/langual_thesaurus.asp?termid=B2112 Mollusca mollusk mollusc *Bivalvia*, in previous centuries referred to as the *Lamellibranchiata* and *Pelecypoda*, is a class of marine and freshwater molluscs that have laterally compressed bodies enclosed by a shell consisting of two hinged parts. Bivalves as a group have no head and they lack some usual molluscan organs like the radula and the odontophore. They include the clams, oysters, cockles, mussels, scallops, and numerous other families that live in saltwater, as well as a number of families that live in freshwater.[https://en.wikipedia.org/wiki/Bivalvia] http://langual.org http://eol.org/pages/2215 http://www.langual.org/langual_thesaurus.asp?termid=B2113 bivalvia lamellibranchiata pelecypod pelecypoda bivalve Echinoderm is the common name given to any member of the phylum *Echinodermata* of marine animals. The adults are recognizable by their (usually five-point) radial symmetry, and include such well-known animals as sea stars, sea urchins, sand dollars, and sea cucumbers, as well as the sea lilies or "stone lilies". [https://en.wikipedia.org/wiki/Echinoderm] http://langual.org EC:No 1637/2001 ECH FAO ASFIS:ECH http://www.langual.org/langual_thesaurus.asp?termid=B2115 Echinodermata Echinodermata Klein, 1734 echinodermata echinoderm A cephalopod is any member of the molluscan class *Cephalopoda* such as a squid, octopus or nautilus. These exclusively marine animals are characterized by bilateral body symmetry, a prominent head, and a set of arms or tentacles modified from the primitive molluscan foot. Fishermen sometimes call them inkfish, referring to their common ability to squirt ink. [https://en.wikipedia.org/wiki/Cephalopod] http://langual.org http://eol.org/pages/2312 http://www.langual.org/langual_thesaurus.asp?termid=B2116 cephalopoda cephalopod *Coelenterata* is an obsolete term encompassing the animal phyla *Cnidaria* (coral animals, true jellies, sea anemones, sea pens, and their allies) and *Ctenophora* (comb jellies). [https://en.wikipedia.org/wiki/Coelenterata] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B2409 coelenterata coelenterate This section and its narrover terms refer to the European Commission food additive regulation according to COMMISSION REGULATION (EU) No 1129/2011 of 11 November 2011 amending Annex II to Regulation (EC) No 1333/2008 of the European Parliament and of the Council by establishing a Union list of food additives [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2011:295:0001:0177:EN:PDF] and its basis, the four Food Additive Directives: the EEC Framework Directive on Food Additives (89/107/EEC), the Directive on colours (94/36/EC), the Directive on sweeteners (94/35/EC) and the 'miscellaneous' Directive (95/2/EC) plus amendments [http://ec.europa.eu/food/fs/sfp/flav_index_en.html] and/or Codex Alimentarius Commission General Standard for Food Additives (CODEX STAN 192, revised 2011) [http://www.codexalimentarius.net/download/standards/4/CXS_192e.pdf]. If used for food supplement substances, thissection and its narrover terms refer to the European Commission regulation in general [http://ec.europa.eu/food/food/labellingnutrition/supplements/index_en.htm] and specifically to the EC Directive on the approximation of the laws of the Members States relating to food supplements (2002/46/EC) [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF]. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B2972 Damion Dooley's note: manysubclasses here are currently originating from LanguaL additives that have not yet been matched to CHEBI ontology terms. If matches are possible they will be implemented over time, at which point the corresponding FoodOn id's will be deprecated. food additive A chemical food component in liquid form. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B2974 liquid Food additive; technological purpose(s): bulking agent, humectant, sequestrant, stabilizer, sweetener. http://langual.org Codex::420(ii) Europe::420 http://www.langual.org/langual_thesaurus.asp?termid=B3286 LanguaL curation note: See "food additive" comments. sorbitol syrup http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3357 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. plant according to family http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3358 feed plant fodder fodder plant forage plant used as fodder http://langual.org CCPR: DPNL 2003:8093 GRIN:30008 GRIN:300085 PLANTS:BRASS2 http://eol.org/pages/4219 http://www.langual.org/langual_thesaurus.asp?termid=B3372 Brassica Brassica L. Brassica sp. Brassica spp. brassica spp. brassica species This section list vitamins and mineral substances which may be used in the manufacture of food supplements. DIRECTIVE 2002/46/EC OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 10 June 2002 on the approximation of the laws of the Member States relating to food supplements. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3749 food supplements, vitamin and mineral substances (ec) DIRECTIVE 2002/46/EC OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 10 June 2002 on the approximation of the laws of the Member States relating to food supplements [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF] and its amendments COMMISSION DIRECTIVE 2006/37/EC [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2006:094:0032:0033:EN:PDF] and COMMISSION REGULATION (EC) No 1170/2009 [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2009:314:0036:0042:EN:PDF]. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3751 food supplements, vitamin substances (ec) DIRECTIVE 2002/46/EC OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 10 June 2002 on the approximation of the laws of the Member States relating to food supplements [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF]. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3761 vitamin b12 DIRECTIVE 2002/46/EC OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 10 June 2002 on the approximation of the laws of the Member States relating to food supplements [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2002:183:0051:0057:EN:PDF]. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B3763 vitamin C http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B4168 plant used for dietary supplements The biological subfamily *Bovinae* includes a diverse group of 10 genera of medium- to large-sized ungulates, including domestic cattle, the bison, African buffalo, the water buffalo, the yak, and the four-horned and spiral-horned antelopes. The evolutionary relationship between the members of the group is obscure, and their classification into loose tribes rather than formal subgroups reflects this uncertainty. General characteristics include cloven hoofs and usually at least one of the sexes of a species having true horns. WIKIPEDIA:Bovinae http://langual.org http://eol.org/pages/2851454 http://www.langual.org/langual_thesaurus.asp?termid=B4374 bovinae bovine A bovid (family *Bovidae*) is any of almost 140 species of cloven-hoofed, ruminant mammal which has males with characteristic unbranching horns covered in a permanent sheath of keratin. The family is widespread, being native to Asia, Africa, Europe and North America, and diverse: members include bison, African buffalo, water buffalo, antelopes, gazelles, sheep, goats, muskoxen, and domestic cattle. WIKIPEDIA:Bovidae http://langual.org http://eol.org/pages/7687 http://www.langual.org/langual_thesaurus.asp?termid=B4381 bovidae bovid The *Cucurbitaceae*, also called cucurbits and the gourd family, are a plant family consisting of about 965 species in around 95 genera, the most important of which are: *Cucurbita* - squash, pumpkin, zucchini, some gourds; *Lagenaria* - calabash, and others that are inedible; *Citrullus* - watermelon (*C. lanatus, C. colocynthis*) and others; *Cucumis* - cucumber (*C. sativus*), various melons; *Luffa* - luffa, loofah http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B4460 cucurbitaceae gourd/squash family Tunicates, previously known as *Urochordata* or urochordates, are members of the *Tunicata*, a subphylum of the phylum *Chordata*. They are marine filter feeders with a saclike morphology. In their respiration and feeding they take in water through an incurrent (or inhalant) siphon and expel the filtered water through an excurrent (or exhalant) siphon. Most adult tunicates are sessile and attached to rocks or similarly suitable surfaces on the ocean floor; others such as salps, doliolids and pyrosomes swim in the pelagic zone as adults. Various species are commonly known as sea squirts or sea pork. WIKIPEDIA:Tunicate http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B4466 oopah sea squirt tunicata tunicate Edible flesh of any type of animal, including poultry and seafood. Excludes parts containing only animal fat, which is indexed under *FAT OR OIL* or under *FAT, TRIM*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0103 Damion Dooley Feb 6, 2017: Good meat cut resources to incorporate for Canada: The CFIA Meat Cuts Manual http://www.inspection.gc.ca/food/labelling/meat-cuts/eng/1300126276015/1300126372856 meat part of animal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0106 organ meat, digestive system A broad term that includes the nutritive sweeteners dextrose, fructose, galactose, lactose, maltose and sucrose, which are simple carbohydrates with molecules composed of one or two saccharide units. Note that on a product label or in a recipe, 'sugar' means *SUCROSE* and should be so indexed. Use the broad term *SUGAR* only if the specific sugar used is not known or not listed in the vocabulary. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0108 sugar Anatomical part of the plant or animal from which a food product or its major ingredient is derived. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0116 LanguaL curation note: "e.g. *LEAF*, *ROOT OR TUBER*, *ORGAN MEAT*, *MILK* OR *EGG*; it also includes components of parts, such as *CREAM*, and extracts, concentrates or isolates, such as *PROTEIN EXTRACT* or *SUGAR*." part of organism Bone, feathers, shell, skin or trim fat. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0122 LanguaL curation note: *BLOOD* AND *INK, AQUATIC ANIMAL* are now listed under organism substance. nonmeat part of animal Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0127 LanguaL curation note: Includes carcass meat, organ meat, and nonmeat parts of animals, as well as the whole animal. animal body or body part http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0129 organ meat, cardiovascular system http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0138 LanguaL curation note: Renamed from *FRUIT OR BERRY, PEEL REMOVED* in LanguaL 2008. fruit, peel removed http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0145 organ meat, urogenital system Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0152 carbohydrate extract, concentrate, or isolate Anatomical part of an animal; includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0164 part of animal The fleshy fruit of any plant. *FRUIT* includes vegetables berries and pods as well. The bulk of a fruit is its fleshy part, which is covered by a peel (skin) and which encloses a core, pit or seeds. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0167 berry berry or fruit (anatomical part) fruit or berry, peel undetermined hip (fruit) infructescence LanguaL curation note: The descriptors under *FRUIT* are arrayed so that the indexer can check first whether the peel is present, removed or undetermined; then check the same informationfor the core, pit or seeds. For juices, beverages or jellies made from fruit, Index the entire part from which the product is derived. Renamed from *FRUIT OR BERRY* in LanguaL 2008. fruit part Bone (endoskeleton) or shell (exoskeleton) of animals, or any part thereof. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0168 shell (animal) bone or shell Carcass meat from any type of animal including poultry and seafood. Includes retail and wholesale cuts other than organ meat. Refers to the whole carcass or parts. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0175 skeletal meat part Extract, concentrate or isolate high in gluten, the predominant protein of wheat or corn. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0177 gluten http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0178 seed part Food substance or component consisting predominantly of mixed glycerol esters of fatty acids and, in far lesser amounts, of fatty acids, sterols and pigments. A fat is a solid at room temperature, an oil is a liquid at room temperature (20 degrees C.). Excludes essential oils. Damion Dooley http://langual.org 2019-06-20T05:09:36Z SUBSET_SIREN:F15008 http://www.langual.org/langual_thesaurus.asp?termid=C0190 http://www.langual.org/langual_thesaurus.asp?termid=H0221 oil or fat subset_siren SIREN DB annotation: * has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) * has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) * derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) fat or oil Poultry, game bird or turtle eggs. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0194 LanguaL curation note: Fish roe are indexed under *OVARY, ROE*. egg or egg component Edible organ meat, including blood and bone marrow. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0218 variety meat organ meat The egg yolk and albumen component of one or more eggs with shell removed. Damion Dooley http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0225 egg (without shell) http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0227 LanguaL curation note: Used for seeds in hard shells rather than pods. Examples include brazil nuts, walnuts, almonds and peanuts. seed(s) in shell or hull A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0228 Damion Dooley's note: Items in this branch will be merged into foodon food product branch. extract, concentrate or isolate of plant or animal http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0229 flesh of fruit LanguaL curation note: Renamed from *FRUIT OR BERRY, PEEL REMOVED, CORE, PIT OR SEED REMOVED* in LanguaL 2008. fruit, peel removed, core, pit or seed removed Extract, concentrate or isolate high in protein; may contain amino acids, polypeptides and enzymes. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0236 http://www.langual.org/langual_thesaurus.asp?termid=H0164 protein extract, concentrate or isolate Meat from organs that do not belong to the cardiovascular, digestive or urogenital system. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0255 organ meat, other systems http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0271 http://www.langual.org/langual_thesaurus.asp?termid=H0280 LanguaL curation note: Used when a sugar syrup or sugar syrup solids is the major ingredient. Sugar syrup is a liquid or semiliquid high in sugar content derived from a plant source through extraction possibly followed by conversion and/or concentration. A sugar syrup usually contains several sugars in varying proportions. Sugar syrup solids are derived by removing water from sugar syrup. sugar syrup or syrup solids http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0272 high fructose syrup The oil produced by pressing or extracting lipids from plant seeds (e.g. grapeseed oil, rapeseed oil, linseed oil) /AM http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0307 seed oil The physical state of the food product (liquid, semiliquid, semisolid, or solid). Solid food products are further subdivided by shape or form. Terms are provided for products that have both liquid and solid components or that incorporate air or other gases. [FDA CFSAN 1995] http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=E0113 Damion Dooley's note: these categories need to be mapped over to PATO phenotypic categories, with a suitable treatment of mixtures of solids that are divided into parts. food physical quality A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*. http://langual.org SUBSET_SIREN:F5105 http://www.langual.org/langual_thesaurus.asp?termid=E0130 fluid SIREN DB annotation: * has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) food (liquid) Refers to natural or formed shape as appropriate, regardless of size, which may vary from very large (e.g., beef carcass) to very small (e.g., poppy seed, yeast cell). http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=E0131 whole http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=E0150 LanguaL curation note: Whole refers not only to a whole plant or animal but also to a whole part as indexed in C. PART OF PLANT OR ANIMAL; examples of whole natural products are: an apple, rice in grain form, an asparagus spear, a spinach leaf, a beef carcass, a dressed chicken, a chicken drumstick, a calf liver. Products may have been slightly modified during processing and preservation (e.g., raisins or a pear that has been peeled and cored). whole, natural shape Used to specifically characterize a food product based on the treatment or processes applied to the product or any indexed ingredient. The processes include adding, substituting or removing components or modifying the food or component, e.g., through fermentation. Multiple values can be assigned. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0111 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. food treatment process Modified by microbial or enzymatic action resulting in molecular changes in any food component. If salt, sugar or other food additive is used to aid in the modification process, index it by the appropriate term under *INGREDIENT ADDED*. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0119 fermented, unspecified microbial/enzymatic modification process http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0141 LanguaL curation note: Used when the food product underwent mechanical, chemical or enzymatic modification that has affected the texture, flavor or other characteristic of the product. food modification process This disjunction is provided for food indexers who used the LanguaL category per guidelines. Currently, by specifying the more specific nut or seed as ingredient instead, this category can be inferred. nut or seed added http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0177 LanguaL curation note: With the exception of peanut (see *PEANUT OR PEANUT BUTTER ADDED*), used when a nut or seed ingredient is the second ingredient in order of predominance. plant seed or nut food product http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0216 vitamin B A fat or oil derived from vegetable material Damion Dooley vegetable fat or oil added http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0263 This is a convenience class inherited from LanguaL vegetable fat or oil Reference "canola oil" or "rapeseed oil" instead. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=H0851 canola or rapeseed oil true The methods contributing to the prevention or retardation of microbial, enzymatic or oxidative spoilage and thus to the extension of shelf life. Index all methods for which information is available, even if a corresponding descriptor has already been used in *H. TREATMENT APPLIED*. Preservation descriptors refer to the finished food as a whole with these exceptions: (1) if the components of a multi-component food, such as cream pie, are preservation by different methods, index all methods; (2) if chemical preservatives are declared on the label, always index them even if it is known that the preservative was introduced through or is only present in a component or ingredient of the food; and (3) if the preservation method for an ingredient is declared on the label (such as brie cheese made from pasteurized milk) index it. Also use *INGREDIENT preservation by THERMAL PROCESSING* or *INGREDIENT preservation by IRRADIATION* when ingredients have been pasteurized, ultrapasteurized, sterilized or irradiated. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=J0107 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. food preservation process The specific container or coating materials in direct contact with the food. [FDA CFSAN 1995] http://langual.org surface http://www.langual.org/langual_thesaurus.asp?termid=N0010 food product contact surface http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=N0050 food contact surface from natural material The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins. citrulline metabolism biological_process GO:0000052 citrulline metabolic process The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins. ISBN:0198506732 The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine. sulfur amino acid metabolism sulphur amino acid metabolic process sulphur amino acid metabolism biological_process GO:0000096 sulfur amino acid metabolic process The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine. GOC:ai Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline. regulation of glutamine family amino acid metabolism biological_process GO:0000820 regulation of glutamine family amino acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid. regulation of arginine metabolism biological_process GO:0000821 regulation of arginine metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid. GOC:go_curators The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). skeletal development biological_process GO:0001501 skeletal system development The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton). GOC:dph GOC:jid GOC:tb The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. Wikipedia:Ossification bone biosynthesis bone formation osteogenesis biological_process GO:0001503 Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'. ossification The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:mtg_mpo PMID:17572649 A homeostatic process in which an organism modulates its internal body temperature. Wikipedia:Thermoregulation thermoregulation biological_process GO:0001659 temperature homeostasis A homeostatic process in which an organism modulates its internal body temperature. GOC:jl thermoregulation GOC:dph GOC:tb The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22. long-chain fatty acid metabolism biological_process GO:0001676 long-chain fatty acid metabolic process The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22. GOC:ajp Replacement ossification wherein bone tissue replaces cartilage. Wikipedia:Endochondral_ossification biological_process GO:0001958 endochondral ossification Replacement ossification wherein bone tissue replaces cartilage. GO_REF:0000034 ISBN:0878932437 The controlled release of a peptide from a cell or a tissue. biological_process GO:0002790 peptide secretion The controlled release of a peptide from a cell or a tissue. GOC:add Any process that modulates the frequency, rate, or extent of peptide secretion. biological_process GO:0002791 regulation of peptide secretion Any process that modulates the frequency, rate, or extent of peptide secretion. GOC:add Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion. down regulation of peptide secretion down-regulation of peptide secretion downregulation of peptide secretion inhibition of peptide secretion biological_process GO:0002792 negative regulation of peptide secretion Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion. GOC:add Any process that activates or increases the frequency, rate, or extent of peptide secretion. up regulation of peptide secretion up-regulation of peptide secretion upregulation of peptide secretion activation of peptide secretion stimulation of peptide secretion biological_process GO:0002793 positive regulation of peptide secretion Any process that activates or increases the frequency, rate, or extent of peptide secretion. GOC:add A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. organ system process biological_process GO:0003008 system process A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. GOC:mtg_cardio A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. Wikipedia:Circulatory_system biological_process GO:0003013 circulatory system process A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism. GOC:mtg_cardio A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular process GO:0005554 molecular function molecular_function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GOC:pdt Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Wikipedia:Enzyme enzyme activity molecular_function GO:0003824 catalytic activity Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GOC:vw ISBN:0198506732 enzyme activity GOC:dph GOC:tb true Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. receptor binding Wikipedia:Ligand_(biochemistry) receptor ligand molecular_function receptor-associated protein activity GO:0005102 Where appropriate, also consider annotating to 'receptor agonist activity ; GO:0048018'. signaling receptor binding Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function. GOC:bf GOC:ceb ISBN:0198506732 The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. Wikipedia:Binding_(molecular) ligand molecular_function GO:0005488 Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. GOC:ceb GOC:mah ISBN:0198506732 Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GO:0001948 GO:0045308 MIPS_funcat:16.01 MIPS_funcat:18.01.07 Reactome:R-HSA-170835 Reactome:R-HSA-170846 protein amino acid binding glycoprotein binding molecular_function GO:0005515 protein binding Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules). GOC:go_curators Reactome:R-HSA-170835 An anchoring protein, ZFYVE9 (SARA), recruits SMAD2/3 Reactome:R-HSA-170846 TGFBR2 recruits TGFBR1 A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GOC:pdt NIF_Subcellular:sao1337158144 The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together. GOC:go_curators subcellular entity NIF_Subcellular:nlx_subcell_100315 A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. https://github.com/geneontology/go-ontology/issues/17776 Wikipedia:Intracellular internal to cell intracellular protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular intracellular anatomical structure A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah OBSOLETE. The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. cell and encapsulating structures NIF_Subcellular:sao1813327414 Wikipedia:Cell_(biology) cellular_component GO:0005623 This term was obsoleted because it was redundant with the root class of the cell ontology, CL:0000000. obsolete cell true OBSOLETE. The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:go_curators A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. MIPS_funcat:70.10 NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GOC:go_curators horsetail nucleus GOC:al GOC:mah GOC:vw PMID:15030757 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. Wikipedia:Cytoplasm cellular_component GO:0005737 cytoplasm All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. ISBN:0198547684 A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. NIF_Subcellular:sao1860313010 Wikipedia:Mitochondrion mitochondria cellular_component GO:0005739 Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.) mitochondrion A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration. GOC:giardia ISBN:0198506732 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. Wikipedia:Vacuole cellular_component vacuolar carboxypeptidase Y GO:0005773 vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GOC:mtg_sensu ISBN:0198506732 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore membrane plasma membrane lipid bilayer cellular_component GO:0005886 plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. ISBN:0716731363 cellular membrane NIF_Subcellular:sao6433132645 plasma membrane lipid bilayer GOC:mah The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. Wikipedia:Cell_cortex cellular_component cell periphery peripheral cytoplasm GO:0005938 cell cortex The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. GOC:mah ISBN:0815316194 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule. jl 2012-10-23T15:40:34Z GO:0044261 GO:0044723 Wikipedia:Carbohydrate_metabolism carbohydrate metabolism multicellular organismal carbohydrate metabolic process biological_process single-organism carbohydrate metabolic process GO:0005975 carbohydrate metabolic process The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule. GOC:mah ISBN:0198506732 The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom. alcohol metabolism biological_process GO:0006066 alcohol metabolic process The chemical reactions and pathways involving alcohols, any of a class of compounds containing one or more hydroxyl groups attached to a saturated carbon atom. ISBN:0198506732 The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage. organic acid metabolism biological_process GO:0006082 organic acid metabolic process The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances. energy pathways biological_process intermediary metabolism metabolic energy generation GO:0006091 generation of precursor metabolites and energy The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances. GOC:jl intermediary metabolism GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates. regulation of carbohydrate metabolism biological_process GO:0006109 regulation of carbohydrate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates. GOC:go_curators Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0055134 cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0006139 nucleobase-containing compound metabolic process Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:ai nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving purines. regulation of purine base metabolic process regulation of purine base metabolism biological_process GO:0006141 regulation of purine nucleobase metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving purines. GOC:go_curators regulation of purine base metabolic process GOC:go_curators The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine. purine base metabolic process purine base metabolism purine metabolic process purine metabolism biological_process GO:0006144 purine nucleobase metabolic process The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine. GOC:go_curators purine base metabolic process GOC:go_curators The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells. GO:0006519 amino acid and derivative metabolism amino acid metabolic process cellular amino acid and derivative metabolic process cellular amino acid metabolism biological_process GO:0006520 cellular amino acid metabolic process The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids. regulation of amino acid metabolism biological_process GO:0006521 regulation of cellular amino acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids. GOC:go_curators The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid. Wikipedia:Arginine arginine metabolism biological_process GO:0006525 arginine metabolic process The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid. GOC:go_curators The chemical reactions and pathways involving glycine, aminoethanoic acid. glycine metabolism biological_process GO:0006544 glycine metabolic process The chemical reactions and pathways involving glycine, aminoethanoic acid. GOC:go_curators The chemical reactions and pathways involving isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid. isoleucine metabolism biological_process GO:0006549 isoleucine metabolic process The chemical reactions and pathways involving isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid. GOC:ai The chemical reactions and pathways involving leucine, 2-amino-4-methylpentanoic acid. leucine metabolism biological_process GO:0006551 leucine metabolic process The chemical reactions and pathways involving leucine, 2-amino-4-methylpentanoic acid. GOC:ai The chemical reactions and pathways involving lysine, 2,6-diaminohexanoic acid. Wikipedia:Lysine lysine metabolism biological_process GO:0006553 lysine metabolic process The chemical reactions and pathways involving lysine, 2,6-diaminohexanoic acid. GOC:go_curators The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins. methionine and threonine metabolic process methionine and threonine metabolism UM-BBD_pathwayID:met methionine metabolism biological_process GO:0006555 methionine metabolic process The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid. phenylalanine metabolic process phenylalanine metabolism L-phenylalanine metabolism biological_process GO:0006558 L-phenylalanine metabolic process The chemical reactions and pathways involving L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid. GOC:jsg GOC:mah The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid. L-serine metabolism biological_process GO:0006563 L-serine metabolic process The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid. GOC:ai GOC:jsg The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid. UM-BBD_pathwayID:tyr Wikipedia:Tyrosine tyrosine metabolism biological_process GO:0006570 tyrosine metabolic process The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid. GOC:go_curators The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid. valine metabolism biological_process GO:0006573 valine metabolic process The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid. GOC:ai The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents. amino acid derivative metabolic process cellular amino acid derivative metabolic process cellular amino acid derivative metabolism cellular modified amino acid metabolism modified amino acid metabolic process modified amino acid metabolism biological_process GO:0006575 cellular modified amino acid metabolic process The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents. GOC:ai cellular modified amino acid metabolism GOC:mah modified amino acid metabolic process GOC:mah modified amino acid metabolism GOC:mah The chemical reactions and pathways involving any betaine, the N-trimethyl derivative of an amino acid. betaine metabolic process betaine metabolism biological_process GO:0006577 amino-acid betaine metabolic process The chemical reactions and pathways involving any betaine, the N-trimethyl derivative of an amino acid. GOC:mah ISBN:0198506732 The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. ornithine metabolism biological_process GO:0006591 ornithine metabolic process The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. GOC:jl ISBN:0192801023 The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. Wikipedia:Lipid_metabolism lipid metabolism biological_process GO:0006629 lipid metabolic process The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids. GOC:ma The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. Wikipedia:Fatty_acid_metabolism fatty acid metabolism biological_process GO:0006631 fatty acid metabolic process The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis. ISBN:0198547684 The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. aromatic compound metabolism aromatic hydrocarbon metabolic process aromatic hydrocarbon metabolism biological_process GO:0006725 cellular aromatic compound metabolic process The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells. GOC:ai ISBN:0198506732 The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems. vitamin metabolism biological_process GO:0006766 vitamin metabolic process The chemical reactions and pathways involving vitamins. Vitamin is a general term for a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. Vitamins may be water-soluble or fat-soluble and usually serve as components of coenzyme systems. GOC:ai The chemical reactions and pathways involving any of a diverse group of vitamins that are soluble in water. water-soluble vitamin metabolism biological_process GO:0006767 water-soluble vitamin metabolic process The chemical reactions and pathways involving any of a diverse group of vitamins that are soluble in water. GOC:jl The chemical reactions and pathways involving of any of a diverse group of vitamins that are soluble in organic solvents and relatively insoluble in water. fat-soluble vitamin metabolism biological_process GO:0006775 fat-soluble vitamin metabolic process The chemical reactions and pathways involving of any of a diverse group of vitamins that are soluble in organic solvents and relatively insoluble in water. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. Wikipedia:Sulfur_metabolism sulfur metabolism sulphur metabolic process sulphur metabolism biological_process GO:0006790 sulfur compound metabolic process The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione. GOC:ai The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). phosphorus metabolism biological_process GO:0006793 phosphorus metabolic process The chemical reactions and pathways involving the nonmetallic element phosphorus or compounds that contain phosphorus, usually in the form of a phosphate group (PO4). GOC:ai The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. MIPS_funcat:01.04 phosphate metabolism biological_process phosphate metabolic process GO:0006796 phosphate-containing compound metabolic process The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid. GOC:ai The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. nitrogen compound metabolism biological_process GO:0006807 nitrogen compound metabolic process The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GOC:jl ISBN:0198506732 The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. jl 2012-12-13T16:25:32Z GO:0015457 GO:0015460 GO:0044765 small molecule transport solute:solute exchange biological_process single-organism transport GO:0006810 Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. transport The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. GOC:dos GOC:dph GOC:jl GOC:mah The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0006811 ion transport The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0006822 biological_process GO:0006820 anion transport The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. biological_process GO:0006869 lipid transport The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. ISBN:0198506732 Any process involved in the maintenance of an internal steady state of ions at the level of a cell. biological_process GO:0006873 cellular ion homeostasis Any process involved in the maintenance of an internal steady state of ions at the level of a cell. GOC:mah Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell. regulation of calcium ion concentration biological_process GO:0006874 cellular calcium ion homeostasis Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell. GOC:ceb GOC:mah Any process involved in the maintenance of an internal steady state of metal ions at the level of a cell. cellular heavy metal ion homeostasis biological_process GO:0006875 cellular metal ion homeostasis Any process involved in the maintenance of an internal steady state of metal ions at the level of a cell. GOC:ai GOC:mah The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GO:0032779 biological_process copper-induced intracellular protein transport GO:0006886 intracellular protein transport The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell. GOC:mah copper-induced intracellular protein transport GOC:al Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). biological_process response to abiotic stress response to biotic stress GO:0006950 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stress Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:mah Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. GO:0002217 GO:0042829 defence response physiological defense response biological_process antimicrobial peptide activity defense/immunity protein activity GO:0006952 defense response Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. GOC:go_curators The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. inflammation Wikipedia:Inflammation biological_process GO:0006954 inflammatory response The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. GO_REF:0000022 ISBN:0198506732 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. jl 2013-12-19T15:25:51Z GO:1902589 organelle organisation single organism organelle organization biological_process organelle organization and biogenesis single-organism organelle organization GO:0006996 organelle organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:mah single organism organelle organization GOC:TermGenie organelle organization and biogenesis GOC:dph GOC:jl GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. mitochondria organization mitochondrion organisation biological_process mitochondrion organization and biogenesis GO:0007005 mitochondrion organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components. GOC:dph GOC:jl GOC:mah GOC:sgd_curators PMID:9786946 mitochondria organization GOC:mah mitochondrion organisation GOC:mah A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrial membrane, either of the lipid bilayer surrounding a mitochondrion. mitochondrial membrane organisation biological_process mitochondrial membrane organization and biogenesis GO:0007006 mitochondrial membrane organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrial membrane, either of the lipid bilayer surrounding a mitochondrion. GOC:ai GOC:dph GOC:jl GOC:mah mitochondrial membrane organization and biogenesis GOC:mah Any process involved in the maintenance of an internal steady state of calcium ions in the vacuole or between a vacuole and its surroundings. biological_process GO:0007036 vacuolar calcium ion homeostasis Any process involved in the maintenance of an internal steady state of calcium ions in the vacuole or between a vacuole and its surroundings. GOC:ai GOC:mah Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. Wikipedia:Cell_signaling biological_process GO:0007154 cell communication Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:mah The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GO:0023033 MIPS_funcat:30 Wikipedia:Signal_transduction signaling cascade signalling cascade biological_process signaling pathway signalling pathway GO:0007165 Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. signal transduction The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell. GOC:go_curators GOC:mtg_signaling_feb11 signalling pathway GOC:mah Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. cell-cell signalling biological_process GO:0007267 cell-cell signaling Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. GOC:dos GOC:mah The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). biological_process GO:0007275 Note that this term was 'developmental process'. multicellular organism development The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:dph GOC:ems GOC:isa_complete GOC:tb The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. Wikipedia:Digestion biological_process GO:0007586 digestion The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:isa_complete ISBN:0198506732 The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. GO:0070261 biological_process hemolymph circulation GO:0008015 blood circulation The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products. GOC:mtg_heart ISBN:0192800825 Any process in which a protein is transported to, or maintained in, a specific location. GO:0008105 protein localisation biological_process asymmetric protein localisation asymmetric protein localization establishment and maintenance of asymmetric protein localization establishment and maintenance of protein localization GO:0008104 protein localization Any process in which a protein is transported to, or maintained in, a specific location. GOC:ai protein localisation GOC:mah asymmetric protein localisation GOC:mah A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. janelomax jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. janelomax jl 2012-10-17T15:46:40Z GO:0044236 GO:0044710 MIPS_funcat:01 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. GOC:go_curators ISBN:0198547684 The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. Wikipedia:Steroid_metabolism steroid metabolism biological_process GO:0008202 steroid metabolic process The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus. ISBN:0198547684 The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues. cholesterol metabolism biological_process GO:0008203 cholesterol metabolic process The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues. ISBN:0198506732 The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0006861 GO:0008644 sugar transport biological_process GO:0008643 carbohydrate transport The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y. GOC:ai The process in which hexose is transported across a membrane. Hexoses are any aldoses with a chain of six carbon atoms in the molecule. bf 2010-04-08T10:27:23Z GO:0008646 GO:0008647 GO:0035428 high-affinity hexose transport low-affinity hexose transport biological_process hexose membrane transport hexose transport GO:0008645 Note that this term is not intended for use in annotating lateral movement within membranes. hexose transmembrane transport The process in which hexose is transported across a membrane. Hexoses are any aldoses with a chain of six carbon atoms in the molecule. GOC:vw The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. jl 2012-10-17T15:52:18Z GO:0044274 GO:0044711 formation Wikipedia:Anabolism anabolism biosynthesis synthesis multicellular organismal biosynthetic process biological_process single-organism biosynthetic process GO:0009058 biosynthetic process The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. GOC:curators ISBN:0198547684 The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline. glutamine family amino acid metabolism biological_process GO:0009064 glutamine family amino acid metabolic process The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline. GOC:ai The chemical reactions and pathways involving amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine. aspartate family amino acid metabolism biological_process GO:0009066 aspartate family amino acid metabolic process The chemical reactions and pathways involving amino acids of the aspartate family, comprising asparagine, aspartate, lysine, methionine and threonine. GOC:ai The chemical reactions and pathways involving amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine. serine family amino acid metabolism biological_process GO:0009069 serine family amino acid metabolic process The chemical reactions and pathways involving amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine. GOC:ai The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan). aromatic amino acid family metabolism biological_process GO:0009072 aromatic amino acid family metabolic process The chemical reactions and pathways involving aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan). GOC:go_curators The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine. branched chain family amino acid metabolism biological_process GO:0009081 branched-chain amino acid metabolic process The chemical reactions and pathways involving amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine. GOC:ai branched chain family amino acid metabolism GOC:ai The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine. nucleobase metabolism biological_process GO:0009112 nucleobase metabolic process The chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine. GOC:ma The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. cobalamin metabolism vitamin B12 metabolic process vitamin B12 metabolism vitamin B12 reduction biological_process GO:0009235 cobalamin metabolic process The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. GOC:go_curators The controlled release of proteins from a cell. GO:0045166 GO:0045731 glycoprotein secretion protein secretion during cell fate commitment protein secretion resulting in cell fate commitment biological_process GO:0009306 protein secretion The controlled release of proteins from a cell. GOC:ai The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. amine metabolism biological_process GO:0009308 amine metabolic process The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. GOC:jl ISBN:0198506732 The chemical reactions and pathways involving carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane. carnitine metabolism vitamin Bt metabolic process vitamin Bt metabolism biological_process GO:0009437 carnitine metabolic process The chemical reactions and pathways involving carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane. GOC:jl ISBN:0198506732 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. response to environmental stimulus biological_process GO:0009605 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to external stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus. GOC:hb The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. embryogenesis and morphogenesis Wikipedia:Morphogenesis anatomical structure organization morphogenesis biological_process GO:0009653 anatomical structure morphogenesis The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. GOC:go_curators ISBN:0521436125 Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. histogenesis and organogenesis biological_process GO:0009887 animal organ morphogenesis Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:dgh GOC:go_curators ISBN:0471245208 ISBN:0721662544 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. regulation of anabolism regulation of biosynthesis regulation of formation regulation of synthesis biological_process GO:0009889 regulation of biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. down regulation of biosynthetic process down-regulation of biosynthetic process downregulation of biosynthetic process negative regulation of anabolism negative regulation of biosynthesis negative regulation of formation negative regulation of synthesis inhibition of biosynthetic process biological_process GO:0009890 negative regulation of biosynthetic process Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. positive regulation of anabolism positive regulation of biosynthesis positive regulation of formation positive regulation of synthesis up regulation of biosynthetic process up-regulation of biosynthetic process upregulation of biosynthetic process activation of biosynthetic process stimulation of biosynthetic process biological_process GO:0009891 positive regulation of biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044252 down regulation of metabolic process down-regulation of metabolic process downregulation of metabolic process negative regulation of metabolism negative regulation of organismal metabolism inhibition of metabolic process inhibition of organismal metabolic process negative regulation of multicellular organismal metabolic process biological_process GO:0009892 negative regulation of metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044253 positive regulation of metabolism up regulation of metabolic process up-regulation of metabolic process upregulation of metabolic process activation of metabolic process positive regulation of multicellular organismal metabolic process positive regulation of organismal metabolism stimulation of metabolic process stimulation of organismal metabolic process up-regulation of organismal metabolic process biological_process GO:0009893 positive regulation of metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0009914 hormone transport The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:tb Any process that modulates the frequency, rate or extent of signal transduction. GO:0035466 biological_process regulation of signaling pathway regulation of signalling pathway GO:0009966 regulation of signal transduction Any process that modulates the frequency, rate or extent of signal transduction. GOC:sm regulation of signalling pathway GOC:mah Any process that activates or increases the frequency, rate or extent of signal transduction. GO:0035468 up regulation of signal transduction up-regulation of signal transduction upregulation of signal transduction activation of signal transduction stimulation of signal transduction biological_process positive regulation of signaling pathway positive regulation of signalling pathway GO:0009967 positive regulation of signal transduction Any process that activates or increases the frequency, rate or extent of signal transduction. GOC:sm positive regulation of signalling pathway GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GO:0035467 down regulation of signal transduction down-regulation of signal transduction downregulation of signal transduction inhibition of signal transduction biological_process negative regulation of signaling pathway negative regulation of signalling pathway GO:0009968 negative regulation of signal transduction Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction. GOC:sm negative regulation of signalling pathway GOC:mah Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. janelomax jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators GOC:isa_complete Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010562 positive regulation of phosphorus metabolic process Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. biological_process GO:0010563 negative regulation of phosphorus metabolic process Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:dph GOC:tb Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. biological_process GO:0010565 regulation of cellular ketone metabolic process Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. positive regulation of organelle organisation biological_process positive regulation of organelle organization and biogenesis GO:0010638 positive regulation of organelle organization Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb positive regulation of organelle organisation GOC:mah positive regulation of organelle organization and biogenesis GOC:mah Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. negative regulation of organelle organisation biological_process negative regulation of organelle organization and biogenesis GO:0010639 negative regulation of organelle organization Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:dph GOC:tb negative regulation of organelle organisation GOC:mah negative regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010646 regulation of cell communication Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010647 positive regulation of cell communication Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. biological_process GO:0010648 negative regulation of cell communication Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. GOC:dph GOC:tb Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. biological_process GO:0010817 regulation of hormone levels Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. GOC:BHF GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. regulation of mitochondrion organisation biological_process GO:0010821 regulation of mitochondrion organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. GOC:dph GOC:tb regulation of mitochondrion organisation GOC:mah Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. positive regulation of mitochondrion organisation biological_process GO:0010822 positive regulation of mitochondrion organization Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. GOC:dph GOC:tb positive regulation of mitochondrion organisation GOC:mah Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. negative regulation of mitochondrion organisation biological_process GO:0010823 negative regulation of mitochondrion organization Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion. GOC:dph GOC:tb negative regulation of mitochondrion organisation GOC:mah Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process regulation of glucose transport GO:0010827 regulation of glucose transmembrane transport Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process positive regulation of glucose transport GO:0010828 positive regulation of glucose transmembrane transport Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:BHF GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process negative regulation of glucose transport GO:0010829 negative regulation of glucose transmembrane transport Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:BHF GOC:dph GOC:tb Any process in which a lipid is transported to, or maintained in, a specific location. lipid localisation biological_process GO:0010876 lipid localization Any process in which a lipid is transported to, or maintained in, a specific location. GOC:BHF GOC:dph GOC:tb lipid localisation GOC:mah Any process involved in the maintenance of an internal steady state of magnesium ions within an organism or cell. tb 2009-05-06T11:47:17Z biological_process GO:0010960 magnesium ion homeostasis Any process involved in the maintenance of an internal steady state of magnesium ions within an organism or cell. GOC:dph GOC:tb A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. Wikipedia:Endomembrane_system cellular_component GO:0012505 endomembrane system A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. GOC:lh The lipid bilayer surrounding any membrane-bounded vesicle in the cell. NIF_Subcellular:sao1153182838 cellular_component GO:0012506 vesicle membrane The lipid bilayer surrounding any membrane-bounded vesicle in the cell. GOC:mah GOC:vesicle The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0015831 enzyme transport biological_process GO:0015031 protein transport The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. vw 2017-02-19T10:41:27Z GO:1905950 biological_process monosaccharide transport GO:0015749 monosaccharide transmembrane transport The process in which a monosaccharide is transported across a lipid bilayer, from one side of a membrane to the other. Monosaccharides are the simplest carbohydrates; they are polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides. GOC:TermGenie GOC:vw GO_REF:0000069 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0015833 peptide transport The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. 2014-03-06T11:37:54Z GO:0098589 GO:0098805 Wikipedia:Biological_membrane membrane region region of membrane whole membrane cellular_component GO:0016020 membrane membrane A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GOC:dos GOC:mah ISBN:0815316194 A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GO:0044235 GO:0071842 cell organisation cellular component organisation at cellular level cellular component organisation in other organism cellular component organization at cellular level cellular component organization in other organism biological_process cell organization and biogenesis GO:0016043 cellular component organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:ai GOC:jl GOC:mah cellular component organisation at cellular level GOC:mah cellular component organisation in other organism GOC:mah cell organization and biogenesis GOC:mah The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. sterol metabolism biological_process GO:0016125 sterol metabolic process The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. ISBN:0198547684 true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity molecular_function GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. Wikipedia:Phosphorylation biological_process GO:0016310 phosphorylation The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. ISBN:0198506732 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2 Reactome:R-HSA-1483089 Reactome:R-HSA-1483186 Reactome:R-HSA-5668414 Reactome:R-HSA-6787403 Reactome:R-HSA-8868783 molecular_function GO:0016740 transferase activity Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. ISBN:0198506732 Reactome:R-HSA-1483089 PE is converted to PS by PTDSS2 Reactome:R-HSA-1483186 PC is converted to PS by PTDSS1 Reactome:R-HSA-5668414 TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK Reactome:R-HSA-6787403 GTPBP3 and MTO1 transform uridine-34 yielding 5-taurinomethyluridine-34 in tRNA Reactome:R-HSA-8868783 TSR3 transfers aminocarboxypropyl group from S-adenosylmethionine to N(1)-methylpseudouridine-1248 of 18SE rRNA yielding N(1)-methyl-N(3)-aminocarboxypropylpseudouridine-1248 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). EC:2.7 molecular_function GO:0016772 Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides. transferase activity, transferring phosphorus-containing groups Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor). GOC:jl ISBN:0198506732 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. regulation of lipid metabolism biological_process GO:0019216 regulation of lipid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. GO:0006632 regulation of fatty acid metabolism biological_process GO:0019217 regulation of fatty acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids. regulation of steroid metabolism biological_process GO:0019218 regulation of steroid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids. GOC:go_curators Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism biological_process regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0019219 regulation of nucleobase-containing compound metabolic process Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. regulation of phosphate metabolism biological_process GO:0019220 regulation of phosphate metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GO:0044246 regulation of metabolism regulation of multicellular organismal metabolic process regulation of organismal metabolic process biological_process GO:0019222 regulation of metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism. GOC:go_curators regulation of organismal metabolic process GOC:tb Any process involved in the maintenance of an internal steady state at the level of the cell. biological_process GO:0019725 cellular homeostasis Any process involved in the maintenance of an internal steady state at the level of the cell. GOC:isa_complete GOC:jl ISBN:0395825172 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). carboxylic acid metabolism biological_process GO:0019752 carboxylic acid metabolic process The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). ISBN:0198506732 immunoglobulin complex A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. immunoglobulin complex B cell receptor complex An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. B cell receptor complex A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0022600 digestive system process A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:isa_complete GOC:jid GOC:mtg_cardio Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. regulation of morphogenesis biological_process GO:0022603 regulation of anatomical structure morphogenesis Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis. GOC:mah Any process that modulates the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process regulation of signaling process regulation of signalling process GO:0023051 regulation of signaling Any process that modulates the frequency, rate or extent of a signaling process. GOC:mtg_signal regulation of signaling process GOC:bf regulation of signalling process GOC:mah The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. janelomax jl 2010-02-16T09:30:50Z GO:0023046 GO:0044700 biological signaling signaling process signalling biological_process signalling process single organism signaling GO:0023052 Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. signaling The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered. GOC:mtg_signal GOC:mtg_signaling_feb11 GOC:signaling signalling process GOC:mah Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z positive regulation of signalling process biological_process positive regulation of signaling process GO:0023056 positive regulation of signaling Any process that activates, maintains or increases the frequency, rate or extent of a signaling process. GOC:mtg_signal positive regulation of signalling process GOC:mah positive regulation of signaling process GOC:bf Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. 2010-02-16T09:30:50Z biological_process negative regulation of signaling process negative regulation of signalling process GO:0023057 negative regulation of signaling Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process. GOC:mtg_signal negative regulation of signaling process GOC:bf negative regulation of signalling process GOC:mah The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. 2010-02-16T09:30:50Z signal secretion biological_process GO:0023061 signal release The process in which a signal is secreted or discharged into the extracellular medium from a cellular source. GOC:mtg_signal signal secretion GOC:bf Any process involved in the maintenance of an internal steady state of cations at the level of a cell. biological_process GO:0030003 cellular cation homeostasis Any process involved in the maintenance of an internal steady state of cations at the level of a cell. GOC:ceb GOC:mah A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. secretory vesicle cellular_component GO:0030141 Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. secretory granule A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. GOC:mah ISBN:0198506732 Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. regulation of bone biosynthesis regulation of bone formation biological_process GO:0030278 regulation of ossification Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. down regulation of ossification down-regulation of ossification downregulation of ossification negative regulation of bone biosynthesis negative regulation of bone formation inhibition of ossification biological_process GO:0030279 negative regulation of ossification Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:go_curators The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. MIPS_funcat:18.02.07 molecular_function GO:0030545 receptor regulator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is changed. GOC:ceb The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. receptor activator activity molecular_function GO:0030546 signaling receptor activator activity The function of interacting (directly or indirectly) with receptors such that the proportion of receptors in the active form is increased. GOC:ceb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. regulation of vitamin metabolism biological_process GO:0030656 regulation of vitamin metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. GOC:mah The lipid bilayer surrounding a cytoplasmic vesicle. cellular_component GO:0030659 cytoplasmic vesicle membrane The lipid bilayer surrounding a cytoplasmic vesicle. GOC:mah The lipid bilayer surrounding a secretory granule. secretory vesicle membrane cellular_component GO:0030667 secretory granule membrane The lipid bilayer surrounding a secretory granule. GOC:mah A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. NIF_Subcellular:sao830981606 cellular_component intracellular membrane GO:0031090 organelle membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GOC:dos GOC:mah intracellular membrane NIF_Subcellular:sao830981606 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. regulation of cellular metabolism biological_process GO:0031323 regulation of cellular metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. down regulation of cellular metabolic process down-regulation of cellular metabolic process downregulation of cellular metabolic process negative regulation of cellular metabolism inhibition of cellular metabolic process biological_process GO:0031324 negative regulation of cellular metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. positive regulation of cellular metabolism up regulation of cellular metabolic process up-regulation of cellular metabolic process upregulation of cellular metabolic process activation of cellular metabolic process stimulation of cellular metabolic process biological_process GO:0031325 positive regulation of cellular metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. regulation of cellular anabolism regulation of cellular biosynthesis regulation of cellular formation regulation of cellular synthesis biological_process GO:0031326 regulation of cellular biosynthetic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. down regulation of cellular biosynthetic process down-regulation of cellular biosynthetic process downregulation of cellular biosynthetic process negative regulation of cellular anabolism negative regulation of cellular biosynthesis negative regulation of cellular formation negative regulation of cellular synthesis inhibition of cellular biosynthetic process biological_process GO:0031327 negative regulation of cellular biosynthetic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. positive regulation of cellular anabolism positive regulation of cellular biosynthesis positive regulation of cellular formation positive regulation of cellular synthesis up regulation of cellular biosynthetic process up-regulation of cellular biosynthetic process upregulation of cellular biosynthetic process activation of cellular biosynthetic process stimulation of cellular biosynthetic process biological_process GO:0031328 positive regulation of cellular biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. regulation of sulfur amino acid metabolism biological_process GO:0031335 regulation of sulfur amino acid metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. down regulation of sulfur amino acid metabolic process down-regulation of sulfur amino acid metabolic process downregulation of sulfur amino acid metabolic process negative regulation of sulfur amino acid metabolism inhibition of sulfur amino acid metabolic process biological_process GO:0031336 negative regulation of sulfur amino acid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. positive regulation of sulfur amino acid metabolism up regulation of sulfur amino acid metabolic process up-regulation of sulfur amino acid metabolic process upregulation of sulfur amino acid metabolic process activation of sulfur amino acid metabolic process stimulation of sulfur amino acid metabolic process biological_process GO:0031337 positive regulation of sulfur amino acid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur amino acids. GOC:mah Any process that modulates the frequency, rate or extent of a defense response. biological_process GO:0031347 regulation of defense response Any process that modulates the frequency, rate or extent of a defense response. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response. down regulation of defense response down-regulation of defense response downregulation of defense response inhibition of defense response biological_process GO:0031348 negative regulation of defense response Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response. GOC:mah Any process that activates or increases the frequency, rate or extent of a defense response. up regulation of defense response up-regulation of defense response upregulation of defense response activation of defense response stimulation of defense response biological_process GO:0031349 positive regulation of defense response Any process that activates or increases the frequency, rate or extent of a defense response. GOC:mah A vesicle found in the cytoplasm of a cell. GO:0016023 NIF_Subcellular:sao180601769 cellular_component cytoplasmic membrane bounded vesicle cytoplasmic membrane-enclosed vesicle cytoplasmic, membrane-bounded vesicle GO:0031410 cytoplasmic vesicle A vesicle found in the cytoplasm of a cell. GOC:ai GOC:mah GOC:vesicles Any small, fluid-filled, spherical organelle enclosed by membrane. GO:0031988 NIF_Subcellular:sao221389602 Wikipedia:Vesicle_(biology) cellular_component membrane-bounded vesicle membrane-enclosed vesicle GO:0031982 vesicle Any small, fluid-filled, spherical organelle enclosed by membrane. GOC:mah GOC:pz GOC:vesicles Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. down regulation of protein binding down-regulation of protein binding downregulation of protein binding inhibition of protein binding biological_process GO:0032091 negative regulation of protein binding Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding. GOC:mah Any process that activates or increases the frequency, rate or extent of protein binding. up regulation of protein binding up-regulation of protein binding upregulation of protein binding activation of protein binding stimulation of protein binding biological_process GO:0032092 positive regulation of protein binding Any process that activates or increases the frequency, rate or extent of protein binding. GOC:mah Any process that modulates the frequency, rate or extent of a response to an external stimulus. biological_process GO:0032101 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to external stimulus Any process that modulates the frequency, rate or extent of a response to an external stimulus. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus. down regulation of response to external stimulus down-regulation of response to external stimulus downregulation of response to external stimulus inhibition of response to external stimulus biological_process GO:0032102 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to external stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus. GOC:mah Any process that activates, maintains or increases the rate of a response to an external stimulus. up regulation of response to external stimulus up-regulation of response to external stimulus upregulation of response to external stimulus activation of response to external stimulus stimulation of response to external stimulus biological_process GO:0032103 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to external stimulus Any process that activates, maintains or increases the rate of a response to an external stimulus. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0032368 regulation of lipid transport Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of lipid transport down-regulation of lipid transport downregulation of lipid transport inhibition of lipid transport biological_process GO:0032369 negative regulation of lipid transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of lipid transport up-regulation of lipid transport upregulation of lipid transport activation of lipid transport stimulation of lipid transport biological_process GO:0032370 positive regulation of lipid transport Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. biological_process GO:0032386 regulation of intracellular transport Any process that modulates the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. down regulation of intracellular transport down-regulation of intracellular transport downregulation of intracellular transport inhibition of intracellular transport biological_process GO:0032387 negative regulation of intracellular transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. up regulation of intracellular transport up-regulation of intracellular transport upregulation of intracellular transport activation of intracellular transport stimulation of intracellular transport biological_process GO:0032388 positive regulation of intracellular transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells. GOC:mah Any biological process, occurring at the level of a multicellular organism, pertinent to its function. jl 2012-09-19T16:07:47Z GO:0044707 GO:0050874 organismal physiological process biological_process single-multicellular organism process GO:0032501 multicellular organismal process Any biological process, occurring at the level of a multicellular organism, pertinent to its function. GOC:curators GOC:dph GOC:isa_complete GOC:tb A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. jl 2012-12-19T12:21:31Z GO:0044767 development biological_process single-organism developmental process GO:0032502 developmental process A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. GOC:isa_complete The directed movement of a protein from one location to another within a lipid bilayer. protein translocation within membrane receptor translocation within membrane receptor transport within lipid bilayer biological_process GO:0032594 protein transport within lipid bilayer The directed movement of a protein from one location to another within a lipid bilayer. GOC:mah The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-). monocarboxylate metabolic process monocarboxylic acid metabolism biological_process GO:0032787 monocarboxylic acid metabolic process The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-). GOC:vk Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. regulation of localisation biological_process GO:0032879 regulation of localization Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location. GOC:mah regulation of localisation GOC:mah Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. regulation of protein localisation biological_process GO:0032880 regulation of protein localization Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location. GOC:dph GOC:mah GOC:tb regulation of protein localisation GOC:mah The controlled release of a substance by a cell. Wikipedia:Secretion cellular secretion biological_process GO:0032940 secretion by cell The controlled release of a substance by a cell. GOC:mah protein-containing complex A ribosome is a protein complex. A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. protein complex protein-containing complex The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. tetrapyrrole metabolism biological_process GO:0033013 tetrapyrrole metabolic process The chemical reactions and pathways involving tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. GOC:mah Any process in which a macromolecule is transported to, or maintained in, a specific location. macromolecule localisation biological_process GO:0033036 macromolecule localization Any process in which a macromolecule is transported to, or maintained in, a specific location. GOC:mah macromolecule localisation GOC:mah Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. regulation of organelle organisation biological_process regulation of organelle organization and biogenesis GO:0033043 regulation of organelle organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle. GOC:mah regulation of organelle organisation GOC:mah regulation of organelle organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. biological_process GO:0033157 regulation of intracellular protein transport Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells. GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines. regulation of amine metabolism biological_process GO:0033238 regulation of cellular amine metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines. negative regulation of amine metabolism biological_process GO:0033239 negative regulation of cellular amine metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines. GOC:mah Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines. positive regulation of amine metabolism biological_process GO:0033240 positive regulation of cellular amine metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines. GOC:mah A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell. biological_process GO:0033500 carbohydrate homeostasis A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. down regulation of kinase activity down-regulation of kinase activity downregulation of kinase activity inhibition of kinase activity kinase inhibitor biological_process GO:0033673 negative regulation of kinase activity Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. up regulation of kinase activity up-regulation of kinase activity upregulation of kinase activity kinase activator stimulation of kinase activity biological_process GO:0033674 positive regulation of kinase activity Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:mah The process in which a carbohydrate is transported across a membrane. carbohydrate membrane transport transmembrane carbohydrate transport biological_process GO:0034219 Note that this term is not intended for use in annotating lateral movement within membranes. carbohydrate transmembrane transport The process in which a carbohydrate is transported across a membrane. GOC:mah transmembrane carbohydrate transport GOC:dph GOC:tb A process in which an ion is transported across a membrane. GO:0099131 ion membrane transport transmembrane ion transport ATP hydrolysis coupled ion transmembrane transport biological_process GO:0034220 Note that this term is not intended for use in annotating lateral movement within membranes. ion transmembrane transport A process in which an ion is transported across a membrane. GOC:mah transmembrane ion transport GOC:dph GOC:tb Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GO:0016249 cellular protein localisation channel localizer activity biological_process GO:0034613 cellular protein localization Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:mah cellular protein localisation GOC:mah channel localizer activity GOC:mah The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. cellular nitrogen compound metabolism biological_process GO:0034641 cellular nitrogen compound metabolic process The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. regulation of membrane transport biological_process GO:0034762 regulation of transmembrane transport Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. down regulation of transmembrane transport down-regulation of transmembrane transport downregulation of transmembrane transport negative regulation of membrane transport inhibition of transmembrane transport biological_process GO:0034763 negative regulation of transmembrane transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. positive regulation of membrane transport up regulation of transmembrane transport up-regulation of transmembrane transport upregulation of transmembrane transport activation of transmembrane transport stimulation of transmembrane transport biological_process GO:0034764 positive regulation of transmembrane transport Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other. GOC:mah Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. regulation of ion membrane transport regulation of transmembrane ion transport biological_process GO:0034765 regulation of ion transmembrane transport Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah regulation of transmembrane ion transport GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. down regulation of transmembrane ion transport down-regulation of transmembrane ion transport downregulation of transmembrane ion transport negative regulation of ion membrane transport negative regulation of transmembrane ion transport inhibition of transmembrane ion transport biological_process GO:0034766 negative regulation of ion transmembrane transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah negative regulation of transmembrane ion transport GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. positive regulation of ion membrane transport positive regulation of transmembrane ion transport up regulation of transmembrane ion transport up-regulation of transmembrane ion transport upregulation of transmembrane ion transport activation of transmembrane ion transport stimulation of transmembrane ion transport biological_process GO:0034767 positive regulation of ion transmembrane transport Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other. GOC:mah The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function. biological_process GO:0035265 organ growth The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function. GOC:bf ISBN:0471245208 ISBN:0721662544 The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. rfoulger 2010-05-14T01:14:37Z GO:0007242 GO:0007243 GO:0023013 GO:0023034 intracellular signaling chain intracellular protein kinase cascade intracellular signal transduction pathway protein kinase cascade signal transmission via intracellular cascade biological_process intracellular signaling cascade intracellular signaling pathway signal transduction via intracellular signaling cascade GO:0035556 intracellular signal transduction The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. GOC:bf GOC:jl GOC:signaling ISBN:3527303782 intracellular signaling chain ISBN:3527303782 intracellular protein kinase cascade GOC:signaling protein kinase cascade GOC:signaling intracellular signaling cascade GOC:signaling The directed movement of a protein to a specific location within the extracellular region. bf 2010-11-09T10:25:08Z establishment of protein localisation in extracellular region establishment of protein localization in extracellular region biological_process GO:0035592 establishment of protein localization to extracellular region The directed movement of a protein to a specific location within the extracellular region. GOC:BHF GOC:bf establishment of protein localisation in extracellular region GOC:mah The regulated release of any steroid that acts as a hormone into the circulatory system. bf 2011-07-20T01:01:00Z biological_process GO:0035929 steroid hormone secretion The regulated release of any steroid that acts as a hormone into the circulatory system. GOC:sl Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation. bf 2011-12-19T01:53:16Z indirect ossification biological_process GO:0036075 replacement ossification Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation. GO_REF:0000034 indirect ossification GO_REF:0000034 The increase in size or mass of an entire organism, a part of an organism or a cell. GO:0048590 biological_process growth pattern non-developmental growth GO:0040007 See also the biological process term 'cell growth ; GO:0016049'. growth The increase in size or mass of an entire organism, a part of an organism or a cell. GOC:bf GOC:ma non-developmental growth GOC:mah Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. biological_process GO:0040008 regulation of growth Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. GOC:ems GOC:mah T cell receptor complex A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. T cell receptor complex The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. ketone metabolism biological_process GO:0042180 cellular ketone metabolic process The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups. GOC:jl ISBN:0787650153 Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. biological_process GO:0042325 regulation of phosphorylation Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule. GOC:jl Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. down regulation of phosphorylation down-regulation of phosphorylation downregulation of phosphorylation inhibition of phosphorylation biological_process GO:0042326 negative regulation of phosphorylation Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule. GOC:jl Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. up regulation of phosphorylation up-regulation of phosphorylation upregulation of phosphorylation activation of phosphorylation stimulation of phosphorylation biological_process GO:0042327 positive regulation of phosphorylation Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule. GOC:jl The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3). vitamin D metabolism calciferol metabolic process calciferol metabolism cholecalciferol metabolic process cholecalciferol metabolism ergocalciferol metabolic process ergocalciferol metabolism biological_process GO:0042359 vitamin D metabolic process The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3). GOC:mah ISBN:0471331309 immunoglobulin complex, circulating An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. antibody antibody immunoglobulin complex, circulating A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme. cellular_component GO:0042588 zymogen granule A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme. GOC:jl ISBN:0198506732 The lipid bilayer surrounding a zymogen granule. cellular_component GO:0042589 zymogen granule membrane The lipid bilayer surrounding a zymogen granule. GOC:jl Any biological process involved in the maintenance of an internal steady state. GO:0032844 GO:0032845 GO:0032846 homeostasis activation of homeostatic process inhibition of homeostatic process biological_process negative regulation of homeostatic process positive regulation of homeostatic process regulation of homeostatic process GO:0042592 homeostatic process Any biological process involved in the maintenance of an internal steady state. GOC:jl ISBN:0395825172 Any process involved in the maintenance of an internal steady state of glucose within an organism or cell. biological_process GO:0042593 glucose homeostasis Any process involved in the maintenance of an internal steady state of glucose within an organism or cell. GOC:go_curators Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur. regulation of sulfur metabolism regulation of sulphur metabolic process regulation of sulphur metabolism biological_process GO:0042762 regulation of sulfur metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving sulfur, the nonmetallic element sulfur or compounds that contain sulfur. GOC:go_curators The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0042886 amide transport The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl ISBN:0198506732 Any process that activates or increases the activity of an enzyme. GO:0048554 MIPS_funcat:18.02.01.01 positive regulation of enzyme activity up regulation of enzyme activity up-regulation of enzyme activity upregulation of enzyme activity activation of enzyme activity activation of metalloenzyme activity positive regulation of metalloenzyme activity stimulation of enzyme activity stimulation of metalloenzyme activity up regulation of metalloenzyme activity up-regulation of metalloenzyme activity upregulation of metalloenzyme activity biological_process GO:0043085 positive regulation of catalytic activity Any process that activates or increases the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw positive regulation of enzyme activity GOC:tb Any process that stops or reduces the activity of an enzyme. GO:0048553 down regulation of enzyme activity down-regulation of enzyme activity down-regulation of metalloenzyme activity downregulation of enzyme activity negative regulation of enzyme activity down regulation of metalloenzyme activity downregulation of metalloenzyme activity inhibition of enzyme activity inhibition of metalloenzyme activity negative regulation of metalloenzyme activity biological_process GO:0043086 negative regulation of catalytic activity Any process that stops or reduces the activity of an enzyme. GOC:ebc GOC:jl GOC:tb GOC:vw negative regulation of enzyme activity GOC:tb Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. cellular_component GO:0043229 intracellular organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle cellular_component GO:0043231 intracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0043269 regulation of ion transport Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of ion transport up-regulation of ion transport upregulation of ion transport activation of ion transport stimulation of ion transport biological_process GO:0043270 positive regulation of ion transport Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of ion transport down-regulation of ion transport downregulation of ion transport inhibition of ion transport biological_process GO:0043271 negative regulation of ion transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Any process that modulates the frequency, rate or extent of protein binding. biological_process GO:0043393 regulation of protein binding Any process that modulates the frequency, rate or extent of protein binding. GOC:go_curators The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). keto acid metabolic process keto acid metabolism ketoacid metabolic process ketoacid metabolism oxo acid metabolic process oxo acid metabolism oxoacid metabolism biological_process GO:0043436 oxoacid metabolic process The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons). Wikipedia:Oxyacid Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances. biological_process GO:0043467 regulation of generation of precursor metabolites and energy Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances. GOC:jl The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. biological_process GO:0043473 pigmentation The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells. GOC:jl Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. biological_process GO:0043549 regulation of kinase activity Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GOC:bf The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-). dicarboxylate metabolic process dicarboxylate metabolism dicarboxylic acid metabolism biological_process GO:0043648 dicarboxylic acid metabolic process The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-). ISBN:0198506732 Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. biological_process GO:0044057 regulation of system process Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system. GOC:jl Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0044058 regulation of digestive system process Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:jl Any process that modulates the frequency, rate or extent of an endocrine process, a process involving the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. regulation of endocrine system process biological_process GO:0044060 regulation of endocrine process Any process that modulates the frequency, rate or extent of an endocrine process, a process involving the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. GOC:jl Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0044070 regulation of anion transport Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:jl Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane jl 2009-04-21T04:07:27Z biological_process GO:0044092 negative regulation of molecular function Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. jane jl 2009-04-21T04:11:06Z biological_process GO:0044093 positive regulation of molecular function Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GO:jl The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group, as carried out by individual cells. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. jl 2009-07-15T11:55:44Z biological_process GO:0044106 cellular amine metabolic process The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group, as carried out by individual cells. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom. GOC:jl The chemical reactions and pathways by which individual cells transform chemical substances. cellular metabolism biological_process intermediary metabolism GO:0044237 cellular metabolic process The chemical reactions and pathways by which individual cells transform chemical substances. GOC:go_curators intermediary metabolism GOC:mah The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. primary metabolism biological_process GO:0044238 primary metabolic process The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. GOC:go_curators http://www.metacyc.org The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. cellular anabolism cellular biosynthesis cellular formation cellular synthesis biological_process GO:0044249 cellular biosynthetic process The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells. GOC:jl The chemical reactions and pathways involving lipids, as carried out by individual cells. cellular lipid metabolism biological_process GO:0044255 cellular lipid metabolic process The chemical reactions and pathways involving lipids, as carried out by individual cells. GOC:jl The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. jl 2010-01-26T12:05:20Z small molecule metabolism biological_process GO:0044281 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule metabolic process The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:vw The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. jl 2010-01-26T12:06:49Z small molecule biosynthesis biological_process GO:0044283 Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides. small molecule biosynthetic process The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule. GOC:curators GOC:pde GOC:vw OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms. CL:0000000 NIF_Subcellular:sao628508602 cellular subcomponent cellular_component protoplast GO:0044464 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cell part obsolete cell part true OBSOLETE. Any constituent part of a cell, the basic structural and functional unit of all organisms. GOC:jl cellular subcomponent NIF_Subcellular:sao628508602 protoplast GOC:mah The directed movement of a protein to a specific location. establishment of protein localisation protein positioning protein recruitment biological_process GO:0045184 establishment of protein localization The directed movement of a protein to a specific location. GOC:bf establishment of protein localisation GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid. down regulation of amino acid metabolic process down-regulation of amino acid metabolic process downregulation of amino acid metabolic process negative regulation of amino acid metabolism inhibition of amino acid metabolic process biological_process GO:0045763 negative regulation of cellular amino acid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid. positive regulation of amino acid metabolism up regulation of amino acid metabolic process up-regulation of amino acid metabolic process upregulation of amino acid metabolic process activation of amino acid metabolic process stimulation of amino acid metabolic process biological_process GO:0045764 positive regulation of cellular amino acid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid. GOC:go_curators Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. positive regulation of bone biosynthesis positive regulation of bone formation up regulation of ossification up-regulation of ossification upregulation of ossification activation of ossification stimulation of ossification biological_process GO:0045778 positive regulation of ossification Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. down regulation of lipid metabolic process down-regulation of lipid metabolic process downregulation of lipid metabolic process negative regulation of lipid metabolism inhibition of lipid metabolic process biological_process GO:0045833 negative regulation of lipid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. positive regulation of lipid metabolism up regulation of lipid metabolic process up-regulation of lipid metabolic process upregulation of lipid metabolic process activation of lipid metabolic process stimulation of lipid metabolic process biological_process GO:0045834 positive regulation of lipid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. down regulation of carbohydrate metabolic process down-regulation of carbohydrate metabolic process downregulation of carbohydrate metabolic process negative regulation of carbohydrate metabolism inhibition of carbohydrate metabolic process biological_process GO:0045912 negative regulation of carbohydrate metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. positive regulation of carbohydrate metabolism up regulation of carbohydrate metabolic process up-regulation of carbohydrate metabolic process upregulation of carbohydrate metabolic process activation of carbohydrate metabolic process stimulation of carbohydrate metabolic process biological_process GO:0045913 positive regulation of carbohydrate metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. down regulation of fatty acid metabolic process down-regulation of fatty acid metabolic process downregulation of fatty acid metabolic process negative regulation of fatty acid metabolism inhibition of fatty acid metabolic process biological_process GO:0045922 negative regulation of fatty acid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. positive regulation of fatty acid metabolism up regulation of fatty acid metabolic process up-regulation of fatty acid metabolic process upregulation of fatty acid metabolic process activation of fatty acid metabolic process stimulation of fatty acid metabolic process biological_process GO:0045923 positive regulation of fatty acid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving fatty acids. GOC:go_curators Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. down regulation of growth down-regulation of growth downregulation of growth inhibition of growth biological_process GO:0045926 negative regulation of growth Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism. GOC:go_curators Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. up regulation of growth up-regulation of growth upregulation of growth activation of growth stimulation of growth biological_process GO:0045927 positive regulation of growth Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism. GOC:go_curators Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045934 negative regulation of nucleobase-containing compound metabolic process Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process biological_process positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GO:0045935 positive regulation of nucleobase-containing compound metabolic process Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids. GOC:go_curators positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. down regulation of phosphate metabolic process down-regulation of phosphate metabolic process downregulation of phosphate metabolic process negative regulation of phosphate metabolism inhibition of phosphate metabolic process biological_process GO:0045936 negative regulation of phosphate metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. positive regulation of phosphate metabolism up regulation of phosphate metabolic process up-regulation of phosphate metabolic process upregulation of phosphate metabolic process activation of phosphate metabolic process stimulation of phosphate metabolic process biological_process GO:0045937 positive regulation of phosphate metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids. down regulation of steroid metabolic process down-regulation of steroid metabolic process downregulation of steroid metabolic process negative regulation of steroid metabolism inhibition of steroid metabolic process biological_process GO:0045939 negative regulation of steroid metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids. positive regulation of steroid metabolism up regulation of steroid metabolic process up-regulation of steroid metabolic process upregulation of steroid metabolic process activation of steroid metabolic process stimulation of steroid metabolic process biological_process GO:0045940 positive regulation of steroid metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving purine nucleobases. down regulation of purine base metabolic process down-regulation of purine base metabolic process downregulation of purine base metabolic process negative regulation of purine base metabolic process negative regulation of purine base metabolism inhibition of purine base metabolic process biological_process GO:0045982 negative regulation of purine nucleobase metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving purine nucleobases. GOC:go_curators negative regulation of purine base metabolic process GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving purine bases. positive regulation of purine base metabolic process positive regulation of purine base metabolism up regulation of purine base metabolic process up-regulation of purine base metabolic process upregulation of purine base metabolic process activation of purine base metabolic process stimulation of purine base metabolic process biological_process GO:0045983 positive regulation of purine nucleobase metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving purine bases. GOC:go_curators Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. positive regulation of vitamin metabolism up regulation of vitamin metabolic process up-regulation of vitamin metabolic process upregulation of vitamin metabolic process activation of vitamin metabolic process stimulation of vitamin metabolic process biological_process GO:0046136 positive regulation of vitamin metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. down regulation of vitamin metabolic process down-regulation of vitamin metabolic process downregulation of vitamin metabolic process negative regulation of vitamin metabolism inhibition of vitamin metabolic process biological_process GO:0046137 negative regulation of vitamin metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a vitamin, one of a number of unrelated organic substances that occur in many foods in small amounts and that are necessary in trace amounts for the normal metabolic functioning of the body. GOC:ai The directed movement of the hexose monosaccharide glucose into a cell or organelle. Wikipedia:Glucose_uptake glucose uptake biological_process GO:0046323 glucose import The directed movement of the hexose monosaccharide glucose into a cell or organelle. GOC:ai glucose uptake GOC:dph GOC:tb Any process that modulates the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. regulation of glucose uptake biological_process GO:0046324 regulation of glucose import Any process that modulates the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. GOC:ai regulation of glucose uptake GOC:dph GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. down regulation of glucose import down-regulation of glucose import downregulation of glucose import negative regulation of glucose uptake inhibition of glucose import biological_process GO:0046325 negative regulation of glucose import Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. GOC:ai negative regulation of glucose uptake GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. positive regulation of glucose uptake up regulation of glucose import up-regulation of glucose import upregulation of glucose import activation of glucose import stimulation of glucose import biological_process GO:0046326 positive regulation of glucose import Any process that activates or increases the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle. GOC:ai GOC:dph GOC:tb positive regulation of glucose uptake GOC:dph GOC:tb The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). heterocycle metabolism biological_process GO:0046483 heterocycle metabolic process The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings). ISBN:0198506732 Any process that modulates the frequency, rate or extent of growth of an organ of an organism. biological_process GO:0046620 regulation of organ growth Any process that modulates the frequency, rate or extent of growth of an organ of an organism. GOC:bf GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism. biological_process GO:0046621 negative regulation of organ growth Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism. GOC:bf GOC:tb Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism. biological_process GO:0046622 positive regulation of organ growth Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism. GOC:bf GOC:tb The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. biological_process GO:0046879 hormone secretion The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells. ISBN:0198506732 Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell. biological_process GO:0046883 regulation of hormone secretion Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell. up regulation of hormone secretion up-regulation of hormone secretion upregulation of hormone secretion activation of hormone secretion stimulation of hormone secretion biological_process GO:0046887 positive regulation of hormone secretion Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell. down regulation of hormone secretion down-regulation of hormone secretion downregulation of hormone secretion inhibition of hormone secretion biological_process GO:0046888 negative regulation of hormone secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell. GOC:ai The controlled release of a substance by a cell or a tissue. biological_process GO:0046903 secretion The controlled release of a substance by a cell or a tissue. GOC:ai The directed movement of substances within a cell. jl 2013-12-18T14:04:50Z GO:1902582 biological_process single organism intracellular transport single-organism intracellular transport GO:0046907 intracellular transport The directed movement of substances within a cell. GOC:ai single organism intracellular transport GOC:TermGenie The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism. cellular ketone body metabolism biological_process GO:0046950 cellular ketone body metabolic process The chemical reactions and pathways involving ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone, as carried out by individual cells. Although 3-hydroxybutyrate is not a ketone, it is classed as a ketone body because it exists in an equilibrium with acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus or in other defects of carbohydrate metabolism. ISBN:0198506732 The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetate and acetyl-CoA. ketone body anabolism ketone body biosynthesis ketone body formation ketone body synthesis biological_process GO:0046951 ketone body biosynthetic process The chemical reactions and pathways resulting in the formation of ketone bodies, any one of the three substances: acetoacetate, D-3-hydroxybutyrate (beta-hydroxybutyrate) or acetone. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetate and acetyl-CoA. ISBN:0198506732 The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). midori 2010-09-13T04:51:59Z GO:0071884 receptor agonist activity signaling molecule signaling receptor ligand activity vitamin D receptor activator activity molecular_function GO:0048018 Definition discussed in https://github.com/geneontology/go-ontology/issues/14220 receptor ligand activity The activity of a gene product that interacts with a receptor to effect a change in the activity of the receptor. Ligands may be produced by the same, or different, cell that expresses the receptor. Ligands may diffuse extracellularly from their point of origin to the receiving cell, or remain attached to an adjacent cell surface (e.g. Notch ligands). GOC:kv GOC:molecular_function_refactoring GOC:pdt receptor agonist activity GOC:molecular_function_refactoring Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. Wikipedia:Organogenesis development of an organ organogenesis biological_process GO:0048513 animal organ development Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GOC:dph GOC:jid Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043119 positive regulation of physiological process up regulation of biological process up-regulation of biological process upregulation of biological process activation of biological process stimulation of biological process biological_process GO:0048518 positive regulation of biological process Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0043118 down regulation of biological process down-regulation of biological process downregulation of biological process negative regulation of physiological process inhibition of biological process biological_process GO:0048519 negative regulation of biological process Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:jid Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051242 positive regulation of cellular physiological process up regulation of cellular process up-regulation of cellular process upregulation of cellular process activation of cellular process stimulation of cellular process biological_process GO:0048522 positive regulation of cellular process Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051243 down regulation of cellular process down-regulation of cellular process downregulation of cellular process negative regulation of cellular physiological process inhibition of cellular process biological_process GO:0048523 negative regulation of cellular process Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:jid Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. biological_process GO:0048583 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to stimulus Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. up regulation of response to stimulus up-regulation of response to stimulus upregulation of response to stimulus activation of response to stimulus stimulation of response to stimulus biological_process GO:0048584 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. positive regulation of response to stimulus Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. down regulation of response to stimulus down-regulation of response to stimulus downregulation of response to stimulus inhibition of response to stimulus biological_process GO:0048585 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. negative regulation of response to stimulus Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. GOC:jid The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. biological_process GO:0048589 developmental growth The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another. GOC:go_curators Any process that modulates the frequency, rate or extent of developmental growth. biological_process GO:0048638 regulation of developmental growth Any process that modulates the frequency, rate or extent of developmental growth. GOC:go_curators Any process that activates, maintains or increases the rate of developmental growth. up regulation of developmental growth up-regulation of developmental growth upregulation of developmental growth activation of developmental growth stimulation of developmental growth biological_process GO:0048639 positive regulation of developmental growth Any process that activates, maintains or increases the rate of developmental growth. GOC:go_curators Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth. down regulation of developmental growth down-regulation of developmental growth downregulation of developmental growth inhibition of developmental growth biological_process GO:0048640 negative regulation of developmental growth Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth. GOC:go_curators The process in which the anatomical structures of the skeleton are generated and organized. skeletal morphogenesis biological_process GO:0048705 skeletal system morphogenesis The process in which the anatomical structures of the skeleton are generated and organized. GOC:dph GOC:dsf GOC:jid GOC:tb skeletal morphogenesis GOC:dph GOC:tb The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. biological_process GO:0048731 system development The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process. GOC:dph GOC:jid The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. development of an anatomical structure biological_process GO:0048856 anatomical structure development The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. GO_REF:0000021 Any process involved in the maintenance of an internal steady state at the level of the multicellular organism. biological_process GO:0048871 multicellular organismal homeostasis Any process involved in the maintenance of an internal steady state at the level of the multicellular organism. GOC:isa_complete Any biological process involved in the maintenance of an internal steady state of a chemical. biological_process GO:0048878 chemical homeostasis Any biological process involved in the maintenance of an internal steady state of a chemical. GOC:isa_complete Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. biological_process GO:0050708 regulation of protein secretion Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. down regulation of protein secretion down-regulation of protein secretion downregulation of protein secretion inhibition of protein secretion biological_process GO:0050709 negative regulation of protein secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. up regulation of protein secretion up-regulation of protein secretion upregulation of protein secretion activation of protein secretion stimulation of protein secretion biological_process GO:0050714 positive regulation of protein secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell. GOC:ai Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. biological_process GO:0050727 regulation of inflammatory response Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. GO:0030236 anti-inflammatory response down regulation of inflammatory response down-regulation of inflammatory response downregulation of inflammatory response inhibition of inflammatory response biological_process GO:0050728 negative regulation of inflammatory response Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response. GOC:ai Any process that activates or increases the frequency, rate or extent of the inflammatory response. up regulation of inflammatory response up-regulation of inflammatory response upregulation of inflammatory response activation of inflammatory response stimulation of inflammatory response biological_process GO:0050729 positive regulation of inflammatory response Any process that activates or increases the frequency, rate or extent of the inflammatory response. GOC:ai Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GO:0050791 regulation of physiological process biological_process GO:0050789 regulation of biological process Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. GOC:ai GOC:go_curators Any process that modulates the activity of an enzyme. GO:0048552 MIPS_funcat:18.02.01 regulation of enzyme activity regulation of metalloenzyme activity biological_process GO:0050790 regulation of catalytic activity Any process that modulates the activity of an enzyme. GOC:ai GOC:ebc GOC:vw Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). biological_process GO:0050793 regulation of developmental process Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:go_curators Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GO:0051244 regulation of cellular physiological process biological_process GO:0050794 regulation of cellular process Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. GOC:go_curators Any process involved in the maintenance of an internal steady state of ions within an organism or cell. GO:2000021 biological_process electrolyte homeostasis negative regulation of crystal formation regulation of ion homeostasis GO:0050801 ion homeostasis Any process involved in the maintenance of an internal steady state of ions within an organism or cell. GOC:ai Any process that modulates the levels of body fluids. biological_process GO:0050878 regulation of body fluid levels Any process that modulates the levels of body fluids. GOC:ai GOC:dph GOC:tb The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. endocrine physiological process endocrine physiology biological_process GO:0050886 endocrine process The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system. ISBN:0721662544 Any process in which nutrients are taken up from the contents of the intestine. biological_process GO:0050892 intestinal absorption Any process in which nutrients are taken up from the contents of the intestine. GOC:ai GOC:dph Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 MIPS_funcat:34.11 physiological response to stimulus biological_process GO:0050896 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GOC:ai GOC:bf Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. biological_process GO:0051046 regulation of secretion Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. up regulation of secretion up-regulation of secretion upregulation of secretion activation of secretion stimulation of secretion biological_process GO:0051047 positive regulation of secretion Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. down regulation of secretion down-regulation of secretion downregulation of secretion inhibition of secretion biological_process GO:0051048 negative regulation of secretion Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051049 regulation of transport Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of transport up-regulation of transport upregulation of transport activation of transport stimulation of transport biological_process GO:0051050 positive regulation of transport Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of transport down-regulation of transport downregulation of transport inhibition of transport biological_process GO:0051051 negative regulation of transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). down regulation of developmental process down-regulation of developmental process downregulation of developmental process inhibition of developmental process biological_process GO:0051093 negative regulation of developmental process Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:ai Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). up regulation of developmental process up-regulation of developmental process upregulation of developmental process activation of developmental process stimulation of developmental process biological_process GO:0051094 positive regulation of developmental process Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). GOC:ai Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. biological_process GO:0051098 regulation of binding Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. up regulation of binding up-regulation of binding upregulation of binding activation of binding stimulation of binding biological_process GO:0051099 positive regulation of binding Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. down regulation of binding down-regulation of binding downregulation of binding inhibition of binding biological_process GO:0051100 negative regulation of binding Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule. GOC:ai Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. regulation of cellular component organisation biological_process regulation of cell organisation regulation of cell organization regulation of cellular component organization and biogenesis GO:0051128 regulation of cellular component organization Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai regulation of cell organisation GOC:mah regulation of cell organization GOC:mah regulation of cellular component organization and biogenesis GOC:mah Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. down regulation of cell organization down-regulation of cell organization downregulation of cell organization inhibition of cell organization biological_process negative regulation of cell organisation negative regulation of cellular component organization and biogenesis GO:0051129 negative regulation of cellular component organization Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai negative regulation of cell organisation GOC:mah negative regulation of cellular component organization and biogenesis GOC:mah Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. positive regulation of cell organisation up regulation of cell organization up-regulation of cell organization upregulation of cell organization activation of cell organization stimulation of cell organization biological_process positive regulation of cellular component organization and biogenesis GO:0051130 positive regulation of cellular component organization Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope. GOC:ai positive regulation of cellular component organization and biogenesis GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. regulation of nitrogen metabolic process regulation of nitrogen metabolism biological_process GO:0051171 regulation of nitrogen compound metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb regulation of nitrogen metabolic process GOC:tb Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. down regulation of nitrogen metabolic process down-regulation of nitrogen metabolic process downregulation of nitrogen metabolic process negative regulation of nitrogen metabolic process negative regulation of nitrogen metabolism inhibition of nitrogen metabolic process biological_process GO:0051172 negative regulation of nitrogen compound metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb negative regulation of nitrogen metabolic process GOC:tb Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. positive regulation of nitrogen metabolic process positive regulation of nitrogen metabolism up regulation of nitrogen metabolic process up-regulation of nitrogen metabolic process upregulation of nitrogen metabolic process activation of nitrogen metabolic process stimulation of nitrogen metabolic process biological_process GO:0051173 positive regulation of nitrogen compound metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds. GOC:ai GOC:tb positive regulation of nitrogen metabolic process GOC:tb Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. regulation of phosphorus metabolism biological_process GO:0051174 regulation of phosphorus metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphorus or compounds containing phosphorus. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. down regulation of sulfur metabolic process down-regulation of sulfur metabolic process downregulation of sulfur metabolic process negative regulation of sulfur metabolism negative regulation of sulphur metabolic process negative regulation of sulphur metabolism inhibition of sulfur metabolic process biological_process GO:0051175 negative regulation of sulfur metabolic process Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. GOC:ai Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. positive regulation of sulfur metabolism positive regulation of sulphur metabolic process positive regulation of sulphur metabolism up regulation of sulfur metabolic process up-regulation of sulfur metabolic process upregulation of sulfur metabolic process activation of sulfur metabolic process stimulation of sulfur metabolic process biological_process GO:0051176 positive regulation of sulfur metabolic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving sulfur or compounds containing sulfur. GOC:ai Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. jl 2013-12-18T13:51:04Z GO:1902578 establishment and maintenance of localization establishment and maintenance of position localisation establishment and maintenance of cellular component location establishment and maintenance of substance location establishment and maintenance of substrate location biological_process single organism localization single-organism localization GO:0051179 localization Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation. GOC:ai GOC:dos localisation GOC:mah single organism localization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. up regulation of protein transport up-regulation of protein transport upregulation of protein transport activation of protein transport stimulation of protein transport biological_process GO:0051222 positive regulation of protein transport Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. biological_process GO:0051223 regulation of protein transport Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. down regulation of protein transport down-regulation of protein transport downregulation of protein transport inhibition of protein transport biological_process GO:0051224 negative regulation of protein transport Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:ai Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation biological_process GO:0051234 establishment of localization Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos establishment of localisation GOC:mah Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. biological_process GO:0051239 regulation of multicellular organismal process Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai GOC:dph GOC:tb Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. up regulation of multicellular organismal process up-regulation of multicellular organismal process upregulation of multicellular organismal process activation of multicellular organismal process stimulation of multicellular organismal process biological_process GO:0051240 positive regulation of multicellular organismal process Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. down regulation of multicellular organismal process down-regulation of multicellular organismal process downregulation of multicellular organismal process inhibition of multicellular organismal process biological_process GO:0051241 negative regulation of multicellular organismal process Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs. GOC:ai Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. transferase regulator biological_process GO:0051338 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. regulation of transferase activity Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. EC:2.-.-.- GOC:ai Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. transferase activator up regulation of transferase activity up-regulation of transferase activity upregulation of transferase activity activation of transferase activity stimulation of transferase activity biological_process GO:0051347 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. positive regulation of transferase activity Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. down regulation of transferase activity down-regulation of transferase activity downregulation of transferase activity transferase inhibitor inhibition of transferase activity biological_process GO:0051348 This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. negative regulation of transferase activity Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor. GOC:ai Any process involved in the maintenance of an internal steady state of calcium ions within the cytoplasm of a cell or between mitochondria and their surroundings. calcium ion homeostasis in mitochondria calcium ion homeostasis in mitochondrion mitochondrial calcium ion concentration regulation regulation of calcium ion concentration in mitochondria regulation of calcium ion concentration in mitochondrion regulation of mitochondrial calcium ion concentration biological_process GO:0051560 mitochondrial calcium ion homeostasis Any process involved in the maintenance of an internal steady state of calcium ions within the cytoplasm of a cell or between mitochondria and their surroundings. GOC:ai GOC:mah A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. jl 2013-12-18T14:04:32Z GO:1902580 cellular localisation establishment and maintenance of cellular localization establishment and maintenance of localization in cell or cell membrane single organism cellular localization intracellular localization localization within cell biological_process single-organism cellular localization GO:0051641 cellular localization A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane. GOC:tb GOC:vw cellular localisation GOC:mah single organism cellular localization GOC:TermGenie Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. establishment of localisation in cell establishment of intracellular localization establishment of localization within cell positioning within cell biological_process establishment of cellular localization GO:0051649 establishment of localization in cell Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. GOC:ai GOC:dos GOC:dph GOC:tb establishment of localisation in cell GOC:mah establishment of cellular localization GOC:dph GOC:tb Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane. establishment and maintenance of localization in membrane establishment and maintenance of position in membrane localisation within membrane localization to membrane positioning within membrane biological_process GO:0051668 localization within membrane Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane. GOC:ai localisation within membrane GOC:mah Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. biological_process GO:0051716 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. cellular response to stimulus Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell. GOC:bf GOC:jl Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell. biological_process GO:0055062 phosphate ion homeostasis Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell. GOC:jid GOC:mah Any process involved in the maintenance of an internal steady state of metal ions within an organism or cell. biological_process GO:0055065 metal ion homeostasis Any process involved in the maintenance of an internal steady state of metal ions within an organism or cell. GOC:ai GOC:jid GOC:mah Any process involved in the maintenance of an internal steady state of monovalent inorganic cations within an organism or cell. biological_process GO:0055067 monovalent inorganic cation homeostasis Any process involved in the maintenance of an internal steady state of monovalent inorganic cations within an organism or cell. GOC:ai GOC:jid GOC:mah Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell. regulation of calcium ion concentration biological_process GO:0055074 calcium ion homeostasis Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell. GOC:ceb GOC:jid GOC:mah Any process involved in the maintenance of an internal steady state of cations within an organism or cell. biological_process GO:0055080 cation homeostasis Any process involved in the maintenance of an internal steady state of cations within an organism or cell. GOC:ceb GOC:jid GOC:mah Any process involved in the maintenance of an internal steady state of anions within an organism or cell. biological_process GO:0055081 anion homeostasis Any process involved in the maintenance of an internal steady state of anions within an organism or cell. GOC:ceb GOC:jid GOC:mah Any biological process involved in the maintenance of an internal steady state of a chemical at the level of the cell. biological_process GO:0055082 cellular chemical homeostasis Any biological process involved in the maintenance of an internal steady state of a chemical at the level of the cell. GOC:isa_complete GOC:jid The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. tb 2015-10-21T13:22:47Z GO:0090662 membrane transport ATP hydrolysis coupled transmembrane transport biological_process GO:0055085 Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. transmembrane transport The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GOC:dph GOC:jid The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide. nucleobase, nucleoside and nucleotide metabolism biological_process nucleobase, nucleoside and nucleotide metabolic process GO:0055086 nucleobase-containing small molecule metabolic process The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide. GOC:vw Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. regulation of cellular localisation biological_process GO:0060341 regulation of cellular localization Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell. GOC:dph GOC:tb regulation of cellular localisation GOC:mah The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. biological_process GO:0060348 bone development The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components. GOC:dph The process in which bones are generated and organized. biological_process GO:0060349 bone morphogenesis The process in which bones are generated and organized. GOC:dph The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone. biological_process GO:0060350 endochondral bone morphogenesis The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone. GOC:dph PMID:11680679 Any process that increases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0060456 positive regulation of digestive system process Any process that increases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:dph GOC:tb Any process that decreases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. biological_process GO:0060457 negative regulation of digestive system process Any process that decreases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism. GOC:dph GOC:tb The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape. dph 2009-04-28T08:42:53Z differential growth biological_process GO:0060560 developmental growth involved in morphogenesis The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape. GOC:dph differential growth GOC:dph The regulated release of a hormone into the circulatory system. dph 2010-01-11T09:03:48Z biological_process GO:0060986 endocrine hormone secretion The regulated release of a hormone into the circulatory system. GOC:dph A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. jl 2010-02-08T02:43:11Z GO:0016044 GO:0044802 cellular membrane organisation cellular membrane organization membrane organisation biological_process membrane organization and biogenesis single-organism membrane organization GO:0061024 membrane organization A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GOC:dph GOC:tb membrane organisation GOC:mah membrane organization and biogenesis GOC:mah Any process that modulates the rate, frequency or extent of a small molecule metabolic process. dph 2018-03-19T14:11:54Z regulation of small molecule metabolism biological_process GO:0062012 regulation of small molecule metabolic process Any process that modulates the rate, frequency or extent of a small molecule metabolic process. GOC:vw Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process. dph 2018-03-19T14:25:10Z positive regulation of small molecule metabolism biological_process GO:0062013 positive regulation of small molecule metabolic process Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process. GOC:vw Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process. dph 2018-03-19T14:27:23Z negative regulation of small molecule metabolism biological_process GO:0062014 negative regulation of small molecule metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process. GOC:vw Any process that modulates a measurable attribute of any biological process, quality or function. regulation biological_process GO:0065007 biological regulation Any process that modulates a measurable attribute of any biological process, quality or function. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. regulation of biological attribute regulation of biological characteristic biological_process GO:0065008 regulation of biological quality Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. GOC:dph GOC:isa_complete GOC:mah GOC:pr GOC:vw Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. regulation of a molecular function biological_process GO:0065009 regulation of molecular function Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding. GOC:isa_complete Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. regulation of establishment of protein localisation biological_process GO:0070201 regulation of establishment of protein localization Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location. GOC:BHF GOC:mah regulation of establishment of protein localisation GOC:mah Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. mah 2009-06-16T04:08:29Z cellular macromolecule localisation biological_process GO:0070727 cellular macromolecule localization Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:mah cellular macromolecule localisation GOC:mah Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. mah 2010-02-25T04:00:13Z protein localisation in extracellular region protein localization in extracellular region biological_process GO:0071692 protein localization to extracellular region Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location. GOC:mah protein localisation in extracellular region GOC:mah The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. mah 2010-03-08T02:15:14Z biological_process GO:0071702 organic substance transport The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon. GOC:mah The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. mah 2010-03-08T03:32:18Z organic molecular entity metabolic process organic molecular entity metabolism organic substance metabolism biological_process GO:0071704 organic substance metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. GOC:mah The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. mah 2010-03-08T03:56:28Z biological_process GO:0071705 nitrogen compound transport The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:mah A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. mah 2010-09-10T01:39:16Z GO:0071841 cellular component organisation or biogenesis cellular component organisation or biogenesis at cellular level cellular component organization or biogenesis at cellular level biological_process GO:0071840 cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. GOC:mah cellular component organisation or biogenesis GOC:mah cellular component organisation or biogenesis at cellular level GOC:mah The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. mah 2010-10-04T01:51:47Z cellular_component GO:0071944 cell periphery The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. GOC:mah Any process involved in the maintenance of an internal steady state of divalent cations at the level of a cell. mah 2010-12-16T01:25:40Z biological_process GO:0072503 Note that this term was split from 'cellular di-, tri-valent inorganic cation homeostasis ; GO:0030005' (sibling term 'cellular trivalent inorganic cation homeostasis' ; GO:0072504'). cellular divalent inorganic cation homeostasis Any process involved in the maintenance of an internal steady state of divalent cations at the level of a cell. GOC:mah Any process involved in the maintenance of an internal steady state of trivalent inorganic anions within an organism or cell. mah 2010-12-16T01:39:39Z biological_process GO:0072506 Note that this term was split from 'di-, tri-valent inorganic anion homeostasis ; GO:0055061' (sibling term 'divalent inorganic anion homeostasis' ; GO:0072505'). trivalent inorganic anion homeostasis Any process involved in the maintenance of an internal steady state of trivalent inorganic anions within an organism or cell. GOC:mah Any process involved in the maintenance of an internal steady state of divalent cations within an organism or cell. mah 2010-12-16T03:22:48Z biological_process GO:0072507 Note that this term was split from 'di-, tri-valent inorganic cation homeostasis ; GO:0055066' (sibling term 'trivalent inorganic cation homeostasis' ; GO:0072508'). divalent inorganic cation homeostasis Any process involved in the maintenance of an internal steady state of divalent cations within an organism or cell. GOC:mah The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof. mah 2011-01-04T03:03:59Z purine and derivative metabolic process purine-containing compound metabolism biological_process GO:0072521 purine-containing compound metabolic process The chemical reactions and pathways involving a purine-containing compound, i.e. any compound that contains purine or a formal derivative thereof. GOC:mah purine-containing compound metabolism GOC:mah Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. dhl 2009-04-22T04:30:52Z biological_process GO:0080090 regulation of primary metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism. PMID:19211694 Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). dhl 2009-05-06T04:51:28Z biological_process GO:0080134 Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. regulation of response to stress Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). GOC:dhl Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. tb 2009-10-23T11:21:38Z biological_process GO:0090087 regulation of peptide transport Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GOC:dph GOC:tb Any process that modulates the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. tb 2009-12-18T10:33:49Z biological_process GO:0090181 regulation of cholesterol metabolic process Any process that modulates the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. GOC:BHF GOC:dph GOC:tb Any process that increases the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. tb 2009-12-23T10:27:37Z biological_process GO:0090205 positive regulation of cholesterol metabolic process Any process that increases the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. GOC:dph GOC:sl GOC:tb Any process that decreases the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. tb 2009-12-23T10:27:37Z biological_process GO:0090206 negative regulation of cholesterol metabolic process Any process that decreases the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. GOC:dph GOC:sl GOC:tb Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. tb 2010-04-16T03:45:07Z biological_process GO:0090316 positive regulation of intracellular protein transport Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. tb 2010-04-16T03:45:07Z biological_process GO:0090317 negative regulation of intracellular protein transport Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells. GOC:tb Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. tb 2010-07-12T11:14:12Z biological_process GO:0090368 regulation of ornithine metabolic process Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis. GOC:dph GOC:jp GOC:tb Any vesicle that is part of the intracellular region. pr 2016-03-29T17:39:45Z cellular_component GO:0097708 intracellular vesicle Any vesicle that is part of the intracellular region. GOC:vesicles The lipid bilayer that forms the outer-most layer of an organelle. dos 2014-02-26T13:41:31Z cellular_component GO:0098588 Examples include the outer membranes of double membrane bound organelles such as mitochondria as well as the bounding membranes of single-membrane bound organelles such as lysosomes. bounding membrane of organelle The lipid bilayer that forms the outer-most layer of an organelle. GOC:dos A membrane that is a (regional) part of the plasma membrane. dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component GO:0098590 Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. plasma membrane region A membrane that is a (regional) part of the plasma membrane. GOC:dos The process in which an anion is transported across a membrane. GO:0099133 ATP hydrolysis coupled anion transmembrane transport biological_process GO:0098656 anion transmembrane transport The process in which an anion is transported across a membrane. GOC:dos GOC:vw Any process involved in the maintenance of an internal steady state of inorganic ions within an organism or cell. biological_process GO:0098771 inorganic ion homeostasis Any process involved in the maintenance of an internal steady state of inorganic ions within an organism or cell. GOC:dos A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. molecular_function GO:0098772 molecular function regulator A molecular function that modulates the activity of a gene product or complex. Examples include enzyme regulators and channel regulators. GOC:dos GOC:pt A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. cellular_component GO:0099503 secretory vesicle A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space. GOC:dos Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. cellular_component GO:0099568 cytoplasmic region Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. GOC:dos The complete extent of cell cortex that underlies some some region of the plasma membrane. perimembrane region cellular_component GO:0099738 cell cortex region The complete extent of cell cortex that underlies some some region of the plasma membrane. GOC:dos Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. hjd 2017-10-27T17:33:05Z biological_process GO:0106064 regulation of cobalamin metabolic process Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom. PMID:29056341 Any process that activates or increases the frequency, rate or extent of a cobalamin metabolic process. hjd 2018-05-01T18:07:12Z biological_process GO:0106121 positive regulation of cobalamin metabolic process Any process that activates or increases the frequency, rate or extent of a cobalamin metabolic process. PMID:29056341 Any process that stops, prevents or reduces the frequency, rate or extent of a cobalamin metabolic process. hjd 2018-05-01T18:12:48Z biological_process GO:0106122 negative regulation of cobalamin metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of a cobalamin metabolic process. PMID:29056341 Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis. kmv 2018-07-05T14:10:14Z biological_process GO:0110110 positive regulation of animal organ morphogenesis Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis. GOC:kmv Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis. kmv 2018-07-05T14:25:21Z biological_process GO:0110111 negative regulation of animal organ morphogenesis Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis. GOC:kmv A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. kmv 2019-08-12T18:01:37Z cellular_component GO:0110165 cellular anatomical entity A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. GOC:kmv The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. pg 2019-05-22T11:20:45Z efflux biological_process GO:0140352 export from cell The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis. GOC:pg The directed movement of a lipid from a cell, into the extracellular region. pg 2019-05-22T11:33:07Z lipid efflux biological_process GO:0140353 lipid export from cell The directed movement of a lipid from a cell, into the extracellular region. GOC:pg Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. bf 2012-02-22T11:40:53Z regulation of receptor ligand biological_process GO:1900120 regulation of receptor binding Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling regulation of receptor ligand GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. bf 2012-02-22T11:40:57Z down regulation of receptor binding down-regulation of receptor binding downregulation of receptor binding inhibition of receptor binding inhibition of receptor ligand biological_process down regulation of receptor-associated protein activity GO:1900121 negative regulation of receptor binding Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling down regulation of receptor binding GOC:TermGenie down-regulation of receptor binding GOC:TermGenie downregulation of receptor binding GOC:TermGenie inhibition of receptor binding GOC:TermGenie inhibition of receptor ligand GOC:TermGenie down regulation of receptor-associated protein activity GOC:TermGenie Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. bf 2012-02-22T11:41:00Z up regulation of receptor binding upregulation of receptor binding activation of receptor binding biological_process GO:1900122 positive regulation of receptor binding Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor. GOC:TermGenie GOC:signaling up regulation of receptor binding GOC:TermGenie upregulation of receptor binding GOC:TermGenie activation of receptor binding GOC:TermGenie The chemical reactions and pathways involving organic cyclic compound. bf 2012-09-14T09:03:51Z organic cyclic compound metabolism biological_process GO:1901360 organic cyclic compound metabolic process The chemical reactions and pathways involving organic cyclic compound. GOC:TermGenie organic cyclic compound metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of tetrapyrrole metabolic process. tt 2012-10-01T14:34:03Z regulation of tetrapyrrole metabolism biological_process GO:1901401 regulation of tetrapyrrole metabolic process Any process that modulates the frequency, rate or extent of tetrapyrrole metabolic process. GOC:TermGenie GOC:mengo_curators regulation of tetrapyrrole metabolism GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole metabolic process. tt 2012-10-01T14:35:11Z down regulation of tetrapyrrole metabolic process down regulation of tetrapyrrole metabolism down-regulation of tetrapyrrole metabolic process down-regulation of tetrapyrrole metabolism downregulation of tetrapyrrole metabolic process downregulation of tetrapyrrole metabolism inhibition of tetrapyrrole metabolism negative regulation of tetrapyrrole metabolism inhibition of tetrapyrrole metabolic process biological_process GO:1901402 negative regulation of tetrapyrrole metabolic process Any process that stops, prevents or reduces the frequency, rate or extent of tetrapyrrole metabolic process. GOC:TermGenie GOC:mengo_curators down regulation of tetrapyrrole metabolic process GOC:TermGenie down regulation of tetrapyrrole metabolism GOC:TermGenie down-regulation of tetrapyrrole metabolic process GOC:TermGenie down-regulation of tetrapyrrole metabolism GOC:TermGenie downregulation of tetrapyrrole metabolic process GOC:TermGenie downregulation of tetrapyrrole metabolism GOC:TermGenie inhibition of tetrapyrrole metabolism GOC:TermGenie negative regulation of tetrapyrrole metabolism GOC:TermGenie inhibition of tetrapyrrole metabolic process GOC:TermGenie Any process that activates or increases the frequency, rate or extent of tetrapyrrole metabolic process. tt 2012-10-01T14:35:29Z activation of tetrapyrrole metabolism positive regulation of tetrapyrrole metabolism up regulation of tetrapyrrole metabolic process up regulation of tetrapyrrole metabolism up-regulation of tetrapyrrole metabolic process up-regulation of tetrapyrrole metabolism upregulation of tetrapyrrole metabolic process upregulation of tetrapyrrole metabolism activation of tetrapyrrole metabolic process biological_process GO:1901403 positive regulation of tetrapyrrole metabolic process Any process that activates or increases the frequency, rate or extent of tetrapyrrole metabolic process. GOC:TermGenie GOC:mengo_curators activation of tetrapyrrole metabolism GOC:TermGenie positive regulation of tetrapyrrole metabolism GOC:TermGenie up regulation of tetrapyrrole metabolic process GOC:TermGenie up regulation of tetrapyrrole metabolism GOC:TermGenie up-regulation of tetrapyrrole metabolic process GOC:TermGenie up-regulation of tetrapyrrole metabolism GOC:TermGenie upregulation of tetrapyrrole metabolic process GOC:TermGenie upregulation of tetrapyrrole metabolism GOC:TermGenie activation of tetrapyrrole metabolic process GOC:TermGenie The chemical reactions and pathways involving organonitrogen compound. pr 2012-11-04T15:17:52Z organonitrogen compound metabolism biological_process GO:1901564 organonitrogen compound metabolic process The chemical reactions and pathways involving organonitrogen compound. GOC:TermGenie GOC:pr organonitrogen compound metabolism GOC:TermGenie The chemical reactions and pathways involving fatty acid derivative. pr 2012-11-04T17:13:36Z fatty acid derivative metabolism biological_process GO:1901568 fatty acid derivative metabolic process The chemical reactions and pathways involving fatty acid derivative. GOC:TermGenie GOC:pr fatty acid derivative metabolism GOC:TermGenie The chemical reactions and pathways resulting in the formation of fatty acid derivative. pr 2012-11-04T17:13:44Z fatty acid derivative anabolism fatty acid derivative biosynthesis fatty acid derivative formation fatty acid derivative synthesis biological_process GO:1901570 fatty acid derivative biosynthetic process The chemical reactions and pathways resulting in the formation of fatty acid derivative. GOC:TermGenie GOC:pr fatty acid derivative anabolism GOC:TermGenie fatty acid derivative biosynthesis GOC:TermGenie fatty acid derivative formation GOC:TermGenie fatty acid derivative synthesis GOC:TermGenie The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. pr 2012-11-05T11:04:40Z organic molecular entity anabolism organic molecular entity biosynthesis organic molecular entity biosynthetic process organic molecular entity formation organic molecular entity synthesis organic substance anabolism organic substance biosynthesis organic substance formation organic substance synthesis biological_process GO:1901576 organic substance biosynthetic process The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon. GOC:TermGenie GOC:pr organic molecular entity anabolism GOC:TermGenie organic molecular entity biosynthesis GOC:TermGenie organic molecular entity formation GOC:TermGenie organic molecular entity synthesis GOC:TermGenie The chemical reactions and pathways involving an alpha-amino acid. tb 2012-11-08T17:39:50Z alpha-amino acid metabolism biological_process GO:1901605 alpha-amino acid metabolic process The chemical reactions and pathways involving an alpha-amino acid. GOC:TermGenie alpha-amino acid metabolism GOC:TermGenie The chemical reactions and pathways involving organic hydroxy compound. pr 2012-11-13T12:54:27Z organic hydroxy compound metabolism biological_process GO:1901615 organic hydroxy compound metabolic process The chemical reactions and pathways involving organic hydroxy compound. GOC:TermGenie GOC:pr organic hydroxy compound metabolism GOC:TermGenie The chemical reactions and pathways involving erythrose 4-phosphate/phosphoenolpyruvate family amino acid. pr 2013-06-13T10:37:38Z erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolism biological_process GO:1902221 erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process The chemical reactions and pathways involving erythrose 4-phosphate/phosphoenolpyruvate family amino acid. GOC:TermGenie GOC:pr erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolism GOC:TermGenie The chemical reactions and pathways involving ketone body. pr 2013-06-13T10:37:54Z ketone body metabolism biological_process GO:1902224 ketone body metabolic process The chemical reactions and pathways involving ketone body. GOC:TermGenie GOC:pr ketone body metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:32:52Z GO:0010627 regulation of intracellular signaling cascade regulation of intracellular signaling chain regulation of intracellular protein kinase cascade regulation of intracellular signal transduction pathway regulation of signal transmission via intracellular cascade biological_process regulation of intracellular signaling pathway regulation of signal transduction via intracellular signaling cascade GO:1902531 regulation of intracellular signal transduction Any process that modulates the frequency, rate or extent of intracellular signal transduction. GOC:TermGenie GOC:dph GOC:signaling GOC:tb regulation of intracellular signaling cascade GOC:TermGenie regulation of intracellular signaling chain GOC:TermGenie regulation of intracellular signal transduction pathway GOC:TermGenie regulation of signal transmission via intracellular cascade GOC:TermGenie regulation of intracellular signaling pathway GOC:TermGenie regulation of signal transduction via intracellular signaling cascade GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:33:01Z GO:0010741 down regulation of intracellular signal transduction down regulation of intracellular signaling chain down-regulation of intracellular signal transduction down-regulation of intracellular signaling chain downregulation of intracellular signal transduction downregulation of intracellular signaling chain negative regulation of intracellular protein kinase cascade negative regulation of intracellular signaling cascade negative regulation of intracellular signaling chain down regulation of intracellular signal transduction pathway down regulation of intracellular signaling cascade down regulation of signal transmission via intracellular cascade down-regulation of intracellular signal transduction pathway downregulation of intracellular signal transduction pathway downregulation of intracellular signaling cascade downregulation of signal transmission via intracellular cascade inhibition of intracellular signal transduction inhibition of intracellular signal transduction pathway inhibition of intracellular signaling cascade inhibition of intracellular signaling chain inhibition of signal transmission via intracellular cascade negative regulation of intracellular signal transduction pathway negative regulation of signal transmission via intracellular cascade biological_process down regulation of intracellular signaling pathway down regulation of signal transduction via intracellular signaling cascade down-regulation of intracellular signaling cascade down-regulation of intracellular signaling pathway down-regulation of signal transduction via intracellular signaling cascade down-regulation of signal transmission via intracellular cascade downregulation of intracellular signaling pathway downregulation of signal transduction via intracellular signaling cascade inhibition of intracellular signaling pathway inhibition of signal transduction via intracellular signaling cascade negative regulation of intracellular signaling pathway negative regulation of signal transduction via intracellular signaling cascade GO:1902532 negative regulation of intracellular signal transduction Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction. GOC:TermGenie GOC:dph GOC:signaling GOC:tb down regulation of intracellular signal transduction GOC:TermGenie down regulation of intracellular signaling chain GOC:TermGenie down-regulation of intracellular signal transduction GOC:TermGenie down-regulation of intracellular signaling chain GOC:TermGenie downregulation of intracellular signal transduction GOC:TermGenie downregulation of intracellular signaling chain GOC:TermGenie negative regulation of intracellular signaling cascade GOC:TermGenie negative regulation of intracellular signaling chain GOC:TermGenie down regulation of intracellular signal transduction pathway GOC:TermGenie down regulation of intracellular signaling cascade GOC:TermGenie down regulation of signal transmission via intracellular cascade GOC:TermGenie down-regulation of intracellular signal transduction pathway GOC:TermGenie downregulation of intracellular signal transduction pathway GOC:TermGenie downregulation of intracellular signaling cascade GOC:TermGenie downregulation of signal transmission via intracellular cascade GOC:TermGenie inhibition of intracellular signal transduction GOC:TermGenie inhibition of intracellular signal transduction pathway GOC:TermGenie inhibition of intracellular signaling cascade GOC:TermGenie inhibition of intracellular signaling chain GOC:TermGenie inhibition of signal transmission via intracellular cascade GOC:TermGenie negative regulation of intracellular signal transduction pathway GOC:TermGenie negative regulation of signal transmission via intracellular cascade GOC:TermGenie down regulation of intracellular signaling pathway GOC:TermGenie down regulation of signal transduction via intracellular signaling cascade GOC:TermGenie down-regulation of intracellular signaling cascade GOC:TermGenie down-regulation of intracellular signaling pathway GOC:TermGenie down-regulation of signal transduction via intracellular signaling cascade GOC:TermGenie down-regulation of signal transmission via intracellular cascade GOC:TermGenie downregulation of intracellular signaling pathway GOC:TermGenie downregulation of signal transduction via intracellular signaling cascade GOC:TermGenie inhibition of intracellular signaling pathway GOC:TermGenie inhibition of signal transduction via intracellular signaling cascade GOC:TermGenie negative regulation of intracellular signaling pathway GOC:TermGenie negative regulation of signal transduction via intracellular signaling cascade GOC:TermGenie Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. bf 2013-12-02T11:33:10Z GO:0010740 positive regulation of intracellular signaling chain up regulation of intracellular signal transduction up regulation of intracellular signaling chain up-regulation of intracellular signal transduction up-regulation of intracellular signaling chain upregulation of intracellular signal transduction upregulation of intracellular signaling chain activation of intracellular signal transduction activation of intracellular signal transduction pathway activation of intracellular signaling cascade activation of intracellular signaling chain activation of signal transmission via intracellular cascade positive regulation of intracellular protein kinase cascade positive regulation of intracellular signal transduction pathway positive regulation of signal transmission via intracellular cascade up regulation of intracellular signal transduction pathway up regulation of signal transmission via intracellular cascade up-regulation of intracellular signal transduction pathway up-regulation of signal transmission via intracellular cascade upregulation of intracellular signal transduction pathway upregulation of signal transmission via intracellular cascade biological_process activation of intracellular signaling pathway activation of signal transduction via intracellular signaling cascade positive regulation of intracellular signaling cascade positive regulation of intracellular signaling pathway positive regulation of signal transduction via intracellular signaling cascade up regulation of intracellular signaling cascade up regulation of intracellular signaling pathway up regulation of signal transduction via intracellular signaling cascade up-regulation of intracellular signaling cascade up-regulation of intracellular signaling pathway up-regulation of signal transduction via intracellular signaling cascade upregulation of intracellular signaling cascade upregulation of intracellular signaling pathway upregulation of signal transduction via intracellular signaling cascade GO:1902533 positive regulation of intracellular signal transduction Any process that activates or increases the frequency, rate or extent of intracellular signal transduction. GOC:BHF GOC:TermGenie GOC:dph GOC:signaling GOC:tb positive regulation of intracellular signaling chain GOC:TermGenie up regulation of intracellular signal transduction GOC:TermGenie up regulation of intracellular signaling chain GOC:TermGenie up-regulation of intracellular signal transduction GOC:TermGenie up-regulation of intracellular signaling chain GOC:TermGenie upregulation of intracellular signal transduction GOC:TermGenie upregulation of intracellular signaling chain GOC:TermGenie activation of intracellular signal transduction GOC:TermGenie activation of intracellular signal transduction pathway GOC:TermGenie activation of intracellular signaling cascade GOC:TermGenie activation of intracellular signaling chain GOC:TermGenie activation of signal transmission via intracellular cascade GOC:TermGenie positive regulation of intracellular signal transduction pathway GOC:TermGenie positive regulation of signal transmission via intracellular cascade GOC:TermGenie up regulation of intracellular signal transduction pathway GOC:TermGenie up regulation of signal transmission via intracellular cascade GOC:TermGenie up-regulation of intracellular signal transduction pathway GOC:TermGenie up-regulation of signal transmission via intracellular cascade GOC:TermGenie upregulation of intracellular signal transduction pathway GOC:TermGenie upregulation of signal transmission via intracellular cascade GOC:TermGenie activation of intracellular signaling pathway GOC:TermGenie activation of signal transduction via intracellular signaling cascade GOC:TermGenie positive regulation of intracellular signaling cascade GOC:TermGenie positive regulation of intracellular signaling pathway GOC:TermGenie positive regulation of signal transduction via intracellular signaling cascade GOC:TermGenie up regulation of intracellular signaling cascade GOC:TermGenie up regulation of intracellular signaling pathway GOC:TermGenie up regulation of signal transduction via intracellular signaling cascade GOC:TermGenie up-regulation of intracellular signaling cascade GOC:TermGenie up-regulation of intracellular signaling pathway GOC:TermGenie up-regulation of signal transduction via intracellular signaling cascade GOC:TermGenie upregulation of intracellular signaling cascade GOC:TermGenie upregulation of intracellular signaling pathway GOC:TermGenie upregulation of signal transduction via intracellular signaling cascade GOC:TermGenie The chemical reactions and pathways involving secondary alcohol. tt 2014-01-22T10:14:52Z secondary alcohol metabolism biological_process GO:1902652 secondary alcohol metabolic process The chemical reactions and pathways involving secondary alcohol. GOC:TermGenie GOC:mengo_curators GO_REF:0000068 PMID:11288200 secondary alcohol metabolism GOC:TermGenie Any process that modulates the frequency, rate or extent of bone development. mr 2014-05-13T22:41:53Z biological_process GO:1903010 regulation of bone development Any process that modulates the frequency, rate or extent of bone development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:22510437 Any process that stops, prevents or reduces the frequency, rate or extent of bone development. mr 2014-05-13T22:42:00Z down regulation of bone development down-regulation of bone development downregulation of bone development inhibition of bone development biological_process GO:1903011 negative regulation of bone development Any process that stops, prevents or reduces the frequency, rate or extent of bone development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:22510437 down regulation of bone development GOC:TermGenie down-regulation of bone development GOC:TermGenie downregulation of bone development GOC:TermGenie inhibition of bone development GOC:TermGenie Any process that activates or increases the frequency, rate or extent of bone development. mr 2014-05-13T22:42:06Z up regulation of bone development up-regulation of bone development upregulation of bone development activation of bone development biological_process GO:1903012 positive regulation of bone development Any process that activates or increases the frequency, rate or extent of bone development. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:22510437 up regulation of bone development GOC:TermGenie up-regulation of bone development GOC:TermGenie upregulation of bone development GOC:TermGenie activation of bone development GOC:TermGenie Any process that modulates the frequency, rate or extent of blood circulation. mr 2014-10-06T18:38:56Z biological_process regulation of hemolymph circulation GO:1903522 regulation of blood circulation Any process that modulates the frequency, rate or extent of blood circulation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:10659969 regulation of hemolymph circulation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation. mr 2014-10-06T18:39:05Z down regulation of blood circulation down-regulation of blood circulation downregulation of blood circulation inhibition of blood circulation biological_process down regulation of hemolymph circulation down-regulation of hemolymph circulation downregulation of hemolymph circulation inhibition of hemolymph circulation negative regulation of hemolymph circulation GO:1903523 negative regulation of blood circulation Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:10659969 down regulation of blood circulation GOC:TermGenie down-regulation of blood circulation GOC:TermGenie downregulation of blood circulation GOC:TermGenie inhibition of blood circulation GOC:TermGenie down regulation of hemolymph circulation GOC:TermGenie down-regulation of hemolymph circulation GOC:TermGenie downregulation of hemolymph circulation GOC:TermGenie inhibition of hemolymph circulation GOC:TermGenie negative regulation of hemolymph circulation GOC:TermGenie Any process that activates or increases the frequency, rate or extent of blood circulation. mr 2014-10-06T18:39:13Z up regulation of blood circulation up-regulation of blood circulation upregulation of blood circulation activation of blood circulation biological_process activation of hemolymph circulation positive regulation of hemolymph circulation up regulation of hemolymph circulation up-regulation of hemolymph circulation upregulation of hemolymph circulation GO:1903524 positive regulation of blood circulation Any process that activates or increases the frequency, rate or extent of blood circulation. GOC:TermGenie GOC:mr GO_REF:0000058 PMID:10659969 up regulation of blood circulation GOC:TermGenie up-regulation of blood circulation GOC:TermGenie upregulation of blood circulation GOC:TermGenie activation of blood circulation GOC:TermGenie activation of hemolymph circulation GOC:TermGenie positive regulation of hemolymph circulation GOC:TermGenie up regulation of hemolymph circulation GOC:TermGenie up-regulation of hemolymph circulation GOC:TermGenie upregulation of hemolymph circulation GOC:TermGenie Any process that modulates the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:24:59Z regulation of cellular secretion biological_process GO:1903530 regulation of secretion by cell Any process that modulates the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 regulation of cellular secretion GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:25:08Z down regulation of cellular secretion down regulation of secretion by cell down-regulation of cellular secretion down-regulation of secretion by cell downregulation of cellular secretion downregulation of secretion by cell negative regulation of cellular secretion inhibition of cellular secretion inhibition of secretion by cell biological_process GO:1903531 negative regulation of secretion by cell Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 down regulation of cellular secretion GOC:TermGenie down regulation of secretion by cell GOC:TermGenie down-regulation of cellular secretion GOC:TermGenie down-regulation of secretion by cell GOC:TermGenie downregulation of cellular secretion GOC:TermGenie downregulation of secretion by cell GOC:TermGenie negative regulation of cellular secretion GOC:TermGenie inhibition of cellular secretion GOC:TermGenie inhibition of secretion by cell GOC:TermGenie Any process that activates or increases the frequency, rate or extent of secretion by cell. pm 2014-10-08T13:25:17Z positive regulation of cellular secretion up regulation of cellular secretion up regulation of secretion by cell up-regulation of cellular secretion up-regulation of secretion by cell upregulation of cellular secretion upregulation of secretion by cell activation of cellular secretion activation of secretion by cell biological_process GO:1903532 positive regulation of secretion by cell Any process that activates or increases the frequency, rate or extent of secretion by cell. GOC:TermGenie GOC:pm GO_REF:0000058 PMID:12130530 positive regulation of cellular secretion GOC:TermGenie up regulation of cellular secretion GOC:TermGenie up regulation of secretion by cell GOC:TermGenie up-regulation of cellular secretion GOC:TermGenie up-regulation of secretion by cell GOC:TermGenie upregulation of cellular secretion GOC:TermGenie upregulation of secretion by cell GOC:TermGenie activation of cellular secretion GOC:TermGenie activation of secretion by cell GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of anion transport. sl 2015-01-12T21:50:20Z down regulation of anion transport down-regulation of anion transport downregulation of anion transport inhibition of anion transport biological_process GO:1903792 negative regulation of anion transport Any process that stops, prevents or reduces the frequency, rate or extent of anion transport. GOC:TermGenie GO_REF:0000058 PMID:11336802 down regulation of anion transport GOC:TermGenie down-regulation of anion transport GOC:TermGenie downregulation of anion transport GOC:TermGenie inhibition of anion transport GOC:TermGenie Any process that activates or increases the frequency, rate or extent of anion transport. sl 2015-01-12T21:50:30Z up regulation of anion transport up-regulation of anion transport upregulation of anion transport activation of anion transport biological_process GO:1903793 positive regulation of anion transport Any process that activates or increases the frequency, rate or extent of anion transport. GOC:TermGenie GO_REF:0000058 PMID:11336802 up regulation of anion transport GOC:TermGenie up-regulation of anion transport GOC:TermGenie upregulation of anion transport GOC:TermGenie activation of anion transport GOC:TermGenie Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. jl 2015-01-20T14:32:14Z regulation of cellular protein localisation regulation of channel localizer activity biological_process GO:1903827 regulation of cellular protein localization Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:TermGenie GOC:vw GO_REF:0000058 regulation of cellular protein localisation GOC:TermGenie regulation of channel localizer activity GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. jl 2015-01-20T14:32:24Z down regulation of cellular protein localisation down regulation of cellular protein localization down-regulation of cellular protein localisation down-regulation of cellular protein localization downregulation of cellular protein localisation downregulation of cellular protein localization negative regulation of cellular protein localisation down regulation of channel localizer activity down-regulation of channel localizer activity downregulation of channel localizer activity inhibition of cellular protein localisation inhibition of cellular protein localization inhibition of channel localizer activity negative regulation of channel localizer activity biological_process GO:1903828 negative regulation of cellular protein localization Any process that stops, prevents or reduces the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of cellular protein localisation GOC:TermGenie down regulation of cellular protein localization GOC:TermGenie down-regulation of cellular protein localisation GOC:TermGenie down-regulation of cellular protein localization GOC:TermGenie downregulation of cellular protein localisation GOC:TermGenie downregulation of cellular protein localization GOC:TermGenie negative regulation of cellular protein localisation GOC:TermGenie down regulation of channel localizer activity GOC:TermGenie down-regulation of channel localizer activity GOC:TermGenie downregulation of channel localizer activity GOC:TermGenie inhibition of cellular protein localisation GOC:TermGenie inhibition of cellular protein localization GOC:TermGenie inhibition of channel localizer activity GOC:TermGenie negative regulation of channel localizer activity GOC:TermGenie Any process that activates or increases the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. jl 2015-01-20T14:32:33Z positive regulation of cellular protein localisation up regulation of cellular protein localisation up regulation of cellular protein localization up-regulation of cellular protein localisation up-regulation of cellular protein localization upregulation of cellular protein localisation upregulation of cellular protein localization activation of cellular protein localisation activation of cellular protein localization activation of channel localizer activity positive regulation of channel localizer activity up regulation of channel localizer activity up-regulation of channel localizer activity upregulation of channel localizer activity biological_process GO:1903829 positive regulation of cellular protein localization Any process that activates or increases the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GOC:TermGenie GOC:vw GO_REF:0000058 positive regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localisation GOC:TermGenie up regulation of cellular protein localization GOC:TermGenie up-regulation of cellular protein localisation GOC:TermGenie up-regulation of cellular protein localization GOC:TermGenie upregulation of cellular protein localisation GOC:TermGenie upregulation of cellular protein localization GOC:TermGenie activation of cellular protein localisation GOC:TermGenie activation of cellular protein localization GOC:TermGenie activation of channel localizer activity GOC:TermGenie positive regulation of channel localizer activity GOC:TermGenie up regulation of channel localizer activity GOC:TermGenie up-regulation of channel localizer activity GOC:TermGenie upregulation of channel localizer activity GOC:TermGenie Any process that modulates the frequency, rate or extent of anion transmembrane transport. pr 2015-02-25T13:52:25Z biological_process GO:1903959 regulation of anion transmembrane transport Any process that modulates the frequency, rate or extent of anion transmembrane transport. GOC:TermGenie GOC:vw GO_REF:0000058 Any process that stops, prevents or reduces the frequency, rate or extent of anion transmembrane transport. pr 2015-02-25T13:52:35Z down regulation of anion transmembrane transport down-regulation of anion transmembrane transport downregulation of anion transmembrane transport inhibition of anion transmembrane transport biological_process GO:1903960 negative regulation of anion transmembrane transport Any process that stops, prevents or reduces the frequency, rate or extent of anion transmembrane transport. GOC:TermGenie GOC:vw GO_REF:0000058 down regulation of anion transmembrane transport GOC:TermGenie down-regulation of anion transmembrane transport GOC:TermGenie downregulation of anion transmembrane transport GOC:TermGenie inhibition of anion transmembrane transport GOC:TermGenie Any process that activates or increases the frequency, rate or extent of anion transmembrane transport. pr 2015-02-25T13:52:44Z up regulation of anion transmembrane transport up-regulation of anion transmembrane transport upregulation of anion transmembrane transport activation of anion transmembrane transport biological_process GO:1903961 positive regulation of anion transmembrane transport Any process that activates or increases the frequency, rate or extent of anion transmembrane transport. GOC:TermGenie GOC:vw GO_REF:0000058 up regulation of anion transmembrane transport GOC:TermGenie up-regulation of anion transmembrane transport GOC:TermGenie upregulation of anion transmembrane transport GOC:TermGenie activation of anion transmembrane transport GOC:TermGenie Any process that modulates the frequency, rate or extent of intestinal absorption. rl 2015-07-13T15:58:47Z biological_process GO:1904478 regulation of intestinal absorption Any process that modulates the frequency, rate or extent of intestinal absorption. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:12469120 Any process that stops, prevents or reduces the frequency, rate or extent of intestinal absorption. rl 2015-07-13T15:58:54Z down regulation of intestinal absorption down-regulation of intestinal absorption downregulation of intestinal absorption inhibition of intestinal absorption biological_process GO:1904479 negative regulation of intestinal absorption Any process that stops, prevents or reduces the frequency, rate or extent of intestinal absorption. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:12469120 down regulation of intestinal absorption GOC:TermGenie down-regulation of intestinal absorption GOC:TermGenie downregulation of intestinal absorption GOC:TermGenie inhibition of intestinal absorption GOC:TermGenie Any process that activates or increases the frequency, rate or extent of intestinal absorption. rl 2015-07-13T15:59:00Z up regulation of intestinal absorption up-regulation of intestinal absorption upregulation of intestinal absorption activation of intestinal absorption biological_process GO:1904480 positive regulation of intestinal absorption Any process that activates or increases the frequency, rate or extent of intestinal absorption. GOC:BHF GOC:TermGenie GOC:rl GO_REF:0000058 PMID:12469120 up regulation of intestinal absorption GOC:TermGenie up-regulation of intestinal absorption GOC:TermGenie upregulation of intestinal absorption GOC:TermGenie activation of intestinal absorption GOC:TermGenie The process in which glucose is transported across a membrane. vw 2015-09-04T17:20:16Z GO:0015758 biological_process glucose transport GO:1904659 glucose transmembrane transport The process in which glucose is transported across a membrane. GOC:TermGenie GO_REF:0000069 PMID:9090050 Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:24Z down regulation of establishment of protein localisation down regulation of establishment of protein localization down regulation of protein positioning down regulation of protein recruitment down-regulation of establishment of protein localisation down-regulation of establishment of protein localization down-regulation of protein positioning down-regulation of protein recruitment downregulation of establishment of protein localisation downregulation of establishment of protein localization downregulation of protein positioning downregulation of protein recruitment negative regulation of establishment of protein localisation negative regulation of protein positioning negative regulation of protein recruitment inhibition of establishment of protein localisation inhibition of establishment of protein localization inhibition of protein positioning inhibition of protein recruitment biological_process GO:1904950 negative regulation of establishment of protein localization Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 down regulation of establishment of protein localisation GOC:TermGenie down regulation of establishment of protein localization GOC:TermGenie down regulation of protein positioning GOC:TermGenie down regulation of protein recruitment GOC:TermGenie down-regulation of establishment of protein localisation GOC:TermGenie down-regulation of establishment of protein localization GOC:TermGenie down-regulation of protein positioning GOC:TermGenie down-regulation of protein recruitment GOC:TermGenie downregulation of establishment of protein localisation GOC:TermGenie downregulation of establishment of protein localization GOC:TermGenie downregulation of protein positioning GOC:TermGenie downregulation of protein recruitment GOC:TermGenie negative regulation of establishment of protein localisation GOC:TermGenie negative regulation of protein positioning GOC:TermGenie negative regulation of protein recruitment GOC:TermGenie inhibition of establishment of protein localisation GOC:TermGenie inhibition of establishment of protein localization GOC:TermGenie inhibition of protein positioning GOC:TermGenie inhibition of protein recruitment GOC:TermGenie Any process that activates or increases the frequency, rate or extent of establishment of protein localization. mec 2016-02-05T09:59:32Z positive regulation of establishment of protein localisation positive regulation of protein positioning positive regulation of protein recruitment up regulation of establishment of protein localisation up regulation of establishment of protein localization up regulation of protein positioning up regulation of protein recruitment up-regulation of establishment of protein localisation up-regulation of establishment of protein localization up-regulation of protein positioning up-regulation of protein recruitment upregulation of establishment of protein localisation upregulation of establishment of protein localization upregulation of protein positioning upregulation of protein recruitment activation of establishment of protein localisation activation of establishment of protein localization activation of protein positioning activation of protein recruitment biological_process GO:1904951 positive regulation of establishment of protein localization Any process that activates or increases the frequency, rate or extent of establishment of protein localization. GOC:TermGenie GO_REF:0000058 PMID:22761445 positive regulation of establishment of protein localisation GOC:TermGenie positive regulation of protein positioning GOC:TermGenie positive regulation of protein recruitment GOC:TermGenie up regulation of establishment of protein localisation GOC:TermGenie up regulation of establishment of protein localization GOC:TermGenie up regulation of protein positioning GOC:TermGenie up regulation of protein recruitment GOC:TermGenie up-regulation of establishment of protein localisation GOC:TermGenie up-regulation of establishment of protein localization GOC:TermGenie up-regulation of protein positioning GOC:TermGenie up-regulation of protein recruitment GOC:TermGenie upregulation of establishment of protein localisation GOC:TermGenie upregulation of establishment of protein localization GOC:TermGenie upregulation of protein positioning GOC:TermGenie upregulation of protein recruitment GOC:TermGenie activation of establishment of protein localisation GOC:TermGenie activation of establishment of protein localization GOC:TermGenie activation of protein positioning GOC:TermGenie activation of protein recruitment GOC:TermGenie Any process that modulates the frequency, rate or extent of lipid localization. rz 2017-02-21T12:12:22Z regulation of lipid localisation biological_process GO:1905952 regulation of lipid localization Any process that modulates the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 regulation of lipid localisation GOC:TermGenie Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. rz 2017-02-21T12:12:41Z down regulation of lipid localisation down regulation of lipid localization down-regulation of lipid localisation down-regulation of lipid localization downregulation of lipid localisation downregulation of lipid localization negative regulation of lipid localisation inhibition of lipid localisation inhibition of lipid localization biological_process GO:1905953 negative regulation of lipid localization Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 down regulation of lipid localisation GOC:TermGenie down regulation of lipid localization GOC:TermGenie down-regulation of lipid localisation GOC:TermGenie down-regulation of lipid localization GOC:TermGenie downregulation of lipid localisation GOC:TermGenie downregulation of lipid localization GOC:TermGenie negative regulation of lipid localisation GOC:TermGenie inhibition of lipid localisation GOC:TermGenie inhibition of lipid localization GOC:TermGenie Any process that activates or increases the frequency, rate or extent of lipid localization. rz 2017-02-21T12:12:49Z positive regulation of lipid localisation up regulation of lipid localisation up regulation of lipid localization up-regulation of lipid localisation up-regulation of lipid localization upregulation of lipid localisation upregulation of lipid localization activation of lipid localisation activation of lipid localization biological_process GO:1905954 positive regulation of lipid localization Any process that activates or increases the frequency, rate or extent of lipid localization. GOC:TermGenie GO_REF:0000058 PMID:17564681 positive regulation of lipid localisation GOC:TermGenie up regulation of lipid localisation GOC:TermGenie up regulation of lipid localization GOC:TermGenie up-regulation of lipid localisation GOC:TermGenie up-regulation of lipid localization GOC:TermGenie upregulation of lipid localisation GOC:TermGenie upregulation of lipid localization GOC:TermGenie activation of lipid localisation GOC:TermGenie activation of lipid localization GOC:TermGenie Any process that modulates the frequency, rate or extent of multicellular organismal development. tb 2010-08-05T11:25:59Z biological_process GO:2000026 regulation of multicellular organismal development Any process that modulates the frequency, rate or extent of multicellular organismal development. GOC:obol Any process that modulates the frequency, rate or extent of animal organ morphogenesis. tb 2010-08-05T11:26:27Z biological_process regulation of histogenesis and organogenesis GO:2000027 regulation of animal organ morphogenesis Any process that modulates the frequency, rate or extent of animal organ morphogenesis. GOC:obol regulation of histogenesis and organogenesis GOC:obol Any process that modulates the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:46Z biological_process GO:2000831 regulation of steroid hormone secretion Any process that modulates the frequency, rate or extent of steroid hormone secretion. GOC:sl Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:50Z biological_process GO:2000832 negative regulation of steroid hormone secretion Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion. GOC:sl Any process that activates or increases the frequency, rate or extent of steroid hormone secretion. bf 2011-07-26T08:38:51Z biological_process GO:2000833 positive regulation of steroid hormone secretion Any process that activates or increases the frequency, rate or extent of steroid hormone secretion. GOC:sl UMLS:C0444868 human_phenotype HP:0000001 Root of all terms in the Human Phenotype Ontology. All Deviation from the norm of height with respect to that which is expected according to age and gender norms. peter 2008-02-27T02:20:00Z UMLS:C4025901 Abnormality of body height human_phenotype HP:0000002 Abnormality of body height Deviation from the norm of height with respect to that which is expected according to age and gender norms. HPO:probinson Abnormality of body height An abnormality of the female internal genitalia. UMLS:C4025900 Abnormality of female internal genitalia human_phenotype HP:0000008 Abnormal morphology of female internal genitalia An abnormality of the female internal genitalia. HPO:probinson Dysfunction of the urinary bladder. HP:0004424 HP:0008731 UMLS:C3806583 Poor bladder function human_phenotype HP:0000009 Functional abnormality of the bladder Dysfunction of the urinary bladder. HPO:probinson Underdevelopment of the uterus. HP:0001154 HP:0008637 SNOMEDCT_US:35850006 UMLS:C0266399 Hypoplastic uterus Rudimentary uterus Small uterus Underdeveloped uterus human_phenotype HP:0000013 Hypoplasia of the uterus Underdevelopment of the uterus. HPO:probinson Small uterus ORCID:0000-0001-5208-3432 Underdeveloped uterus ORCID:0000-0001-5208-3432 An abnormality of the urinary bladder. UMLS:C0149632 human_phenotype HP:0000014 Abnormality of the bladder An abnormality of the urinary bladder. HPO:probinson Diverticulum (sac or pouch) in the wall of the urinary bladder. MSH:C562406 SNOMEDCT_US:197866008 UMLS:C0156273 Bladder diverticula human_phenotype HP:0000015 Bladder diverticulum Diverticulum (sac or pouch) in the wall of the urinary bladder. HPO:probinson Bladder diverticula HPO:skoehler An abnormality of the male internal genitalia. UMLS:C4025899 human_phenotype HP:0000022 The internal genital structures of the male including the testis, epididymis, vas deferens, seminal vesicle, ejaculatory duct, bulbourethral gland, and the prostate. Abnormality of male internal genitalia An abnormality of the male internal genitalia. HPO:probinson The presence of inflammation of the prostate. MSH:D011472 SNOMEDCT_US:9713002 UMLS:C0033581 Inflammation of the prostate human_phenotype HP:0000024 Prostatitis The presence of inflammation of the prostate. HPO:probinson Inflammation of the prostate ORCID:0000-0001-5208-3432 UMLS:C4025898 human_phenotype HP:0000025 Functional abnormality of male internal genitalia The presence of inflammation of the epididymis. MSH:D004823 SNOMEDCT_US:31070006 UMLS:C0014534 human_phenotype HP:0000031 Epididymitis The presence of inflammation of the epididymis. HPO:probinson An abnormality of male external genitalia. UMLS:C4025897 human_phenotype HP:0000032 Abnormality of male external genitalia An abnormality of male external genitalia. HPO:probinson An anomaly of the testicle (the male gonad). SNOMEDCT_US:55631001 UMLS:C0266423 Abnormality of the testis Anomaly of the testes human_phenotype HP:0000035 Abnormal testis morphology An anomaly of the testicle (the male gonad). HPO:probinson Abnormality of the testis UMLS:C4025896 Abnormality of the penis human_phenotype HP:0000036 Abnormality of the penis Abnormality of the penis Penile length more than 2 SD above the mean for age. SNOMEDCT_US:88673001 UMLS:C0269011 Enlarged penis Long penis human_phenotype HP:0000040 Penile length is the distance between the midline attachment of the gently stretched, flaccid penis above the pubic symphysis and tip of the glans. Long penis Enlarged penis Long penis Lack of external genitalia in a male or female individual. UMLS:C1848869 Absent external genitalia human_phenotype HP:0000042 Absent external genitalia Lack of external genitalia in a male or female individual. HPO:probinson Absent external genitalia UMLS:C4025895 human_phenotype HP:0000045 Abnormality of the scrotum SNOMEDCT_US:204912007 UMLS:C0431659 Hypoplastic scrotum Smaller than typical growth of scrotum human_phenotype HP:0000046 Scrotal hypoplasia Smaller than typical growth of scrotum https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 Midline indentation or cleft of the scrotum. SNOMEDCT_US:236780002 UMLS:C0341787 Cleft of scrotum Scrotal cleft human_phenotype HP:0000048 A testis may or may not be present in each half of the scrotum. Bifid scrotum Midline indentation or cleft of the scrotum. HPO:probinson PMID:23650202 Cleft of scrotum ORCID:0000-0001-5208-3432 Underdevelopment of part or all of the male external reproductive organs (which include the penis, the scrotum and the urethra). HP:0008710 HP:0008721 UMLS:C1852534 Hypoplastic male genitalia Small male external genitalia Underdeveloped male genitalia human_phenotype HP:0000050 Hypoplastic male external genitalia Underdevelopment of part or all of the male external reproductive organs (which include the penis, the scrotum and the urethra). HPO:probinson Small male external genitalia Underdeveloped male genitalia ORCID:0000-0001-5208-3432 The presence of abnormally large testes. UMLS:C1263023 Large testicles Large testis human_phenotype HP:0000053 Macroorchidism The presence of abnormally large testes. HPO:probinson Large testis An abnormality of the female external genitalia. UMLS:C4021822 Abnormal female external genitalia human_phenotype HP:0000055 Abnormality of female external genitalia An abnormality of the female external genitalia. HPO:probinson Abnormal female external genitalia HPO:skoehler An abnormality of the clitoris. UMLS:C4025893 Abnormality of the clit human_phenotype HP:0000056 Abnormality of the clitoris An abnormality of the clitoris. HPO:probinson Abnormality of the clit ORCID:0000-0001-5208-3432 Developmental hypoplasia of the clitoris. UMLS:C1844527 Hypoplastic clitoris Small clitoris Underdeveloped clit human_phenotype HP:0000060 Clitoral hypoplasia Developmental hypoplasia of the clitoris. HPO:probinson Small clitoris Underdeveloped clit ORCID:0000-0001-5208-3432 An abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder. HP:0006001 UMLS:C1840382 Abnormality of the ureters Ureter issue Ureteral anomalies human_phenotype HP:0000069 Abnormality of the ureter An abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder. HPO:probinson A developmental anomaly characterized by the presence of two, instead of one, ureter connecting a kidney to the bladder. SNOMEDCT_US:49496001 UMLS:C0221365 Double ureter human_phenotype HP:0000073 Ureteral duplication A developmental anomaly characterized by the presence of two, instead of one, ureter connecting a kidney to the bladder. HPO:curators Double ureter A congenital anomaly of the urinary tract, in which the kidney is duplicated and is drained via two separate renal pelves and ureters. peter 2008-02-25T12:45:00Z SNOMEDCT_US:30275001 UMLS:C0266298 Extra kidney human_phenotype Supernumerary kidney HP:0000075 Renal duplication A congenital anomaly of the urinary tract, in which the kidney is duplicated and is drained via two separate renal pelves and ureters. HPO:probinson Extra kidney ORCID:0000-0001-5208-3432 An abnormality of the kidney. MSH:D007674 SNOMEDCT_US:44513007 SNOMEDCT_US:90708001 UMLS:C0022658 UMLS:C0266292 Abnormal kidney Abnormality of the kidney Renal anomalies Renal anomaly human_phenotype HP:0000077 The kidney is a paired organ whose primary function is the production of urine. Abnormality of the kidney An abnormality of the kidney. HPO:probinson Abnormal kidney Abnormality of the kidney An abnormality of the genital system. UMLS:C0281966 UMLS:C0744356 Genital abnormalities Genital abnormality Genital anomalies Genital defects human_phenotype Abnormality of the reproductive system HP:0000078 Abnormality of the genital system An abnormality of the genital system. HPO:probinson Genital abnormalities Genital abnormality Genital anomalies Genital defects Abnormality of the reproductive system An abnormality of the urinary system. UMLS:C4021821 Urinary tract abnormalities Urinary tract abnormality Urinary tract anomalies human_phenotype HP:0000079 Abnormality of the urinary system An abnormality of the urinary system. HPO:probinson Urinary tract abnormalities Urinary tract abnormality Urinary tract anomalies An abnormal functionality of the genital system. Abnormality of genital physiology UMLS:C4020896 UMLS:C4021820 Abnormality of reproductive system physiology Genital functional abnormality human_phenotype HP:0000080 Abnormality of reproductive system physiology An abnormal functionality of the genital system. HPO:probinson Abnormality of genital physiology Abnormality of reproductive system physiology Genital functional abnormality A duplication of the collecting system of the kidney, defined as a kidney with two (instead of, normally, one) pyelocaliceal systems. The pyelocaliceal system is comprised of the renal pelvis and calices. The duplicated renal collecting system can be associated with a single ureter or with double ureters. In the latter case, the two ureters empty separately into the bladder or fuse to form a single ureteral orifice. peter 2008-02-25T12:45:00Z UMLS:C1858565 Double collecting system Double urinary collecting systems on intravenous pyelography Duplex collecting system Duplicated renal collecting system human_phenotype HP:0000081 Duplicated collecting system A duplication of the collecting system of the kidney, defined as a kidney with two (instead of, normally, one) pyelocaliceal systems. The pyelocaliceal system is comprised of the renal pelvis and calices. The duplicated renal collecting system can be associated with a single ureter or with double ureters. In the latter case, the two ureters empty separately into the bladder or fuse to form a single ureteral orifice. HPO:probinson Hypoplasia of the kidney. HP:0001968 HP:0004741 HP:0008641 SNOMEDCT_US:32659003 UMLS:C0266295 Hypoplastic kidney Hypoplastic kidneys Small kidneys Underdeveloped kidneys human_phenotype HP:0000089 Oligomeganephronic renal hypoplasia differs from simple hypoplasia, in which the renal mass is reduced but the number of nephrons is normal. Renal hypoplasia Hypoplasia of the kidney. HPO:probinson Small kidneys Underdeveloped kidneys ORCID:0000-0001-5208-3432 An abnormality of the renal tubules. UMLS:C4021826 Abnormality of the renal tubule Morphologic abnormality of the renal tubules human_phenotype HP:0000091 The renal tubules are reabsorptive canals that are involved in the secreting, collecting, and conducting of the urine. Abnormal renal tubule morphology An abnormality of the renal tubules. HPO:probinson A height above that which is expected according to age and gender norms. peter 2008-02-27T02:21:00Z HP:0001527 HP:0003515 HP:0003516 SNOMEDCT_US:248328003 UMLS:C0241240 Accelerated linear growth Increased body height Increased linear growth Tall stature human_phenotype HP:0000098 Tall stature A height above that which is expected according to age and gender norms. HPO:probinson Increased body height Tall stature Agenesis, that is, failure of the kidney to develop during embryogenesis and development. HP:0000785 HP:0004745 HP:0008680 Fyler:4503 SNOMEDCT_US:204942005 UMLS:C0542519 Absent kidney Missing kidney Renal aplasia human_phenotype HP:0000104 Renal agenesis can occur as a unilateral or bilateral trait. Renal agenesis Agenesis, that is, failure of the kidney to develop during embryogenesis and development. HPO:probinson Absent kidney Missing kidney ORCID:0000-0001-6908-9849 An abnormal increase in the size of the kidney. SNOMEDCT_US:300444006 UMLS:C0542518 Enlarged kidney Large kidneys Nephromegaly Renal enlargement human_phenotype Large kidney HP:0000105 The main causes of large kidney are hydronephrosis, polycystic disease, renal cell carcinoma, nephroblastoma/Wilm's tumor (in children), and solitary cysts. If possible, a specific term should be used instead of this one. There are several ways of diagnosing enlarged kidney including intravenous urography. Enlarged kidney An abnormal increase in the size of the kidney. HPO:probinson Enlarged kidney Large kidneys A fluid filled sac in the kidney. HP:0000088 HP:0000109 MSH:D052177 UMLS:C0022679 UMLS:C3887499 Kidney cyst human_phenotype Cystic kidney disease Cystic kidneys Renal cysts HP:0000107 Renal cyst A fluid filled sac in the kidney. Eurenomics:fschaefer Kidney cyst https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 Cystic kidney disease Cystic kidneys HPO:skoehler Renal cysts HPO:skoehler The presence of developmental dysplasia of the kidney. HP:0000116 HP:0004721 MSH:C563261 SNOMEDCT_US:204949001 UMLS:C1619700 UMLS:C3536714 Dysplastic kidneys Renal adysplasia human_phenotype HP:0000110 Renal dysplasia The presence of developmental dysplasia of the kidney. HPO:probinson A phenotypic abnormality. UMLS:C4021819 Organ abnormality human_phenotype HP:0000118 This is the root of the phenotypic abnormality subontology of the HPO. Phenotypic abnormality A phenotypic abnormality. HPO:probinson The presence of any abnormality of the genitourinary system. HP:0008658 HP:0008688 HP:0008704 HP:0008713 MSH:D014564 SNOMEDCT_US:287085006 SNOMEDCT_US:42030000 UMLS:C0042063 UMLS:C0080276 UMLS:C4020895 Abnormality of the GU system Genitourinary abnormality Genitourinary tract anomalies Genitourinary tract malformation Urogenital abnormalities Urogenital anomalies human_phenotype Genitourinary disease Genitourinary dysplasia HP:0000119 Abnormality of the genitourinary system The presence of any abnormality of the genitourinary system. HPO:curators Abnormality of the GU system Nephrocalcinosis is the deposition of calcium salts in renal parenchyma. MSH:D009397 SNOMEDCT_US:48638002 UMLS:C0027709 UMLS:C4280679 Too much calcium deposited in kidneys human_phenotype Increased calcium level in kidney HP:0000121 Nephrocalcinosis can be intratubular or interstitial, and can be diagnosed by means of a radiologic exam (plain radiographs, ultrasonograms, or computed tomography scans) or via microscopic examination of the renal tissues. The term nephrocalcinosis most often applies to a generalized increase in renal calcium content. Nephrocalcinosis Nephrocalcinosis is the deposition of calcium salts in renal parenchyma. HPO:probinson Too much calcium deposited in kidneys https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 Increased calcium level in kidney ORCID:0000-0001-5208-3432 The presence of inflammation affecting the kidney. HP:0008634 MSH:D009393 SNOMEDCT_US:52845002 UMLS:C0027697 Kidney inflammation human_phenotype HP:0000123 Nephritis The presence of inflammation affecting the kidney. HPO:probinson Kidney inflammation ORCID:0000-0001-6908-9849 An abnormality of the uterus. HP:0008630 HP:0008692 MSH:C562565 SNOMEDCT_US:37849005 UMLS:C0266383 Abnormality of the uterus Uterine abnormalities Uterine malformations human_phenotype HP:0000130 Abnormality of the uterus An abnormality of the uterus. HPO:probinson Abnormality of the uterus Uterine abnormalities Uterine malformations The presence of a leiomyoma of the uterus. HP:0008642 MSH:D007889 NCIT:C3157 SNOMEDCT_US:146801000119103 SNOMEDCT_US:44598004 SNOMEDCT_US:95315005 UMLS:C0042133 Benign uterine leiomyomas Uterine fibroid human_phenotype HP:0000131 Leiomyoma is a benign neoplasm derived from smooth muscle cells. Uterine leiomyoma The presence of a leiomyoma of the uterus. HPO:probinson HP:0003243 MSH:D006059 MSH:D006060 SNOMEDCT_US:205681004 SNOMEDCT_US:38804009 SNOMEDCT_US:83579008 SNOMEDCT_US:95219002 UMLS:C0018051 UMLS:C0018055 UMLS:C0687149 Mixed gonadal dysgenesis Pure gonadal dysgenesis human_phenotype HP:0000133 Gonadal dysgenesis The presence of a bifid uterus. UMLS:C1850327 human_phenotype HP:0000136 A uterus that is divided into two lateral horns as a result of imperfect fusion of the paramesonephric ducts. Bifid uterus The presence of a bifid uterus. HPO:probinson An abnormality of the ovary. MSH:D010049 SNOMEDCT_US:5552004 UMLS:C0029928 UMLS:C4021818 Abnormality of the ovaries Abnormality of the ovary human_phenotype Ovarian disease HP:0000137 Abnormality of the ovary An abnormality of the ovary. HPO:probinson Abnormality of the ovaries Abnormality of the ovary Ovarian disease The presence of one or more cysts of the ovary. HP:0000146 MSH:D010048 SNOMEDCT_US:79883001 UMLS:C0029927 Cystic abnormalities of the ovaries Cystic ovaries Ovarian cyst Ovarian cystic abnormality human_phenotype HP:0000138 Ovarian cyst The presence of one or more cysts of the ovary. HPO:probinson Ovarian cyst Any structural abnormality of the vagina. HP:0008650 UMLS:C1856023 Vaginal malformation human_phenotype HP:0000142 Abnormal vagina morphology Any structural abnormality of the vagina. HPO:probinson Aplasia of the uterus. SNOMEDCT_US:248942000 UMLS:C0425913 Absent uterus uterus absent human_phenotype HP:0000151 Aplasia of the uterus Aplasia of the uterus. HPO:probinson Absent uterus uterus absent An abnormality of head and neck. UMLS:C4021817 Abnormality of head or neck Head and neck abnormality human_phenotype HP:0000152 Abnormality of head or neck An abnormality of head and neck. HPO:probinson Abnormality of head or neck Head and neck abnormality An abnormality of the mouth. MSH:D009056 SNOMEDCT_US:128334002 UMLS:C0026633 Abnormal mouth Abnormality of the mouth human_phenotype HP:0000153 Abnormality of the mouth An abnormality of the mouth. HPO:probinson Abnormal mouth HPO:skoehler Abnormality of the mouth Any abnormality of the tongue. UMLS:C0878638 Abnormal tongue Abnormality of the tongue Glossal abnormality Lingual abnormality Tongue abnormality human_phenotype HP:0000157 Abnormality of the tongue Any abnormality of the tongue. HPO:probinson Abnormal tongue HPO:skoehler Abnormality of the tongue Glossal abnormality ORCID:0000-0001-5889-4463 Lingual abnormality ORCID:0000-0001-5889-4463 Tongue abnormality Increased length and width of the tongue. HP:0000203 Glossal hypertrophy Lingual hyperplasia Lingual hypertrophy MSH:D008260 SNOMEDCT_US:25273001 UMLS:C0024421 Abnormally large tongue Hyperplasia of the tongue Hypertrophy of the tongue Increased size of tongue Large tongue Tongue hypertrophy human_phenotype HP:0000158 Normal standards do not exist. Large size usually leads to protrusion of the tongue. This is an acknowledged bundled term, but due to its frequent usage and relative paucity of situations that would call for separate individual assessments of tongue dimensions, the bundled term is retained. Micrognathia may give the false appearance of a large tongue. Macroglossia Increased length and width of the tongue. PMID:19125428 Glossal hypertrophy ORCID:0000-0001-5889-4463 Lingual hyperplasia ORCID:0000-0001-5889-4463 Lingual hypertrophy ORCID:0000-0001-5889-4463 Abnormally large tongue ORCID:0000-0001-5889-4463 Increased size of tongue ORCID:0000-0001-5889-4463 Large tongue An abnormality of the lip. UMLS:C2183966 Abnormal lip Abnormality of the lip Lip abnormality Anomaly of lip Deformity of lip Malformation of lip human_phenotype HP:0000159 Abnormal lip morphology An abnormality of the lip. HPO:probinson Abnormal lip HPO:skoehler Abnormality of the lip Lip abnormality Anomaly of lip ORCID:0000-0001-5889-4463 Deformity of lip ORCID:0000-0001-5889-4463 Malformation of lip ORCID:0000-0001-5889-4463 Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth. UMLS:C4025887 Abnormality of the oral cavity human_phenotype HP:0000163 Abnormal oral cavity morphology Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth. HPO:probinson Abnormality of the oral cavity Any abnormality of the teeth. HP:0001567 HP:0006296 HP:0006348 MSH:D014071 SNOMEDCT_US:422775003 UMLS:C0040427 UMLS:C0262444 Abnormal dentition Abnormal teeth Dental abnormalities Dental abnormality Dental anomalies human_phenotype Abnormality of the teeth Dental problem Dental problems Tooth abnormalities HP:0000164 Any abnormality of the primary (deciduous) or permanent teeth. Abnormality of the dentition Any abnormality of the teeth. HPO:ibailleulforestier Abnormal dentition Abnormal teeth Dental abnormalities Dental abnormality Dental anomalies Abnormality of the teeth Dental problem Dental problems Tooth abnormalities Decreased length and width of the tongue. HP:0000226 HP:0009079 MSH:D014060 SNOMEDCT_US:249380003 SNOMEDCT_US:32614006 UMLS:C0025988 UMLS:C0426492 Abnormally small tongue Decreased size of tongue Hypoglossia Hypoplasia of the tongue Hypoplastic tongue Lingual hypoplasia Rudimentary tongue Small tongue Underdevelopment of the tongue human_phenotype HP:0000171 Normal standards do not exist. The term aglossia is often used for extremely small tongue, but a nubbin of tongue tissue is almost always present and aglossia in sensu strictu is extremely rare. This is an acknowledged bundled term, but due to its frequent usage and relative paucity of situations that would call for separate individual assessments of tongue dimensions, the bundled term is retained. Microglossia Decreased length and width of the tongue. PMID:19125428 Abnormally small tongue ORCID:0000-0001-5889-4463 Underdevelopment of the tongue ORCID:0000-0001-5889-4463 An abnormality of the lower lip. UMLS:C4025883 Abnormality of lower lip Anomaly of the lower lip Deformity of the lower lip Malformation of the lower lip human_phenotype HP:0000178 Abnormality of lower lip An abnormality of the lower lip. HPO:probinson Abnormality of lower lip Anomaly of the lower lip ORCID:0000-0001-5889-4463 Deformity of the lower lip ORCID:0000-0001-5889-4463 Malformation of the lower lip ORCID:0000-0001-5889-4463 A facial appearance characterized by a permanently or nearly permanently opened mouth. SNOMEDCT_US:262016004 UMLS:C0240379 Gaped jawed appearance Gaped mouthed appearance Open mouth Slack jawed appearance human_phenotype Open mouth appearance HP:0000194 Open mouth A facial appearance characterized by a permanently or nearly permanently opened mouth. HPO:probinson Gaped jawed appearance ORCID:0000-0001-5889-4463 Gaped mouthed appearance ORCID:0000-0001-5889-4463 Open mouth Slack jawed appearance ORCID:0000-0001-5889-4463 Open mouth appearance HPO:skoehler The presence of a cleft in the oral cavity, the two main types of which are cleft lip and cleft palate. In cleft lip, there is the congenital failure of the maxillary and median nasal processes to fuse, forming a groove or fissure in the lip. In cleft palate, there is a congenital failure of the palate to fuse properly, forming a grooved depression or fissure in the roof of the mouth. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately. SNOMEDCT_US:253983005 SNOMEDCT_US:66948001 UMLS:C0158646 UMLS:C4021813 Cleft of the mouth Oral clefting Cleft lip, cleft palate human_phenotype Cleft lip/palate HP:0000202 Oral cleft The presence of a cleft in the oral cavity, the two main types of which are cleft lip and cleft palate. In cleft lip, there is the congenital failure of the maxillary and median nasal processes to fuse, forming a groove or fissure in the lip. In cleft palate, there is a congenital failure of the palate to fuse properly, forming a grooved depression or fissure in the roof of the mouth. Clefts of the lip and palate can occur individually or together. It is preferable to code each defect separately. HPO:probinson PMID:21331089 Cleft of the mouth ORCID:0000-0001-5889-4463 The presence of a triangular form of the mouth. UMLS:C1849341 Triangular mouth Triangular shaped mouth Triangular shaped oral aperture human_phenotype HP:0000207 Triangular mouth The presence of a triangular form of the mouth. HPO:probinson Triangular mouth Triangular shaped mouth Triangular shaped oral aperture ORCID:0000-0001-5889-4463 An abnormality of the head. UMLS:C4021812 Abnormal head Abnormality of the head Head abnormality human_phenotype HP:0000234 Abnormality of the head An abnormality of the head. HPO:probinson Abnormal head HPO:skoehler Abnormality of the head Head abnormality Any abnormality of the fontanelles (the regions covered by a thick membrane that normally ossify in the first two years of life) or the cranial sutures (the fibrous joints in which the articulating bones or cartilages of the skull are connected by sutural ligaments). UMLS:C4025876 human_phenotype HP:0000235 Fontanels are the fibrous, membrane-covered gaps created when more than two cranial bones are juxtaposed, as opposed to sutures, which are narrow seams of fibrous connective tissue that separate the flat bones of the skull. At birth, an infant has six fontanels (the anterior and posterior, two mastoid, and two sphenoid). The anterior fontanel is the largest and most important for clinical evaluation. The average size of the anterior fontanel is 2.1 cm, and the median time of closure is 13.8 months. Abnormality of the fontanelles or cranial sutures Any abnormality of the fontanelles (the regions covered by a thick membrane that normally ossify in the first two years of life) or the cranial sutures (the fibrous joints in which the articulating bones or cartilages of the skull are connected by sutural ligaments). HPO:probinson PMID:12825844 Hydrocephalus is an active distension of the ventricular system of the brain resulting from inadequate passage of CSF from its point of production within the cerebral ventricles to its point of absorption into the systemic circulation. HP:0007189 HP:0008503 MSH:D006849 SNOMEDCT_US:230745008 UMLS:C0020255 Hydrocephaly Nonsyndromal hydrocephalus Too much cerebrospinal fluid in the brain human_phenotype HP:0000238 Hydrocephalus results from an imbalance between the rate of production of cerebrospinal fluid (CSF), mainly in the choroid plexus, and its reabsorption in the subarchnoid space over brain and spinal cord. Hydrocephalus Hydrocephalus is an active distension of the ventricular system of the brain resulting from inadequate passage of CSF from its point of production within the cerebral ventricles to its point of absorption into the systemic circulation. HPO:probinson PMID:18211712 PMID:19410151 Too much cerebrospinal fluid in the brain orcid.org/0000-0002-6548-5200 In newborns, the two frontal bones, two parietal bones, and one occipital bone are joined by fibrous sutures, which form a small posterior fontanelle, and a larger, diamond-shaped anterior fontanelle. These regions allow for the skull to pass the birth canal and for later growth. The fontanelles gradually ossify, whereby the posterior fontanelle usually closes by eight weeks and the anterior fontanelle by the 9th to 16th month of age. Large fontanelles are diagnosed if the fontanelles are larger than age-dependent norms. HP:0004473 SNOMEDCT_US:276709006 UMLS:C0456132 UMLS:C4072820 UMLS:C4072821 UMLS:C4072822 Enlarged fontanelles Large fontanel Large fontanelle Large fontanels Persistent wide fontanel Wide fontanelles Large bregma sutures Large, late-closing fontanelle Wide bregma sutures human_phenotype HP:0000239 There are six membrane-covered openings between the cranial sutures in the incompletely ossified skull of the fetus or newborn infant that normally close sometime after birth (anterior fontanel, cranial fontanel, mastoid fontanel, posterior fontanel, sphenoidal fontanel). Large fontanelles In newborns, the two frontal bones, two parietal bones, and one occipital bone are joined by fibrous sutures, which form a small posterior fontanelle, and a larger, diamond-shaped anterior fontanelle. These regions allow for the skull to pass the birth canal and for later growth. The fontanelles gradually ossify, whereby the posterior fontanelle usually closes by eight weeks and the anterior fontanelle by the 9th to 16th month of age. Large fontanelles are diagnosed if the fontanelles are larger than age-dependent norms. HPO:probinson Wide fontanelles ORCID:0000-0001-5889-4463 Large bregma sutures ORCID:0000-0001-5889-4463 Large, late-closing fontanelle ORCID:0000-0001-5889-4463 Wide bregma sutures ORCID:0000-0001-5889-4463 Any abnormality of the size of the skull. Abnormality of head size UMLS:C4025874 Abnormality of cranium size Abnormality of skull size human_phenotype HP:0000240 Abnormality of skull size Any abnormality of the size of the skull. HPO:curators Abnormality of head size ORCID:0000-0001-5889-4463 Abnormality of cranium size ORCID:0000-0001-5889-4463 Abnormality of skull size Wedge-shaped, or triangular head, with the apex of the triangle at the midline of the forehead and the base of the triangle at the occiput. Triangular head shape Wedge shaped head MSH:D003398 SNOMEDCT_US:28740008 UMLS:C0265535 UMLS:C4280665 UMLS:C4280666 Triangular cranium shape Triangular skull shape Wedge shaped cranium Wedge shaped skull human_phenotype HP:0000243 This shape should be assessed from above, with the examiner looking down on the head of the patient. Trigonocephaly can be caused by premature fusion of the metopic suture. Trigonocephaly Wedge-shaped, or triangular head, with the apex of the triangle at the midline of the forehead and the base of the triangle at the occiput. PMID:19125436 Triangular head shape ORCID:0000-0001-5889-4463 Wedge shaped head ORCID:0000-0001-5889-4463 Triangular cranium shape ORCID:0000-0001-5889-4463 Triangular skull shape ORCID:0000-0001-5889-4463 Wedge shaped cranium ORCID:0000-0001-5889-4463 Wedge shaped skull ORCID:0000-0001-5889-4463 An abnormal increase of density of the bones making up the calvaria. UMLS:C1854834 Dense skull cap human_phenotype HP:0000250 Dense calvaria An abnormal increase of density of the bones making up the calvaria. HPO:curators Dense skull cap ORCID:0000-0001-5889-4463 Head circumference below 2 standard deviations below the mean for age and gender. HP:0001366 HP:0005485 HP:0005489 HP:0005497 Abnormally small head Decreased size of head Small head Small skull Fyler:4310 SNOMEDCT_US:271611007 UMLS:C0424688 Abnormally small cranium Abnormally small skull Decreased circumference of cranium Decreased size of cranium Decreased size of skull Reduced head circumference Small head circumference small calvarium small cranium human_phenotype HP:0000252 Head circumference is measured from just above the glabella (the most prominent point on the frontal bone above the root of the nose) to the most posterior prominent point of the occipital bone using a tape measure. Some standard charts are organized by centiles [Hall et al. [2007]], others by standard deviations [Farkas, [1981]]. It is important to add an indication of how far below the normal standard the head circumference is if an accurate assessment of this can be made. Microcephaly is an absolute term. The term relative microcephaly can be used when the head size centile is less than the centile for height, for example, head size at the 3rd centile with height at the 75% for age and sex. On prenatal ultrasound, microcephaly is diagnosed if the head circumference or the biparietal diameter is more than three standard deviations below the mean. Microcephaly Head circumference below 2 standard deviations below the mean for age and gender. PMID:19125436 PMID:25465325 PMID:9683597 Abnormally small head ORCID:0000-0001-5889-4463 Decreased size of head ORCID:0000-0001-5889-4463 Small head ORCID:0000-0001-5889-4463 Small skull ORCID:0000-0001-5889-4463 Abnormally small cranium ORCID:0000-0001-5889-4463 Abnormally small skull ORCID:0000-0001-5889-4463 Decreased circumference of cranium ORCID:0000-0001-5889-4463 Decreased size of cranium ORCID:0000-0001-5889-4463 Decreased size of skull ORCID:0000-0001-5889-4463 Reduced head circumference Small head circumference small calvarium ORCID:0000-0001-5889-4463 small cranium ORCID:0000-0001-5889-4463 Progressive microcephaly is diagnosed when the head circumference falls progressively behind age- and gender-dependent norms. UMLS:C1850456 Microcephaly, postnatal, progressive Microcephaly, progressive Progressively abnormally small cranium Progressively abnormally small skull human_phenotype HP:0000253 Progressive microcephaly Progressive microcephaly is diagnosed when the head circumference falls progressively behind age- and gender-dependent norms. HPO:probinson Microcephaly, progressive HPO:skoehler Progressively abnormally small cranium ORCID:0000-0001-5889-4463 Progressively abnormally small skull ORCID:0000-0001-5889-4463 Occipitofrontal (head) circumference greater than 97th centile compared to appropriate, age matched, sex-matched normal standards. Alternatively, a apparently increased size of the cranium. HP:0005491 HP:0005496 HP:0200135 Big calvaria Big cranium Big head Big skull Increased size of head Large calvaria Large cranium Large skull Fyler:4335 UMLS:C4083076 UMLS:C4255213 UMLS:C4280663 UMLS:C4280664 Increased size of cranium Increased size of skull Large head Large head circumference Macrocrania Megacephaly human_phenotype HP:0000256 Macrocephaly can be due to hydrocephalus (increased CFSF), megalencephaly (increased brain volume) or thickening of the skull. Head circumference is measured from just above the glabella (the most prominent point on the frontal bone above the root of the nose) to the most posterior prominent point of the occipital bone using a tape measure. Some standard charts are organized by centiles [Hall et al. [2007]], others by standard deviations [Farkas, [1981]]. It is important to add an indication of how far above the normal standard the head circumference is if an accurate assessment of this can be made. Macrocephaly is an absolute term. The term relative macrocephaly can be used when the head size centile exceeds the centile for height, for example, head size at the 75th centile with height at the 5th centile for age and sex. Macrocephaly Occipitofrontal (head) circumference greater than 97th centile compared to appropriate, age matched, sex-matched normal standards. Alternatively, a apparently increased size of the cranium. PMID:19125436 Big calvaria ORCID:0000-0001-5889-4463 Big cranium ORCID:0000-0001-5889-4463 Big head ORCID:0000-0001-5889-4463 Big skull ORCID:0000-0001-5889-4463 Increased size of head ORCID:0000-0001-5889-4463 Large calvaria ORCID:0000-0001-5889-4463 Large cranium ORCID:0000-0001-5889-4463 Large skull ORCID:0000-0001-5889-4463 Increased size of cranium ORCID:0000-0001-5889-4463 Increased size of skull ORCID:0000-0001-5889-4463 Large head Large head circumference Megacephaly ORCID:0000-0001-5208-3432 An abnormality of the face. Abnormality of the countenance Abnormality of the physiognomy Abnormality of the visage Disorder of face SNOMEDCT_US:118930001 SNOMEDCT_US:32003007 SNOMEDCT_US:398206004 SNOMEDCT_US:398302004 UMLS:C0266617 UMLS:C1290857 UMLS:C4025871 Abnormal face Abnormality of the face Facial abnormality Disorder of the face human_phenotype Anomaly of face Anomaly of the face Facial anomaly HP:0000271 Abnormality of the face An abnormality of the face. HPO:probinson Abnormality of the countenance ORCID:0000-0001-5889-4463 Abnormality of the physiognomy ORCID:0000-0001-5889-4463 Abnormality of the visage ORCID:0000-0001-5889-4463 Disorder of face ORCID:0000-0001-5889-4463 Abnormal face HPO:skoehler Abnormality of the face Facial abnormality ORCID:0000-0001-5889-4463 Disorder of the face ORCID:0000-0001-5889-4463 Anomaly of face ORCID:0000-0001-5889-4463 Anomaly of the face ORCID:0000-0001-5889-4463 Facial anomaly ORCID:0000-0001-5889-4463 A face that is short (HP:0011219) and narrow (HP:0000275). UMLS:C1855538 Facial hypoplasia Hypoplasia of face Microface Microfacies Short and narrow face Small face Small facies human_phenotype HP:0000274 This term represents a combination of two terms, short face and narrow face. Small face A face that is short (HP:0011219) and narrow (HP:0000275). HP:probinson Facial hypoplasia ORCID:0000-0001-5889-4463 Hypoplasia of face ORCID:0000-0001-5889-4463 Microface ORCID:0000-0001-5889-4463 Microfacies ORCID:0000-0001-5889-4463 Short and narrow face ORCID:0000-0001-5889-4463 Small face Small facies ORCID:0000-0001-5889-4463 Facial height (length) is more than 2 standard deviations above the mean (objective); or, an apparent increase in the height (length) of the face (subjective). HP:0000334 UMLS:C1836047 Elongation of face Increased height of face Increased length of face Increased vertical dimension of face Long face Long facies Vertical Facial Excess Vertical elongation of face Vertical enlargement of face Vertical excess of face Vertical hyperplasia of face Vertical overgrowth of face human_phenotype HP:0000276 Objective measurement of the face height is made with sliding calipers from the nasion, just above the depth of the nasal root, to the gnathion, the inferior border of the mandible, both in the midline. Note that long face is distinct from narrow face. Long face Facial height (length) is more than 2 standard deviations above the mean (objective); or, an apparent increase in the height (length) of the face (subjective). PMID:19125436 Elongation of face ORCID:0000-0001-5889-4463 Increased height of face ORCID:0000-0001-5889-4463 Increased length of face ORCID:0000-0001-5889-4463 Increased vertical dimension of face ORCID:0000-0001-5889-4463 Long face Long facies ORCID:0000-0001-5889-4463 Vertical Facial Excess ORCID:0000-0001-5889-4463 Vertical elongation of face ORCID:0000-0001-5889-4463 Vertical enlargement of face ORCID:0000-0001-5889-4463 Vertical excess of face ORCID:0000-0001-5889-4463 Vertical hyperplasia of face ORCID:0000-0001-5889-4463 Vertical overgrowth of face ORCID:0000-0001-5889-4463 UMLS:C4025866 Abnormality of facial fat Deformity of facial adipose tissue Malformation of facial adipose tissue human_phenotype HP:0000291 Abnormality of facial adipose tissue Abnormality of facial fat Deformity of facial adipose tissue ORCID:0000-0001-5889-4463 Malformation of facial adipose tissue ORCID:0000-0001-5889-4463 Increased prominence or roundness of soft tissues between zygomata and mandible. HP:0002262 HP:0004427 UMLS:C1866231 UMLS:C2748653 UMLS:C3806443 UMLS:C4280647 UMLS:C4280648 Apple cheeks Big cheeks Full cheeks Increased size of cheeks Large cheeks human_phenotype Chubby cheeks Hyperplasia of cheeks Hypertrophy of cheeks Puffy cheeks HP:0000293 Full cheeks Increased prominence or roundness of soft tissues between zygomata and mandible. DDD:awilkie Apple cheeks Big cheeks Full cheeks Increased size of cheeks ORCID:0000-0001-5889-4463 Large cheeks Chubby cheeks ORCID:0000-0001-5889-4463 Hyperplasia of cheeks ORCID:0000-0001-5889-4463 Hypertrophy of cheeks ORCID:0000-0001-5889-4463 Puffy cheeks ORCID:0000-0001-5889-4463 An anomaly of a muscle that is innervated by the facial nerve (the seventh cranial nerve). UMLS:C4025865 Abnormality of facial muscles Facial muscle issue human_phenotype HP:0000301 Facial muscles control facial expression and are innervated by the seventh cranial nerve. Facial muscles around the eye are responsible for eye blink and eyelid closure. Abnormality of facial musculature An anomaly of a muscle that is innervated by the facial nerve (the seventh cranial nerve). HPO:probinson Abnormality of facial muscles ORCID:0000-0001-5889-4463 Facial muscle issue An anomaly of the midface, which is a region and not an anatomical term. It extends, superiorly, from the inferior orbital margin to, inferiorly, the level of nasal base. It is formed by the maxilla (upper jaw) and zygoma and cheeks and malar region. Traditionally, the nose and premaxilla are not included in the midface. UMLS:C4021811 Abnormality of the midface Anomaly of the midface Deformity of the midface Malformation of the midface human_phenotype HP:0000309 Abnormality of the midface An anomaly of the midface, which is a region and not an anatomical term. It extends, superiorly, from the inferior orbital margin to, inferiorly, the level of nasal base. It is formed by the maxilla (upper jaw) and zygoma and cheeks and malar region. Traditionally, the nose and premaxilla are not included in the midface. HPO:probinson PMID:19125436 Abnormality of the midface Deformity of the midface ORCID:0000-0001-5889-4463 Malformation of the midface ORCID:0000-0001-5889-4463 HP:0000284 UMLS:C4025863 Abnormality of the eye region Abnormality of the region around the eyes Anomaly of the orbital region of the face Deformity of the orbital region of the face Malformation of the orbital region of the face human_phenotype HP:0000315 Abnormality of the orbital region Abnormality of the eye region ORCID:0000-0001-5889-4463 Abnormality of the region around the eyes ORCID:0000-0001-5889-4463 Anomaly of the orbital region of the face ORCID:0000-0001-5889-4463 Deformity of the orbital region of the face ORCID:0000-0001-5889-4463 Malformation of the orbital region of the face ORCID:0000-0001-5889-4463 An abnormality of the external ear. HP:0001752 SNOMEDCT_US:275259005 UMLS:C0266589 UMLS:C1846460 Abnormal pinnae Abnormality of the auricle Abnormality of the external ear Abnormality of the outer ear Ear anomalies External ear malformations Malformed pinnae Outer ear abnormality human_phenotype HP:0000356 Abnormality of the outer ear An abnormality of the external ear. HPO:probinson Abnormality of the external ear Abnormality of the outer ear Ear anomalies External ear malformations Outer ear abnormality Abnormal location of the ear. UMLS:C4021810 Abnormal location of ears External ear position defect human_phenotype HP:0000357 Abnormal location of ears Abnormal location of the ear. HPO:probinson Abnormal location of ears An abnormality of the inner ear. UMLS:C4021809 Abnormality of the inner ear Inner ear abnormality human_phenotype HP:0000359 Abnormality of the inner ear An abnormality of the inner ear. HPO:probinson Abnormality of the inner ear Inner ear abnormality In otosclerosis, a callus of bone accumulates on the stapes creating a partial fixation. This limits the movement of the stapes bone, which results in hearing loss. MSH:D010040 SNOMEDCT_US:11543004 UMLS:C0029899 human_phenotype HP:0000362 Otosclerosis cannot be seen on an office examination. The audiogram indicates a conductive type of hearing loss. Testing of the stapedial reflexes indicates limited or no movement of the bones of hearing. Otosclerosis In otosclerosis, a callus of bone accumulates on the stapes creating a partial fixation. This limits the movement of the stapes bone, which results in hearing loss. HPO:probinson PMID:15931303 An abnormality of the nose. SNOMEDCT_US:128274005 SNOMEDCT_US:72089000 UMLS:C0240547 UMLS:C0265736 UMLS:C2235909 Abnormality of the nose Anomaly of the nose Nasal abnormality Nasal anomaly Deformity of the nose Malformation of the nose Nasal deformity Nasal malformation human_phenotype HP:0000366 Abnormality of the nose An abnormality of the nose. HPO:probinson Abnormality of the nose Anomaly of the nose ORCID:0000-0001-5889-4463 Nasal abnormality ORCID:0000-0001-5889-4463 Nasal anomaly ORCID:0000-0001-5889-4463 Deformity of the nose ORCID:0000-0001-5889-4463 Malformation of the nose ORCID:0000-0001-5889-4463 Nasal deformity ORCID:0000-0001-5889-4463 Nasal malformation ORCID:0000-0001-5889-4463 Upper insertion of the ear to the scalp below an imaginary horizontal line drawn between the inner canthi of the eye and extending posteriorly to the ear. SNOMEDCT_US:95515009 UMLS:C0239234 Low set ears Low-set ears Lowset ears Melotia human_phenotype HP:0000369 Low-set ears Upper insertion of the ear to the scalp below an imaginary horizontal line drawn between the inner canthi of the eye and extending posteriorly to the ear. HPO:probinson PMID:19152421 Low set ears Low-set ears Lowset ears An abnormality of the middle ear. UMLS:C1861141 Middle ear abnormalities Middle ear abnormality human_phenotype HP:0000370 Abnormality of the middle ear An abnormality of the middle ear. HPO:probinson An abnormality of the External acoustic tube (also known as the auditory canal). UMLS:C4021807 Auditory canal abnormality human_phenotype HP:0000372 Abnormality of the auditory canal An abnormality of the External acoustic tube (also known as the auditory canal). HPO:probinson An abnormality of the cochlea. UMLS:C4025858 Abnormality of cochlea human_phenotype HP:0000375 The cochlea is an inner ear structure comprised of a snail-shell like structure divided into three fluid-filled parts. Two are canals for the transmission of pressure and in the third is the organ of Corti, which detects pressure impulses and responds with electrical impulses which travel along the auditory nerve to the brain. Abnormal cochlea morphology An abnormality of the cochlea. HPO:probinson An abnormality of the pinna, which is also referred to as the auricle or external ear. HP:0000390 HP:0000398 HP:0004465 HP:0008562 HP:0008566 HP:0008567 HP:0008580 HP:0008582 HP:0008602 SNOMEDCT_US:253255002 UMLS:C0431483 UMLS:C0857379 Abnormal form of ears Abnormally shaped ears Auricular malformation Deformed auricles Deformed ears Dysplastic ears Malformation of auricle Malformed auricles Malformed ears Malformed external ears Minor malformation of the auricles Poorly defined conchae human_phenotype HP:0000377 The term 'dysplastic' is no longer accepted as a descriptor for an ear with unusual morphology. Each specific anatomical component of the ear should be described when the ear is thought to be abnormal in appearance. Abnormality of the pinna An abnormality of the pinna, which is also referred to as the auricle or external ear. HPO:probinson Abnormally shaped ears Auricular malformation Deformed ears Malformed ears Inflammation or infection of the middle ear. MSH:D010033 SNOMEDCT_US:65363002 UMLS:C0029882 Middle ear infection human_phenotype HP:0000388 Otitis media Inflammation or infection of the middle ear. HPO:probinson Middle ear infection ORCID:0000-0001-6908-9849 Median longitudinal ear length greater than two standard deviations above the mean and median ear width greater than two standard deviations above the mean (objective); or, apparent increase in length and width of the pinna (subjective). HP:0000382 HP:0000386 HP:0000401 HP:0001755 SNOMEDCT_US:275480001 SNOMEDCT_US:69056000 UMLS:C0152421 UMLS:C0554972 UMLS:C1835581 UMLS:C1848570 UMLS:C1850189 UMLS:C1855062 UMLS:C1860838 Large ears Large pinnae human_phenotype HP:0000400 This is acknowledged to be a bundled term but retained here because of its usefulness in practice. Ear length is determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. If only length is increased the term Long ear should be used. Macrotia Median longitudinal ear length greater than two standard deviations above the mean and median ear width greater than two standard deviations above the mean (objective); or, apparent increase in length and width of the pinna (subjective). PMID:19152421 Large ears Increased volume and globular shape of the anteroinferior aspect of the nose. HP:0000443 MSH:C538354 UMLS:C0240543 UMLS:C1834118 UMLS:C1855751 Bulbous nose human_phenotype Bulbous nasal tip Potato nose HP:0000414 This is a bundled term, but as it is useful in practice it is kept here. This alteration of size and shape may be limited to the tip, but may involve the lower third of the nose. If only the width of the nasal tip is increased this should be coded as Broad nasal tip. Bulbous nose Increased volume and globular shape of the anteroinferior aspect of the nose. PMID:19152422 Bulbous nose Potato nose ORCID:0000-0001-5889-4463 Abnormality of the choanae (the posterior nasal apertures). UMLS:C4025855 human_phenotype HP:0000415 Abnormality of the choanae Abnormality of the choanae (the posterior nasal apertures). HPO:curators Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose. COHD:318556 EFO:0003895 ICD10:R04.0 ICD9:784.7 MSH:D004844 NCIT:C26766 SNOMEDCT_US:12441001 SNOMEDCT_US:249366005 UMLS:C0014591 Bloody nose Frequent nosebleeds Nasal hemorrhage Nose bleed Nose bleeding Nosebleed human_phenotype HP:0000421 Epistaxis Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose. HPO:probinson Bloody nose ORCID:0000-0001-5889-4463 Frequent nosebleeds Nasal hemorrhage NCIT:C26766 Nose bleed NCIT:C26766 Nose bleeding Nosebleed NCIT:C26766 An abnormality of the Ala of nose. UMLS:C2227020 UMLS:C4021804 UMLS:C4280631 UMLS:C4280632 Abnormality of the nasal ala Abnormality of the nasal alar cartilage Deformity of the nasal ala Deformity of the nasal alar cartilage Malformation of the nasal ala Malformation of the nasal alar cartilage human_phenotype HP:0000429 The nasal ala is the tissue comprising the lateral boundary of the nose, inferiorly, surrounding the naris. Abnormality of the nasal alae An abnormality of the Ala of nose. HPO:probinson PMID:19152422 Abnormality of the nasal alar cartilage ORCID:0000-0001-5889-4463 Deformity of the nasal ala ORCID:0000-0001-5889-4463 Deformity of the nasal alar cartilage ORCID:0000-0001-5889-4463 Malformation of the nasal ala ORCID:0000-0001-5889-4463 Malformation of the nasal alar cartilage ORCID:0000-0001-5889-4463 Thinned, deficient, or excessively arched ala nasi. HP:0004497 HP:0004507 HP:0005276 HP:0005277 HP:0005286 UMLS:C1834055 Ala nasi, underdeveloped Alar cartilage hypoplasia Decreased size of nasal alae Hypoplastic alae nasae Hypoplastic alae nasi Hypoplastic alar cartilage Hypoplastic alar nasae Hypoplastic nares Hypoplastic nasal alae Hypoplastic nasal wings Hypoplastic nostrils Nasal cartilage hypoplasia Small nasal alae Thin hypoplastic alae nasi Underdeveloped tissue around nostril human_phenotype HP:0000430 The alae nasi are the lateral portions of the nose or the wings of the nostrils, which partly encircle the nostrils (nares). They are usually about the width of the columella, but vary greatly depending on the shape of the nostril. Note that individuals may be described as having a Cleft ala nasi, but have a severely underdeveloped ala nasi. In an underdeveloped ala the continuity of the tissue encircling the nostril is undisturbed while in a cleft it is disrupted. With severe hypoplasia of the nasal alae, the nasal tip may appear depressed. Underdeveloped nasal alae Thinned, deficient, or excessively arched ala nasi. PMID:19152422 Decreased size of nasal alae ORCID:0000-0001-5889-4463 Small nasal alae ORCID:0000-0001-5889-4463 Underdeveloped tissue around nostril https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 UMLS:C4025854 Abnormality of mucosa of nose Abnormality of mucous membrane of nose Abnormality of nasal mucous membrane Abnormality of the nasal mucosa HP:0000433 Abnormal nasal mucosa morphology Abnormality of mucosa of nose ORCID:0000-0001-5889-4463 Abnormality of mucous membrane of nose ORCID:0000-0001-5889-4463 Abnormality of nasal mucous membrane ORCID:0000-0001-5889-4463 Abnormality of the nasal mucosa An abnormality of the nasal tip. UMLS:C4025852 Abnormality of the nasal tip Abnormality of tip of nose Deformity of the nasal tip Deformity of tip of nose Malformation of the nasal tip Malformation of tip of nose human_phenotype HP:0000436 The nasal tip is located at the junction of the inferior margin of the nasal ridge and the columella. Commonly, it is the part of the nose furthest from the plane of the face. In rare circumstances, such as markedly prominent and convex nasal profiles, other parts of the ridge may be further removed from the facial plane. Abnormality of the nasal tip An abnormality of the nasal tip. HPO:probinson PMID:19152422 Abnormality of the nasal tip Abnormality of tip of nose ORCID:0000-0001-5889-4463 Deformity of the nasal tip ORCID:0000-0001-5889-4463 Deformity of tip of nose ORCID:0000-0001-5889-4463 Malformation of the nasal tip ORCID:0000-0001-5889-4463 Malformation of tip of nose ORCID:0000-0001-5889-4463 UMLS:C1839765 Triangular nasal tip Triangular shaped tip of nose human_phenotype HP:0000451 Triangular nasal tip Triangular nasal tip Triangular shaped tip of nose ORCID:0000-0001-5889-4463 A splitting of the nasal tip. Visually assessable vertical indentation, cleft, or depression of the nasal tip. HP:0005282 SNOMEDCT_US:249326006 UMLS:C0426428 UMLS:C4020890 Bifid tip of nose Cleft nasal tip human_phenotype Cleft tip of nose Notched nasal tip Notched tip of nose HP:0000456 This is a rare congenital deformity due to failure of the paired nasal processes to fuse to a single midline organ during early gestation. Bifid nasal tip A splitting of the nasal tip. Visually assessable vertical indentation, cleft, or depression of the nasal tip. HPO:sdoelken PMID:19152422 Bifid tip of nose ORCID:0000-0001-5889-4463 Cleft nasal tip ORCID:0000-0001-5889-4463 Cleft tip of nose ORCID:0000-0001-5889-4463 Notched nasal tip Notched tip of nose ORCID:0000-0001-5889-4463 An abnormality of the neck. SNOMEDCT_US:298390003 SNOMEDCT_US:40052002 UMLS:C0266623 UMLS:C0575167 UMLS:C4280628 Abnormality of the neck Anomaly of the neck Deformity of the neck Malformation of the neck human_phenotype HP:0000464 Abnormality of the neck An abnormality of the neck. HPO:probinson Abnormality of the neck Anomaly of the neck ORCID:0000-0001-5889-4463 Deformity of the neck ORCID:0000-0001-5889-4463 Malformation of the neck ORCID:0000-0001-5889-4463 An increased amount of subcutaneous fat tissue around the neck. UMLS:C4025850 Increased fat around the neck human_phenotype HP:0000468 Increased adipose tissue around the neck An increased amount of subcutaneous fat tissue around the neck. HPO:probinson Increased fat around the neck ORCID:0000-0001-5889-4463 Diminished length of the neck. HP:0005992 HP:0200137 SNOMEDCT_US:95427009 UMLS:C0521525 Cervical shortening Decreased cervical height Decreased cervical length Decreased length of neck Short neck human_phenotype HP:0000470 Short neck Diminished length of the neck. HPO:probinson Cervical shortening ORCID:0000-0001-5889-4463 Decreased cervical height ORCID:0000-0001-5889-4463 Decreased cervical length ORCID:0000-0001-5889-4463 Decreased length of neck ORCID:0000-0001-5889-4463 Short neck Dysplasia affecting the vasculature of the gastrointestinal tract. UMLS:C0854242 GI angiodysplasia human_phenotype HP:0000471 Gastrointestinal angiodysplasia Dysplasia affecting the vasculature of the gastrointestinal tract. HPO:probinson GI angiodysplasia Increased inferior-superior length of the neck. UMLS:C1839816 Cervical elongation Elongated neck Increased cervical length Increased length of neck Long neck human_phenotype HP:0000472 Long neck Increased inferior-superior length of the neck. HPO:probinson Cervical elongation ORCID:0000-0001-5889-4463 Elongated neck ORCID:0000-0001-5889-4463 Increased cervical length ORCID:0000-0001-5889-4463 Increased length of neck ORCID:0000-0001-5889-4463 Long neck Any abnormality of the eye, including location, spacing, and intraocular abnormalities. MSH:D005124 MSH:D005128 SNOMEDCT_US:19416009 SNOMEDCT_US:371405004 SNOMEDCT_US:371409005 UMLS:C0015393 UMLS:C0015397 Abnormal eye Abnormality of the eye human_phenotype Eye disease HP:0000478 Abnormality of the eye Any abnormality of the eye, including location, spacing, and intraocular abnormalities. HPO:probinson Abnormal eye HPO:skoehler Abnormality of the eye Eye disease A structural abnormality of the retina. HP:0007938 MSH:D012164 SNOMEDCT_US:29555009 UMLS:C0035300 UMLS:C0035309 Abnormal retina Abnormality of the retina Anomaly of the retina Retina issue human_phenotype Retinal disease HP:0000479 Abnormal retinal morphology A structural abnormality of the retina. HPO:probinson Abnormal retina HPO:skoehler Retina issue A notch or cleft of the retina. HP:0007808 SNOMEDCT_US:39302008 UMLS:C0240896 Hole in the back of the eye human_phenotype HP:0000480 Retinal coloboma A notch or cleft of the retina. HPO:probinson Hole in the back of the eye ORCID:0000-0002-6548-5200 Any abnormality of the cornea, which is the transparent tissue at the front of the eye that covers the iris, pupil, and anterior chamber. HP:0007771 HP:0007972 UMLS:C1855670 UMLS:C4020889 Abnormality of the cornea Corneal abnormalities Corneal abnormality human_phenotype Cornela disease HP:0000481 Abnormal cornea morphology Any abnormality of the cornea, which is the transparent tissue at the front of the eye that covers the iris, pupil, and anterior chamber. HPO:probinson A congenital abnormality of the cornea in which the cornea and the anterior segment of the eye are smaller than normal. The horizontal diameter of the cornea does not reach 10 mm even in adulthood. HP:0100688 SNOMEDCT_US:26098002 UMLS:C0266544 UMLS:C1167713 Cornea of eye less than 10mm in diameter Decreased corneal diameter human_phenotype HP:0000482 Note that the cornea's diameter is normally about 9.5-10.0 mm at birth and reaches 10.0-12-5 mm in adulthood. Microcornea A congenital abnormality of the cornea in which the cornea and the anterior segment of the eye are smaller than normal. The horizontal diameter of the cornea does not reach 10 mm even in adulthood. HPO:probinson Cornea of eye less than 10mm in diameter https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 An enlargement of the cornea with normal clarity and function. Megalocornea is diagnosed with a horizontal corneal diameter of 12 mm or more at birth or 13 mm or more after two years of age. HP:0007660 MSH:C562829 SNOMEDCT_US:204118005 SNOMEDCT_US:268158009 UMLS:C0344530 UMLS:C1167712 Anterior megalophthalmos Enlarged cornea Increased corneal diameter Macrocornea human_phenotype HP:0000485 Megalocornea An enlargement of the cornea with normal clarity and function. Megalocornea is diagnosed with a horizontal corneal diameter of 12 mm or more at birth or 13 mm or more after two years of age. HPO:curators Enlarged cornea ORCID:0000-0001-5208-3432 An abnormality of the lens. MSH:D007905 SNOMEDCT_US:10810001 UMLS:C0023308 UMLS:C0549651 Abnormality of the lens Lens issue human_phenotype Lens disease HP:0000517 Abnormality of the lens An abnormality of the lens. HPO:probinson Abnormality of the lens Lens issue Lens disease An abnormality of the iris, which is the pigmented muscular tissue between the cornea and the lens, that is perforated by an opening called the pupil. UMLS:C4025845 Abnormality of the iris human_phenotype HP:0000525 Abnormality iris morphology An abnormality of the iris, which is the pigmented muscular tissue between the cornea and the lens, that is perforated by an opening called the pupil. HPO:probinson Abnormality of the iris Abnormality of the iris characterized by, typically bilateral, complete or partial iris hypoplasia. The phenotype ranges from mild defects of anterior iris stroma only to almost complete absence of the iris. HP:0011498 MSH:D015783 SNOMEDCT_US:69278003 UMLS:C0003076 Absent iris human_phenotype HP:0000526 Aniridia Abnormality of the iris characterized by, typically bilateral, complete or partial iris hypoplasia. The phenotype ranges from mild defects of anterior iris stroma only to almost complete absence of the iris. HPO:probinson PMID:24138039 PMID:25313118 PMID:29850208 UManchester:psergouniotis Absent iris ORCID:0000-0001-5208-3432 Absence of the globe or eyeball. HP:0001485 HP:0007664 Fyler:4864 MSH:D000853 SNOMEDCT_US:204099004 SNOMEDCT_US:7183006 UMLS:C0003119 Absence of eyeballs Absence of globes of eyes Anophthalmia, clinical Clinical anophthalmia, unilateral/bilateral Failure of development of eyeball Missing eyeball Missing globe of eye No eyeball No globe of eye Ocular absence human_phenotype HP:0000528 Anophthalmia Absence of the globe or eyeball. DDD:ncarter Absence of eyeballs ORCID:0000-0001-5889-4463 Absence of globes of eyes ORCID:0000-0001-5889-4463 Failure of development of eyeball ORCID:0000-0001-5889-4463 Missing eyeball ORCID:0000-0001-5208-3432 ORCID:0000-0001-5889-4463 Missing globe of eye ORCID:0000-0001-5208-3432 ORCID:0000-0001-5889-4463 No eyeball ORCID:0000-0001-5208-3432 ORCID:0000-0001-5889-4463 No globe of eye ORCID:0000-0001-5208-3432 ORCID:0000-0001-5889-4463 Ocular absence ORCID:0000-0001-5208-3432 ORCID:0000-0001-5889-4463 An abnormality of the choroid and retina. HP:0001145 HP:0007888 UMLS:C4025844 Chorioretinal abnormality human_phenotype HP:0000532 The choroid is the vascular layer of the eye, located between the retina and the sclera. Abnormal chorioretinal morphology An abnormality of the choroid and retina. HPO:probinson An abnormality of the uvea, the vascular layer of the eyeball. UMLS:C4025842 Abnormality of the uvea human_phenotype HP:0000553 Abnormal uvea morphology An abnormality of the uvea, the vascular layer of the eyeball. HPO:probinson Inflammation of one or all portions of the uveal tract. MSH:D014605 SNOMEDCT_US:128473001 UMLS:C0042164 human_phenotype HP:0000554 The uvea is the pigmented middle layer of the eye consisting of the iris and ciliary body together with the choroid. Uveitis Inflammation of one or all portions of the uveal tract. HPO:curators Absence of a region of the retina, retinal pigment epithelium, and choroid. HP:0000611 HP:0007718 HP:0007784 HP:0007956 SNOMEDCT_US:39302008 UMLS:C0240896 Birth defect that causes a hole in the innermost layer at the back of the eye Choroidoretinal coloboma human_phenotype Choroid coloboma Choroidal coloboma Coloboma of choroid HP:0000567 Chorioretinal coloboma Absence of a region of the retina, retinal pigment epithelium, and choroid. HPO:probinson Birth defect that causes a hole in the innermost layer at the back of the eye orcid.org/0000-0002-6548-5200 A developmental anomaly characterized by abnormal smallness of one or both eyes. HP:0007996 Decreased size of eyeball Decreased size of globe of eye Fyler:4877 MSH:D008850 SNOMEDCT_US:204108000 SNOMEDCT_US:61142002 UMLS:C0026010 UMLS:C4280625 UMLS:C4280808 Abnormally small eyeball Abnormally small globe of eye Microphthalmos human_phenotype Nanophthalmos HP:0000568 Microphthalmia A developmental anomaly characterized by abnormal smallness of one or both eyes. HPO:probinson Decreased size of eyeball ORCID:0000-0001-5889-4463 Decreased size of globe of eye ORCID:0000-0001-5889-4463 Abnormally small eyeball ORCID:0000-0001-5889-4463 Abnormally small globe of eye ORCID:0000-0001-5889-4463 Hemorrhage occurring within the retina. MSH:D012166 SNOMEDCT_US:28998008 UMLS:C0035317 Retinal bleeding Retinal haemorrhage Retinal hemorrhages human_phenotype HP:0000573 The type of retinal hemorrhage and its clinical appearance depends on its location within the retina. Retinal hemorrhage Hemorrhage occurring within the retina. HPO:gcarletti Retinal bleeding Retinal haemorrhage Retinal hemorrhages ORCID:0000-0002-0736-9199 A developmental defect characterized by a cleft of some portion of the eye or ocular adnexa. HP:0007767 HP:0007995 Fyler:4311 MSH:D003103 SNOMEDCT_US:92828000 SNOMEDCT_US:93390002 UMLS:C0009363 Notched pupil Ocular coloboma Ocular colobomas human_phenotype HP:0000589 Coloboma A developmental defect characterized by a cleft of some portion of the eye or ocular adnexa. HPO:probinson Notched pupil An abnormality of the sclera. Abnormality of the outer white part of eyeball UMLS:C4025840 Abnormality of the sclera human_phenotype HP:0000591 Abnormal sclera morphology An abnormality of the sclera. HPO:probinson Abnormality of the outer white part of eyeball ORCID:0000-0001-5208-3432 Abnormality of the anterior chamber, which is the space in the eye that is behind the cornea and in front of the iris. SNOMEDCT_US:204142009 UMLS:C3152182 Abnormality of the anterior chamber Anterior chamber anomalies Ocular anterior chamber abnormality human_phenotype HP:0000593 Abnormal anterior chamber morphology Abnormality of the anterior chamber, which is the space in the eye that is behind the cornea and in front of the iris. HPO:probinson An abnormality of the ear. SNOMEDCT_US:275259005 UMLS:C0266589 Abnormality of the ear Ear anomaly human_phenotype HP:0000598 Either a morphological abnormality or hearing deficit. This should be split more cleanly in the future. Abnormality of the ear An abnormality of the ear. HPO:probinson Abnormality of the ear An anomaly of the pharynx, i.e., of the tubular structure extending from the base of the skull superiorly to the esophageal inlet inferiorly. UMLS:C4025838 HP:0000600 The pharynx is tubular structure extending from base of skull superiorly to esophageal inlet inferiorly, and is composed of three distinct areas: the nasopharynx, the oropharynx, and the hypopharynx, with the pharyngeal walls being composed of the superior, middle, and inferior pharyngeal constrictor muscles. It is part of the digestive system and of the conducting zone of the respiratory system. Abnormality of the pharynx An anomaly of the pharynx, i.e., of the tubular structure extending from the base of the skull superiorly to the esophageal inlet inferiorly. HPO:probinson Any structural abnormality of the choroid. HP:0001122 MSH:D015862 UMLS:C0008521 UMLS:C4025836 Abnormality of the choroid human_phenotype Choroid disease HP:0000610 Abnormal choroid morphology Any structural abnormality of the choroid. HPO:probinson A coloboma of the iris. HP:0007744 HP:0007748 UMLS:C0240063 Cat eye Coloboma of iris Coloboma of the iris Keyhole iris human_phenotype HP:0000612 Iris coloboma A coloboma of the iris. HPO:probinson PMID:19369671 Cat eye ORCID:0000-0001-6908-9849 An abnormality of the nasolacrimal drainage system, which serves as a conduit for tear flow from the external eye to the nasal cavity. UMLS:C4025835 Abnormality of the nasolacrimal system human_phenotype HP:0000614 The nasolacrimal system consists of the puncta, canaliculi, lacrimal sac, and nasolacrimal duct. Abnormal nasolacrimal system morphology An abnormality of the nasolacrimal drainage system, which serves as a conduit for tear flow from the external eye to the nasal cavity. DDD:ncarter UMLS:C4021802 Abnormality of retinal arteries Retinal arterial abnormality human_phenotype HP:0000630 Abnormal retinal artery morphology Abnormality of retinal arteries Retinal arterial abnormality Atrophy of the eyeball with blindness and decreased intraocular pressure due to end-stage intraocular disease. SNOMEDCT_US:4229009 UMLS:C0271007 human_phenotype HP:0000667 Phthisis bulbi refers to atrophy and degeneration of a blind eye. Phthisis bulbi Atrophy of the eyeball with blindness and decreased intraocular pressure due to end-stage intraocular disease. HPO:probinson The congenital absence of all teeth. HP:0006484 MSH:D000848 SNOMEDCT_US:16958000 SNOMEDCT_US:26624006 UMLS:C0399352 UMLS:C4280622 Anodontia vera Complete agenesis of all teeth Dental agenesis Failure of development of all teeth Complete anodontia Total anodontia human_phenotype Missing all teeth Total absence of all teeth HP:0000674 Anodontia can affect both primary and permanent teeth. Alternatively, there can be anodontia of just the permanent teeth. Anodontia must be distinguished from non-erupted teeth. Anodontia The congenital absence of all teeth. HPO:ibailleulforestier Anodontia vera ORCID:0000-0001-5889-4463 Complete agenesis of all teeth ORCID:0000-0001-5889-4463 Failure of development of all teeth ORCID:0000-0001-5889-4463 Complete anodontia ORCID:0000-0001-5889-4463 Total anodontia ORCID:0000-0001-5889-4463 Missing all teeth ORCID:0000-0001-5889-4463 Total absence of all teeth ORCID:0000-0001-5889-4463 Developmental hypoplasia of teeth. HP:0000688 HP:0006281 HP:0006307 Decreased size of teeth Underdevelopment of teeth UMLS:C0235357 UMLS:C4280611 Hypoplastic teeth human_phenotype HP:0000685 Hypoplasia of teeth Developmental hypoplasia of teeth. HPO:ibailleulforestier Decreased size of teeth ORCID:0000-0001-5889-4463 Underdevelopment of teeth ORCID:0000-0001-5889-4463 Decreased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD below mean. Alternatively, an apparently decreased maximum width of tooth. Decreased size of tooth Hypotrophic tooth Small tooth SNOMEDCT_US:32337007 UMLS:C0240340 UMLS:C4280611 UMLS:C4280612 Decreased width of tooth Small teeth human_phenotype HP:0000691 Standard reference has means and standard deviations by gender [Moyers et al, 1976]. It is easy to measure the width of teeth, for which reason the definition of microdontia can be made with reference to the width of the tooth. However, microdontia means that the overall size of the tooth is decreased. In microdontia, the gaps between the teeth, particularly the anterior upper and lower teeth, are increased, creating diastemata. This should be assessed and coded separately. Microdontia Decreased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD below mean. Alternatively, an apparently decreased maximum width of tooth. HPO:ibailleulforestier PMID:19125428 Decreased size of tooth ORCID:0000-0001-5889-4463 Hypotrophic tooth ORCID:0000-0001-5889-4463 Small tooth ORCID:0000-0001-5889-4463 Decreased width of tooth ORCID:0000-0001-5889-4463 Developmental dysplasia of dentin. MSH:D003811 SNOMEDCT_US:196286005 UMLS:C0011436 human_phenotype HP:0000703 This term is kept for convenience since it is often used to refer to the phenotype of discolored, fragile teeth in the medical literature. Dentinogenesis imperfecta is a disorder of tooth development. This condition causes the teeth to be discolored (most often a blue-gray or yellow-brown color) and translucent. Teeth are also weaker than normal, making them prone to rapid wear, breakage, and loss. Dentinogenesis imperfecta Developmental dysplasia of dentin. HPO:ibailleulforestier An abnormality of the nervous system. HP:0001333 HP:0006987 Brain and/or spinal cord issue MSH:D009421 SNOMEDCT_US:88425004 UMLS:C0497552 Abnormality of the nervous system Neurologic abnormalities Neurological abnormality human_phenotype HP:0000707 The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system. Abnormality of the nervous system An abnormality of the nervous system. HPO:probinson Brain and/or spinal cord issue Abnormality of the nervous system Neurologic abnormalities Neurological abnormality An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities. HP:0000715 HP:0002368 HP:0002456 MSH:D000066553 MSH:D001526 SNOMEDCT_US:25786006 SNOMEDCT_US:277843001 UMLS:C0004941 UMLS:C0233514 Behavioral abnormality Behavioral changes Behavioral disorders Behavioral disturbances Behavioral problems Behavioral/psychiatric abnormalities Behavioural abnormality Behavioural/Psychiatric abnormality Psychiatric disorders Psychiatric disturbances human_phenotype Behavioral symptoms HP:0000708 Behavioral abnormality An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities. HPO:probinson Behavioral abnormality Behavioral changes Behavioral disorders Behavioral disturbances Behavioral problems Behavioral/psychiatric abnormalities Behavioural abnormality Behavioural/Psychiatric abnormality Psychiatric disorders Psychiatric disturbances Behavioral symptoms A state of unease characterized by diffuse motor activity or motion subject to limited control, nonproductive or disorganized behavior, and subjective distress. SNOMEDCT_US:162221009 UMLS:C3887611 Restlessness human_phenotype HP:0000711 Restlessness A state of unease characterized by diffuse motor activity or motion subject to limited control, nonproductive or disorganized behavior, and subjective distress. PMID:28332736 Restlessness A state of exceeding restlessness and excessive motor activity associated with mental distress or a feeling of inner tension. SNOMEDCT_US:24199005 UMLS:C0085631 human_phenotype HP:0000713 Agitation A state of exceeding restlessness and excessive motor activity associated with mental distress or a feeling of inner tension. PMID:29630205 SNOMEDCT_US:112082005 UMLS:C0233522 Inappropriate behavior Inappropriate behaviour human_phenotype HP:0000719 Inappropriate behavior Inappropriate behavior Inappropriate behaviour A structural abnormality of the peripheral nervous system, which is composed of the nerves that lead to or branch off from the central nervous system. This includes the cranial nerves (olfactory and optic nerves are technically part of the central nervous system). HP:0003483 MSH:D010523 SNOMEDCT_US:302226006 SNOMEDCT_US:42658009 UMLS:C0031117 UMLS:C4025831 Abnormal peripheral nervous system structure Peripheral nervous system disease HP:0000759 The peripheral nervous system is divided into autonomic and somatic components, which both include afferent (sensory) and efferent (motor) nerves. Abnormal peripheral nervous system morphology A structural abnormality of the peripheral nervous system, which is composed of the nerves that lead to or branch off from the central nervous system. This includes the cranial nerves (olfactory and optic nerves are technically part of the central nervous system). HPO:probinson Abnormal peripheral nervous system structure Any abnormality of the thorax (the region of the body formed by the sternum, the thoracic vertebrae and the ribs). HP:0100655 UMLS:C4021797 Abnormality of the chest Abnormality of the thorax Structural abnormality of the chest wall HP:0000765 Abnormal thorax morphology Any abnormality of the thorax (the region of the body formed by the sternum, the thoracic vertebrae and the ribs). HPO:probinson Abnormality of the chest An abnormality of the breast. UMLS:C4025829 Abnormality of the breast human_phenotype HP:0000769 Abnormality of the breast An abnormality of the breast. HPO:probinson Abnormality of the breast An anomaly of the rib. HP:0006618 UMLS:C1842083 Abnormality of the ribs Rib abnormalities Rib anomalies human_phenotype HP:0000772 Abnormality of the ribs An anomaly of the rib. HPO:probinson Abnormality of the ribs Rib abnormalities Reduced rib length. HP:0000899 HP:0000908 HP:0009750 SNOMEDCT_US:249696007 UMLS:C0426817 Hypoplastic ribs Rib hypoplasia Short ribs human_phenotype HP:0000773 Short ribs Reduced rib length. HPO:probinson Short ribs Any abnormality of the diaphragm, the sheet of skeletal muscle that separates the thoracic cavity from the abdominal cavity. HP:0005204 UMLS:C1848873 Abnormality of the diaphragm Diaphragm issues Diaphragmatic defect human_phenotype HP:0000775 Abnormality of the diaphragm Any abnormality of the diaphragm, the sheet of skeletal muscle that separates the thoracic cavity from the abdominal cavity. HPO:probinson Abnormality of the diaphragm Diaphragm issues Diaphragmatic defect Abnormality of the thymus, an organ located in the upper anterior portion of the chest cavity just behind the sternum and whose main function is to provide an environment for T lymphocyte maturation. SNOMEDCT_US:93297002 UMLS:C0262650 UMLS:C0685891 Abnormality of the thymus human_phenotype HP:0000777 Abnormality of the thymus Abnormality of the thymus, an organ located in the upper anterior portion of the chest cavity just behind the sternum and whose main function is to provide an environment for T lymphocyte maturation. HPO:probinson Abnormality of the thymus Underdevelopment of the thymus. SNOMEDCT_US:93297002 UMLS:C0685891 UMLS:C4228227 Small thymus Thymic hypoplasia Thymus hypoplasia HP:0000778 Hypoplasia of the thymus Underdevelopment of the thymus. HPO:curators Small thymus ORCID:0000-0001-5208-3432 Any abnormality of the scapula, also known as the shoulder blade. UMLS:C4025828 Abnormality of the shoulder blade HP:0000782 Abnormal scapula morphology Any abnormality of the scapula, also known as the shoulder blade. HPO:probinson Abnormality of the shoulder blade ORCID:0000-0001-5208-3432 The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine). High urine occult blood MSH:D006417 SNOMEDCT_US:34436003 SNOMEDCT_US:53298000 UMLS:C0018965 Blood in urine human_phenotype HP:0000790 Hematuria The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine). HPO:curators High urine occult blood Blood in urine ORCID:0000-0001-5208-3432 An abnormality of the urethra, i.e., of the tube which connects the urinary bladder to the outside of the body. UMLS:C4025826 Urethra issue human_phenotype HP:0000795 Abnormality of the urethra An abnormality of the urethra, i.e., of the tube which connects the urinary bladder to the outside of the body. HPO:probinson Urethra issue Cysts of the cortex of the kidney. UMLS:C1969144 Cortical cysts human_phenotype HP:0000803 Renal cortical cysts Cysts of the cortex of the kidney. Eurenomics:fschaefer UMLS:C4025825 Abnormal external genitalia human_phenotype HP:0000811 Abnormal external genitalia Abnormal external genitalia An anomaly of the adnexa, uterus, and vagina (in female) or seminal tract and prostate (in male). UMLS:C4025824 Abnormal internal genitalia human_phenotype HP:0000812 Abnormal internal genitalia An anomaly of the adnexa, uterus, and vagina (in female) or seminal tract and prostate (in male). HPO:probinson Abnormal internal genitalia An abnormality of the endocrine system. MSH:D004700 SNOMEDCT_US:362969004 UMLS:C0014130 UMLS:C4025823 human_phenotype Endocrine system disease HP:0000818 The endocrine system is composed of glands that secrete hormones directly into the bloodstream and includes the following glands: thyroid, parathyroids, adrenals, pancreas, gonads (testicles and ovaries), and pituitary. Many other organs, such as the kidney, liver, and heart, have secondary endocrine functions. Abnormality of the endocrine system An abnormality of the endocrine system. HPO:probinson A group of abnormalities characterized by hyperglycemia and glucose intolerance. HP:0004908 HP:0008217 HP:0008234 HP:0008260 MSH:D003920 SNOMEDCT_US:73211009 UMLS:C0011849 human_phenotype HP:0000819 Diabetes mellitus A group of abnormalities characterized by hyperglycemia and glucose intolerance. HPO:probinson An abnormality of the thyroid gland. MSH:D013959 SNOMEDCT_US:14304000 UMLS:C0040128 Abnormality of the thyroid gland Thyroid abnormality human_phenotype Thyroid disease HP:0000820 Abnormality of the thyroid gland An abnormality of the thyroid gland. HPO:probinson Abnormality of the thyroid gland Thyroid abnormality Thyroid disease The presence of chronic increased pressure in the systemic arterial system. HP:0004949 HP:0005126 MSH:D006973 SNOMEDCT_US:24184005 SNOMEDCT_US:38341003 UMLS:C0020538 UMLS:C0497247 Systemic hypertension human_phenotype High blood pressure HP:0000822 Hypertension is sustained elevation of resting systolic BP (140 mm Hg or higher), diastolic BP (90 mm Hg or higher), or both. Hypertension The presence of chronic increased pressure in the systemic arterial system. HPO:probinson High blood pressure ORCID:0000-0001-5208-3432 An abnormality of the parathyroid gland. MSH:D010279 SNOMEDCT_US:73132005 UMLS:C0030517 UMLS:C4025822 human_phenotype Parathyroid disease HP:0000828 There are four parathyroid glands, which are small endocrine glands located in the neck behind the thyroid gland that produce parathyroid hormone. Abnormality of the parathyroid gland An abnormality of the parathyroid gland. HPO:curators A condition caused by a deficiency of parathyroid hormone characterized by hypocalcemia and hyperphosphatemia. HP:0000856 HP:0008292 MSH:D007011 SNOMEDCT_US:36976004 UMLS:C0020626 Decreased parathyroid hormone secretion Low parathyroid hormone human_phenotype HP:0000829 Hypoparathyroidism A condition caused by a deficiency of parathyroid hormone characterized by hypocalcemia and hyperphosphatemia. HPO:probinson Decreased parathyroid hormone secretion https://orcid.org/0000-0002-6548-5200 A condition of reduced function of the anterior pituitary gland characterized by decreased secretion of one or more of the pituitary hormones growth hormone, thyroid-stimulating hormone, adrenocorticotropic hormone, prolactin, luteinizing hormone, and follicle-stimulating hormone. UMLS:C4025821 human_phenotype HP:0000830 Anterior hypopituitarism A condition of reduced function of the anterior pituitary gland characterized by decreased secretion of one or more of the pituitary hormones growth hormone, thyroid-stimulating hormone, adrenocorticotropic hormone, prolactin, luteinizing hormone, and follicle-stimulating hormone. HPO:probinson Abnormality of the adrenal glands, i.e., of the endocrine glands located at the top of the kindneys. MSH:D000307 SNOMEDCT_US:30171000 UMLS:C0001621 UMLS:C4021794 Adrenal abnormalities human_phenotype Adrenal gland disease HP:0000834 Abnormality of the adrenal glands Abnormality of the adrenal glands, i.e., of the endocrine glands located at the top of the kindneys. HPO:probinson Adrenal abnormalities Adrenal gland disease Developmental hypoplasia of the adrenal glands. MSH:C538429 SNOMEDCT_US:237774001 UMLS:C0342491 UMLS:C1846223 Adrenal gland hypoplasia Hypoplastic adrenal glands Small adrenal glands human_phenotype HP:0000835 Adrenal hypoplasia Developmental hypoplasia of the adrenal glands. HPO:probinson Small adrenal glands Excessive production of parathyroid hormone (PTH) by the parathyroid glands. MSH:D006961 SNOMEDCT_US:66999008 UMLS:C0020502 Elevated blood parathyroid hormone level human_phenotype HP:0000843 Hyperparathyroidism Excessive production of parathyroid hormone (PTH) by the parathyroid glands. HPO:probinson Elevated blood parathyroid hormone level ORCID:0000-0001-5208-3432 UMLS:C4025820 human_phenotype HP:0000849 Adrenocortical abnormality An enlargement of the thyroid gland. MSH:D006042 SNOMEDCT_US:3716002 UMLS:C0018021 Enlarged thyroid gland in neck Goitre Thyroid goiter human_phenotype HP:0000853 Goiter An enlargement of the thyroid gland. HPO:probinson Enlarged thyroid gland in neck https://orcid.org/0000-0002-6548-5200 Goitre Developmental hypoplasia of the parathyroid gland. UMLS:C1389851 Small parathyroid glands Underdeveloped parathyroid glands human_phenotype HP:0000860 Parathyroid hypoplasia Developmental hypoplasia of the parathyroid gland. HPO:probinson Small parathyroid glands ORCID:0000-0001-5208-3432 Underdeveloped parathyroid glands ORCID:0000-0001-5208-3432 Abnormality of the pituitary gland (also known as hypophysis), which is an endocrine gland that protrudes from the bottom of the hypothalamus at the base of the brain. The pituitary gland secretes the hormones ACTH, TSH, PRL, GH, endorphins, FSH, LH, oxytocin, and antidiuretic hormone. The secretion of hormones from the anterior pituitary is under the strict control of hypothalamic hormones, and the posterior pituitary is essentially an extension of the hypothalamus, so that hypothalamus and pituitary gland may be regarded as a functional unit. HP:0000838 HP:0000844 UMLS:C4025819 human_phenotype HP:0000864 Abnormality of the hypothalamus-pituitary axis Abnormality of the pituitary gland (also known as hypophysis), which is an endocrine gland that protrudes from the bottom of the hypothalamus at the base of the brain. The pituitary gland secretes the hormones ACTH, TSH, PRL, GH, endorphins, FSH, LH, oxytocin, and antidiuretic hormone. The secretion of hormones from the anterior pituitary is under the strict control of hypothalamic hormones, and the posterior pituitary is essentially an extension of the hypothalamus, so that hypothalamus and pituitary gland may be regarded as a functional unit. DDD:spark A pituitary functional deficit affecting all the anterior pituitary hormones (growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone, luteinizing hormone, adrenocorticotropic hormone, and prolactin). MSH:C580003 SNOMEDCT_US:32390006 UMLS:C0242343 human_phenotype HP:0000871 Panhypopituitarism HPO:skoehler A pituitary functional deficit affecting all the anterior pituitary hormones (growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone, luteinizing hormone, adrenocorticotropic hormone, and prolactin). HPO:probinson PMID:12466332 Underdeveloped scapula. HP:0000906 HP:0006616 UMLS:C1846434 Hypoplastic scapula Scapular hypoplasia Short scapulae Small scapula Small scapulae Small shoulder blade human_phenotype HP:0000882 Hypoplastic scapulae Underdeveloped scapula. HPO:probinson Small shoulder blade ORCID:0000-0001-5208-3432 Malformation of the rib cage. UMLS:C1838659 Deformed rib cage human_phenotype HP:0000886 Deformed rib cage Malformation of the rib cage. HPO:probinson Deformed rib cage A bifid rib refers to cleavage of the sternal end of a rib, usually unilateral. Bifid ribs are usually asymptomatic, and are often discovered incidentally by chest x-ray. SNOMEDCT_US:66102006 UMLS:C0265695 Cleft ribs Split ribs human_phenotype HP:0000892 Bifid ribs A bifid rib refers to cleavage of the sternal end of a rib, usually unilateral. Bifid ribs are usually asymptomatic, and are often discovered incidentally by chest x-ray. HPO:probinson Cleft ribs ORCID:0000-0001-5208-3432 Split ribs ORCID:0000-0001-5208-3432 A developmental anomaly with absence of one or more ribs. HP:0000881 HP:0006627 SNOMEDCT_US:249695006 UMLS:C0426816 Absent ribs Decreased rib number Missing ribs human_phenotype HP:0000921 Missing ribs A developmental anomaly with absence of one or more ribs. HPO:probinson Absent ribs Decreased rib number Missing ribs An abnormality of the skeletal system. UMLS:C4021790 Abnormality of the skeletal system Skeletal abnormalities Skeletal anomalies human_phenotype HP:0000924 Abnormality of the skeletal system An abnormality of the skeletal system. HPO:probinson Abnormality of the skeletal system Skeletal abnormalities Skeletal anomalies Any abnormality of the vertebral column. UMLS:C4020882 UMLS:C4021789 Abnormal spine Abnormal vertebral column Abnormality of the spine Abnormality of the vertebral column Abnormality of the backbone HP:0000925 Abnormality of the vertebral column Any abnormality of the vertebral column. HPO:probinson Abnormal spine HPO:skoehler Abnormal vertebral column Abnormality of the spine Abnormality of the vertebral column Abnormality of the backbone An abnormality of the skull, the bony framework of the head which is comprised of eight cranial and fourteen facial bones. UMLS:C0235942 Abnormality of the skull Abnormality of the skull bones human_phenotype HP:0000929 Abnormal skull morphology An abnormality of the skull, the bony framework of the head which is comprised of eight cranial and fourteen facial bones. HPO:probinson Abnormality of the skull Abnormality of the skull bones ORCID:0000-0001-5889-4463 Osteopenia is a term to define bone density that is not normal but also not as low as osteoporosis. By definition from the World Health Organization osteopenia is defined by bone densitometry as a T score -1 to -2.5. HP:0002768 HP:0002799 HP:0002800 MSH:D001851 SNOMEDCT_US:312894000 SNOMEDCT_US:78441005 UMLS:C0029453 UMLS:C0747078 Generalized osteopenia human_phenotype HP:0000938 Osteopenia Osteopenia is a term to define bone density that is not normal but also not as low as osteoporosis. By definition from the World Health Organization osteopenia is defined by bone densitometry as a T score -1 to -2.5. HPO:probinson PMID:21234807 An abnormality of the structure or form of the diaphysis, i.e., of the main or mid-section (shaft) of a long bone. HP:0006504 UMLS:C4021787 Abnormal shape of shaft of long bone Abnormality involving the diaphyses of the limbs Abnormality of shaft of long bone of the limbs Abnormality of the diaphyses Anomaly of the limb diaphyses Anomaly of the limb diaphyses morphology human_phenotype HP:0000940 Abnormal diaphysis morphology An abnormality of the structure or form of the diaphysis, i.e., of the main or mid-section (shaft) of a long bone. HPO:probinson Abnormal shape of shaft of long bone ORCID:0000-0001-5208-3432 Abnormality of shaft of long bone of the limbs ORCID:0000-0001-5208-3432 UMLS:C4025815 Short shaft of long bone human_phenotype HP:0000941 Short diaphyses Short shaft of long bone ORCID:0000-0001-5208-3432 An abnormality of one or more metaphysis, i.e., of the somewhat wider portion of a long bone that is adjacent to the epiphyseal growth plate and grows during childhood. HP:0006506 UMLS:C4025814 Abnormality of the wide portion of a long bone human_phenotype HP:0000944 Abnormality of the metaphysis An abnormality of one or more metaphysis, i.e., of the somewhat wider portion of a long bone that is adjacent to the epiphyseal growth plate and grows during childhood. HPO:probinson Abnormality of the wide portion of a long bone ORCID:0000-0001-5208-3432 Underdevelopment of the ilium. HP:0003176 HP:0003178 Small wings of the pelvic girdle UMLS:C1861218 UMLS:C4280607 Short and small iliac bones Small iliac bones human_phenotype HP:0000946 Hypoplastic ilia Underdevelopment of the ilium. HPO:probinson Small wings of the pelvic girdle ORCID:0000-0001-5208-3432 An abnormality of the skin. HP:0001478 HP:0001479 HP:0005591 HP:0006736 HP:0007415 HP:0007580 MSH:D012868 MSH:D012871 SNOMEDCT_US:199879009 SNOMEDCT_US:95320005 UMLS:C0037268 UMLS:C0037274 Abnormality of the skin dermatopathy dermopathy human_phenotype Skin abnormality HP:0000951 Abnormality of the skin An abnormality of the skin. HPO:probinson Abnormality of the skin dermatopathy HPO:skoehler dermopathy HPO:skoehler A darkening of the skin related to an increase in melanin production and deposition. HP:0007527 MSH:D017495 SNOMEDCT_US:4830009 SNOMEDCT_US:49765009 UMLS:C0162834 Cutaneous hyperpigmentation Hyperpigmented lesion Increased skin pigmentation Patchy darkened skin Skin hyperpigmentation Melanoderma Melanodermia HP:0000953 Hyperpigmentation of the skin A darkening of the skin related to an increase in melanin production and deposition. HPO:probinson Hyperpigmented lesion https://orcid.org/0000-0001-5208-3432 Patchy darkened skin Eczema is a form of dermatitis. The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding. HP:0001481 MSH:D004485 SNOMEDCT_US:281104002 SNOMEDCT_US:43116000 UMLS:C0013595 Eczema human_phenotype HP:0000964 Eczema has several forms including atopic dermatitis, contact dermatitis, dyshidrotic eczema, nummular eczema, seborrheic dermatitis, and stasis dermatitis. Eczema Eczema is a form of dermatitis. The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding. HPO:probinson Eczema Ectodermal dysplasia is a group of conditions in which there is abnormal development of the skin, hair, nails, teeth, or sweat glands. HP:0007615 MSH:D004476 SNOMEDCT_US:254154003 SNOMEDCT_US:8654005 UMLS:C0013575 human_phenotype HP:0000968 This term is kept in the HPO for now as 'ectodermal dysplasia' has been recorded as a phenotypic of other disorders such as DEAFNESS WITH ANHIDROTIC ECTODERMAL DYSPLASIA (MIM125050). Nevertheless it is preferable to use precise descriptions of the phenotypic abnormalities and this term should not be used for new annotations. It will be made obsolete in the future. Ectodermal dysplasia Ectodermal dysplasia is a group of conditions in which there is abnormal development of the skin, hair, nails, teeth, or sweat glands. HPO:probinson Any structural abnormality of the sweat gland. MSH:D013543 SNOMEDCT_US:88232005 UMLS:C0038986 UMLS:C0262643 UMLS:C4020881 Abnormality of the sweat gland human_phenotype Abnormalities of sweating Sweat gland disease HP:0000971 Abnormal sweat gland morphology Any structural abnormality of the sweat gland. HPO:probinson Abnormality of the sweat gland Abnormalities of sweating HPO:skoehler Sweat gland disease A oval and round, colored (usually medium-to dark brown, reddish brown, or flesh colored) lesion. Typically, a melanocytic nevus is less than 6 mm in diameter, but may be much smaller or larger. Noncancerous mole MSH:D009508 SNOMEDCT_US:21119008 SNOMEDCT_US:400096001 UMLS:C0027962 UMLS:C4280269 Beauty mark Melanocytic naevus Melanocytic nevi Nevocellular nevi Pigmented naevi Pigmented nevi human_phenotype HP:0000995 Melanocytic nevi are commonly known as moles. The majority of moles appear during the first 20 to 30 years of a person's life, however, some may be present when the baby is born. The average human has from 10 to 14 moles. Moles can develop on the scalp, under the nails, armpits, virtually anywhere on the body. The total number of moles a person can have usually varies during his or her lifetime. Melanocytic nevus A oval and round, colored (usually medium-to dark brown, reddish brown, or flesh colored) lesion. Typically, a melanocytic nevus is less than 6 mm in diameter, but may be much smaller or larger. HPO:probinson Noncancerous mole ORCID:0000-0001-5208-3432 Beauty mark ORCID:0000-0001-6908-9849 Hypertrichosis is increased hair growth that is abnormal in quantity or location. Excessive hair growth Increased hair growth on body MSH:D006983 SNOMEDCT_US:271607001 SNOMEDCT_US:29966009 UMLS:C0020555 human_phenotype HP:0000998 Hypertrichosis Hypertrichosis is increased hair growth that is abnormal in quantity or location. HPO:probinson Excessive hair growth ORCID:0000-0001-5208-3432 Increased hair growth on body https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 An abnormality of the pigmentation of the skin. HP:0007582 HP:0200045 UMLS:C1260926 Abnormal pigmentation Abnormal skin color Abnormal skin pigmentation Abnormality of pigmentation Abnormality of skin pigmentation Pigmentary changes Pigmentary skin changes Pigmentation anomaly human_phenotype HP:0001000 Abnormality of skin pigmentation An abnormality of the pigmentation of the skin. HPO:probinson Abnormal pigmentation Abnormal skin color ORCID:0000-0001-6908-9849 Abnormal skin pigmentation HPO:skoehler Abnormality of pigmentation Abnormality of skin pigmentation Pigmentary changes Pigmentary skin changes Pigmentation anomaly UMLS:C4025813 Abnormality of fatty tissue below the skin human_phenotype HP:0001001 Abnormality of subcutaneous fat tissue Abnormality of fatty tissue below the skin ORCID:0000-0001-5208-3432 Abnormally increased hair growth referring to a male pattern of body hair (androgenic hair). MSH:D006628 SNOMEDCT_US:399939002 UMLS:C0019572 Excessive hairiness human_phenotype HP:0001007 Hirsutism Abnormally increased hair growth referring to a male pattern of body hair (androgenic hair). HPO:sdoelken Excessive hairiness https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 A reduction of skin color related to a decrease in melanin production and deposition. HP:0005589 HP:0007604 HP:0007622 MSH:D017496 SNOMEDCT_US:18655006 SNOMEDCT_US:201284005 SNOMEDCT_US:23006000 SNOMEDCT_US:89031001 UMLS:C0162835 Hypopigmentation Hypopigmented skin Patchy lightened skin human_phenotype Skin hypopigmentation HP:0001010 Hypopigmentation of the skin A reduction of skin color related to a decrease in melanin production and deposition. HPO:probinson Patchy lightened skin An abnormality of the biliary tree. MSH:D001660 SNOMEDCT_US:105997008 UMLS:C0005424 UMLS:C0549613 human_phenotype Biliary tract disease HP:0001080 Biliary tract abnormality An abnormality of the biliary tree. HPO:probinson Diffusely large eye (with megalocornea) without glaucoma. HP:0200093 SNOMEDCT_US:246920008 UMLS:C0423221 UMLS:C1855852 UMLS:C4280603 Increased size of eyes Large eyes Megalophthalmos human_phenotype Increased size of palpebral fissures Large eyeballs Large of palpebral fissures HP:0001090 Note that Increased size of palpebral fissues is not a synonym of this term. Abnormally large globe Diffusely large eye (with megalocornea) without glaucoma. HPO:probinson Increased size of eyes ORCID:0000-0001-5889-4463 Large eyes Increased size of palpebral fissures ORCID:0000-0001-5889-4463 Large eyeballs ORCID:0000-0001-5889-4463 Large of palpebral fissures ORCID:0000-0001-5889-4463 Any structural abnormality of the fundus of the eye. UMLS:C4025804 Abnormality of the fundus human_phenotype HP:0001098 Abnormal fundus morphology Inflammation of the iris. MSH:D007500 SNOMEDCT_US:65074000 UMLS:C0022081 Inflammation of iris human_phenotype HP:0001101 Iritis Inflammation of the iris. HPO:probinson Inflammation of iris ORCID:0000-0001-5208-3432 Any abnormality of the size or morphology of the cornea. UMLS:C4025802 human_phenotype HP:0001120 Abnormality of corneal size Any abnormality of the size or morphology of the cornea. HPO:curators An abnormality affecting one or both hands. HP:0005858 MSH:D006226 SNOMEDCT_US:299033004 UMLS:C0018564 Abnormal hands Abnormality of the hand Hand anomalies Hand deformities human_phenotype HP:0001155 Abnormality of the hand An abnormality affecting one or both hands. HPO:probinson Abnormal hands HPO:skoehler Abnormality of the hand Hand anomalies Hand deformities Digits that appear disproportionately short compared to the hand/foot. The word brachydactyly is used here to describe a series distinct patterns of shortened digits (brachydactyly types A-E). This is the sense used here. HP:0001189 HP:0001201 HP:0005630 HP:0005657 HP:0005727 HP:0006017 HP:0006128 HP:0100667 MSH:D059327 SNOMEDCT_US:43476002 UMLS:C0221357 Brachydactyly syndrome Short fingers or toes human_phenotype HP:0001156 Brachydactyly Digits that appear disproportionately short compared to the hand/foot. The word brachydactyly is used here to describe a series distinct patterns of shortened digits (brachydactyly types A-E). This is the sense used here. HPO:probinson Short fingers or toes orcid.org/0000-0002-6548-5200 A kind of polydactyly characterized by the presence of a supernumerary finger or fingers. MEDDRA:10036064 SNOMEDCT_US:81793007 UMLS:C0158733 Extra finger Finger polydactyly Polydactyly of the hand Supernumerary finger human_phenotype HP:0001161 Hand polydactyly A kind of polydactyly characterized by the presence of a supernumerary finger or fingers. HPO:probinson MEDDRA:10036064 Polydactyly of fingers Extra finger ORCID:0000-0001-6908-9849 Supernumerary finger ORCID:0000-0001-6908-9849 Supernumerary digits located at the ulnar side of the hand (that is, on the side with the fifth finger). HP:0004698 HP:0005763 HP:0009984 SNOMEDCT_US:205131007 UMLS:C0431904 Extra little finger Extra pinkie finger Extra pinky finger Polydactyly affecting the 5th finger Postaxial polydactyly of fingers Postaxial polydactyly of hand Postaxial polydactyly of hands human_phenotype HP:0001162 Postaxial hand polydactyly Supernumerary digits located at the ulnar side of the hand (that is, on the side with the fifth finger). HPO:sdoelken Extra little finger ORCID:0000-0001-5208-3432 Extra pinkie finger ORCID:0000-0001-5208-3432 Extra pinky finger ORCID:0000-0001-5208-3432 An abnormality of the metacarpal bones. UMLS:C4021785 Abnormality of the long bone of hand Anomaly of the metacarpal bones human_phenotype HP:0001163 Abnormality of the metacarpal bones An abnormality of the metacarpal bones. HPO:probinson Abnormality of the long bone of hand ORCID:0000-0001-5208-3432 An anomaly of a finger. HP:0003035 UMLS:C2674737 Abnormalities of the fingers Abnormality of finger human_phenotype HP:0001167 Abnormality of finger An anomaly of a finger. HPO:probinson Abnormalities of the fingers Abnormality of finger An abnormal structure of the first digit of the hand. MSH:C536903 SNOMEDCT_US:299130003 UMLS:C0575897 Abnormality of the thumb Abnormality of the thumbs Thumb deformity human_phenotype HP:0001172 Abnormal thumb morphology Abnormality of the thumb Abnormality of the thumbs Thumb deformity HP:0002820 HP:0006044 HP:0006219 SNOMEDCT_US:249752003 UMLS:C0426870 Disproportionately large hands Large hands large hand human_phenotype HP:0001176 Large hands Large hands large hand Supernumerary digits located at the radial side of the hand. Polydactyly (supernumerary digits) involving the thumb occurs in many distinct forms of high variability and severity. Ranging from fleshy nubbins over varying degrees of partial duplication/splitting to completely duplicated or even triplicated thumbs or preaxial (on the radial side of the hand) supernumerary digits. HP:0005629 HP:0005634 HP:0006182 HP:0009604 MSH:C536332 SNOMEDCT_US:205135003 SNOMEDCT_US:445216006 UMLS:C1395852 Extra thumb Polydactyly affecting the thumb Preaxial polydactyly of hands Supernumerary thumb thumb polydactyly human_phenotype HP:0001177 Preaxial hand polydactyly Supernumerary digits located at the radial side of the hand. Polydactyly (supernumerary digits) involving the thumb occurs in many distinct forms of high variability and severity. Ranging from fleshy nubbins over varying degrees of partial duplication/splitting to completely duplicated or even triplicated thumbs or preaxial (on the radial side of the hand) supernumerary digits. HPO:probinson Extra thumb ORCID:0000-0001-6908-9849 Supernumerary thumb ORCID:0000-0001-6908-9849 A developmental defect resulting in the presence of fewer than the normal number of fingers. SNOMEDCT_US:71358006 UMLS:C0728895 Hand has less than 5 fingers human_phenotype HP:0001180 Hand oligodactyly A developmental defect resulting in the presence of fewer than the normal number of fingers. HPO:probinson Hand has less than 5 fingers https://orcid.org/0000-0002-6548-5200 An abnormality affecting the carpal bones of the wrist (scaphoid, lunate, triquetral, pisiform, trapezium, trapezoid, capitate, hamate). Abnormal wrist bones UMLS:C1840535 Abnormal carpal bones Anomalous carpal bones Carpal bone anomalies human_phenotype HP:0001191 Abnormality of the carpal bones An abnormality affecting the carpal bones of the wrist (scaphoid, lunate, triquetral, pisiform, trapezium, trapezoid, capitate, hamate). HPO:probinson Abnormal wrist bones ORCID:0000-0001-5208-3432 UMLS:C4048199 human_phenotype HP:0001193 Ulnar deviation of the hand or of fingers of the hand An abnormality of the placenta (the organ that connects the developing fetus to the uterine wall) or of the umbilical cord (the cord that connects the fetus to the placenta). UMLS:C4025798 Abnormalities of placenta or umbilical cord human_phenotype HP:0001194 Abnormalities of placenta or umbilical cord An abnormality of the placenta (the organ that connects the developing fetus to the uterine wall) or of the umbilical cord (the cord that connects the fetus to the placenta). HPO:curators Abnormalities of placenta or umbilical cord Decreased length of the umbilical cord. SNOMEDCT_US:59795007 UMLS:C0266786 Short umbilical cord human_phenotype HP:0001196 Short umbilical cord Decreased length of the umbilical cord. HPO:probinson Short umbilical cord An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. UMLS:C4025797 Abnormality of prenatal development or birth human_phenotype HP:0001197 Because of the close link between prenatal developmental abnormalities and abnormalities of the birth process, a single term is chosen to subsume both classes of abnormality. Abnormality of prenatal development or birth An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. HPO:probinson Abnormality of prenatal development or birth An abnormal structure of the tip (end) of a finger. UMLS:C4025796 Abnormality of the fingertips human_phenotype HP:0001211 Abnormal fingertip morphology Abnormality of the fingertips Ossification of carpal bones occurs later than age-adjusted norms. UMLS:C1841684 UMLS:C4280599 Carpal delayed ossification Delayed carpal bone age Delayed carpal ossification Delayed maturation of carpal bones human_phenotype Delayed maturation of wrist bone HP:0001216 Delayed ossification of carpal bones Ossification of carpal bones occurs later than age-adjusted norms. HPO:probinson Delayed maturation of wrist bone ORCID:0000-0001-5208-3432 Chronic loss of joint motion in an interphalangeal joint of a finger due to structural changes in non-bony tissue. UMLS:C4021784 Interphalangeal joint flexion contractures human_phenotype HP:0001220 Interphalangeal joint contracture of finger Chronic loss of joint motion in an interphalangeal joint of a finger due to structural changes in non-bony tissue. HPO:probinson A chronic loss of wrist joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevent normal movement of the joints of the wrist. HP:0006049 HP:0006137 SNOMEDCT_US:202275008 UMLS:C0409345 Wrist contracture Wrist flexion deformity human_phenotype HP:0001239 Wrist flexion contracture A chronic loss of wrist joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevent normal movement of the joints of the wrist. HPO:probinson A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. HP:0001275 HP:0001303 HP:0002125 HP:0002182 HP:0002279 HP:0002306 HP:0002348 HP:0002391 HP:0002417 HP:0002430 HP:0002431 HP:0002432 HP:0002434 HP:0002437 HP:0002466 HP:0002479 HP:0002794 HP:0006997 HP:0010520 MSH:D004827 MSH:D012640 SNOMEDCT_US:128613002 SNOMEDCT_US:246545002 SNOMEDCT_US:313307000 SNOMEDCT_US:84757009 SNOMEDCT_US:91175000 UMLS:C0014544 UMLS:C0036572 Epileptic seizure Seizures human_phenotype Epilepsy HP:0001250 A type of electrographic seizure has been proposed in neonates which does not have a clinical correlate, it is electrographic only. The term epilepsy is not used to describe recurrent febrile seizures. Epilepsy presumably reflects an abnormally reduced seizure threshold. Seizure A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. HPO:probinson PMID:15816939 Seizures Seizures Epilepsy Inflammation of the meninges. MSH:D008581 SNOMEDCT_US:7180009 UMLS:C0025289 human_phenotype HP:0001287 Meningitis Inflammation of the meninges. HPO:probinson Structural abnormality affecting one or more of the cranial nerves, which emerge directly from the brain stem. HP:0003480 UMLS:C1854510 UMLS:C4020872 Abnormality of cranial nerve Abnormality of the cranial nerves Cranial nerve disease Cranial nerve involvement human_phenotype Cranial nerve abnormality HP:0001291 Abnormal cranial nerve morphology Structural abnormality affecting one or more of the cranial nerves, which emerge directly from the brain stem. HPO:probinson Abnormality of cranial nerve https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0001-5889-4463 Any structural abnormality of the cerebellum. UMLS:C0742038 UMLS:C1866129 Abnormality of the cerebellum Cerebellar abnormalities Cerebellar abnormality Cerebellar anomaly Cerebellar signs human_phenotype HP:0001317 A malformed cerebellum may be abnormally small, dysplastic, or unusually large. The vermis and both hemispheres may be equally or disproportionately affected. Primary malformations of the pons, midbrain, and supratentorial structures are also seen in a substantial subset of patients. The wide range in morphological presentations results from the diversity of causes, including chromosomal abnormalities, specific genetic syndromes, and extrinsic factors. Abnormal cerebellum morphology Any structural abnormality of the cerebellum. HPO:probinson PMID:27160001 Abnormality of the cerebellum Cerebellar abnormalities Cerebellar abnormality Cerebellar anomaly Underdevelopment of the cerebellum. HP:0006806 HP:0006910 HP:0007038 HP:0007053 MSH:C562568 SNOMEDCT_US:16026008 UMLS:C0266470 Congenital cerebellar hypoplasia Hypoplasia of cerebellum Hypoplastic cerebellum Small cerebellum Underdeveloped cerebellum human_phenotype HP:0001321 By prenatal ultrasound, cerebellar hypoplasia is diagnosed if the cerebellum measures more than two standard deviations below the mean. In adults, cerebellar hypoplasia is typically diagnosed by computer tomography or magnetic resonance imaging. Cerebellar hypoplasia can be diagnosed if there is a small cerebellum with fissures of normal size compared with the folia (this is a distinguishing characteristic compared with cerebellar atrophy). Cerebellar hypoplasia (CH) refers to an underdevelopment of the cerebellum. This category of cerebellar malformation is distinct from Dandy Walker malformation in that it does not involve a concurrent enlargement of the posterior fossa, and almost all individuals exhibit cognitive and motor impairments. Cerebellar hypoplasia Underdevelopment of the cerebellum. HPO:probinson PMID:27160001 Small cerebellum ORCID:0000-0001-5208-3432 Underdeveloped cerebellum ORCID:0000-0001-5208-3432 Hemorrhage into the parenchyma of the brain. HP:0002137 MSH:D002543 MSH:D020300 SNOMEDCT_US:230706003 SNOMEDCT_US:274100004 UMLS:C0553692 UMLS:C2937358 Bleeding in brain Cerebral haemorrhage Intracerebral hemorrhage human_phenotype Hemorrhagic stroke HP:0001342 A cerebral hemorrhage (or intracerebral hemorrhage, ICH), is a type of intracranial hemorrhage that occurs within the brain tissue itself. Cerebral hemorrhage Hemorrhage into the parenchyma of the brain. HPO:gcarletti Bleeding in brain https://orcid.org/0000-0002-6548-5200 Cerebral haemorrhage Hemorrhagic stroke ORCID:0000-0001-6908-9849 A localized defect in the bone of the skull resulting from abnormal embryological development. The defect is covered by normal skin. In some cases, skull x-rays have shown underlying lytic bone lesions which have closed before the age of one year. UMLS:C4025787 UMLS:C4280595 UMLS:C4280596 Cranial defect Skull defect Calvarial defect human_phenotype HP:0001362 Calvarial skull defect A localized defect in the bone of the skull resulting from abnormal embryological development. The defect is covered by normal skin. In some cases, skull x-rays have shown underlying lytic bone lesions which have closed before the age of one year. HPO:probinson Cranial defect ORCID:0000-0001-5889-4463 Skull defect Calvarial defect ORCID:0000-0001-5889-4463 An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join. MSH:D007592 SNOMEDCT_US:399269003 UMLS:C0022408 UMLS:C0240083 Abnormal shape of joints Abnormality of the joints Anomaly of the joints human_phenotype Joint disease HP:0001367 Abnormal joint morphology An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join. HPO:probinson Abnormal shape of joints ORCID:0000-0001-5208-3432 Abnormality of the joints Anomaly of the joints Joint disease Inflammation of a joint. MSH:D001168 SNOMEDCT_US:3723001 UMLS:C0003864 Arthritis Joint inflammation human_phenotype HP:0001369 Arthritis Inflammation of a joint. HPO:probinson Arthritis Joint inflammation ORCID:0000-0002-6548-5200 A flexion contracture is a bent (flexed) joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints. HP:0001372 HP:0001381 HP:0005053 HP:0005189 HP:0005660 MSH:D003286 SNOMEDCT_US:203598005 SNOMEDCT_US:385522000 SNOMEDCT_US:55033002 SNOMEDCT_US:57048009 SNOMEDCT_US:7890003 SNOMEDCT_US:88565003 UMLS:C0009917 UMLS:C0009918 UMLS:C0333068 UMLS:C1850530 Contracture Flexed joint that cannot be straightened Flexion contractures Flexion contractures of joints Joint contracture Joint contractures human_phenotype Contractures HP:0001371 Flexion contracture A flexion contracture is a bent (flexed) joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints. HPO:probinson Flexed joint that cannot be straightened Contractures HPO:skoehler A reduction in the freedom of movement of one or more joints. HP:0003101 UMLS:C1857108 Decreased joint mobility Decreased mobility of joints Limitation of joint mobility Limited joint mobility Limited joint motion human_phenotype HP:0001376 Limitation of joint mobility A reduction in the freedom of movement of one or more joints. HPO:probinson Decreased joint mobility Decreased mobility of joints Limitation of joint mobility Limited joint mobility Limited joint motion The ability of a joint to move beyond its normal range of motion. HP:0001378 HP:0005034 SNOMEDCT_US:298181000 UMLS:C1844820 Double-Jointed Extensible joints Flexible joints Hyperextensible joints Increased joint mobility Increased mobility of joints Joint hyperextensibility human_phenotype HP:0001382 Joint hypermobility The ability of a joint to move beyond its normal range of motion. HPO:probinson Double-Jointed Flexible joints Increased mobility of joints An abnormality of the hip joint. UMLS:C4020870 Abnormality of the hip joint human_phenotype Abnormality of the hip joints HP:0001384 Abnormality of the hip joint An abnormality of the hip joint. HPO:probinson Abnormality of the hip joint Abnormality of the hip joints The presence of developmental dysplasia of the hip. HP:0008787 Abnormal formation of the hip MSH:D006618 SNOMEDCT_US:48334007 SNOMEDCT_US:52781008 UMLS:C0019555 Congenital hip dysplasia human_phenotype HP:0001385 Hip dysplasia The presence of developmental dysplasia of the hip. HPO:probinson Abnormal formation of the hip https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 An abnormality of the liver. MSH:D008107 SNOMEDCT_US:235856003 UMLS:C0023895 UMLS:C4021780 Abnormal liver Abnormality of the liver Liver abnormality human_phenotype Liver disease HP:0001392 Abnormality of the liver An abnormality of the liver. HPO:probinson Abnormal liver Abnormality of the liver Liver abnormality Liver disease SNOMEDCT_US:85057007 UMLS:C0267834 Liver cysts human_phenotype HP:0001407 Hepatic cysts Liver cysts peter 2008-04-07T10:59:00Z UMLS:C4025786 Abnormal hand muscles human_phenotype HP:0001421 Abnormality of the musculature of the hand Abnormal hand muscles ORCID:0000-0001-5208-3432 peter 2008-04-07T10:18:00Z HP:0004300 UMLS:C4021779 Abnormal calf muscles Abnormality of calf musculature human_phenotype HP:0001430 Abnormality of the calf musculature Abnormal calf muscles ORCID:0000-0001-5208-3432 Simultaneous enlargement of the liver and spleen. peter 2008-02-20T10:51:00Z SNOMEDCT_US:36760000 UMLS:C0019214 Enlarged liver and spleen human_phenotype HP:0001433 Hepatosplenomegaly Simultaneous enlargement of the liver and spleen. HPO:probinson Enlarged liver and spleen ORCID:0000-0001-5208-3432 peter 2008-04-07T10:19:00Z HP:0004301 UMLS:C4021778 Abnormality of shoulder musculature human_phenotype HP:0001435 Abnormality of the shoulder girdle musculature Abnormality of shoulder musculature An anomaly of the musculature of foot. peter 2008-04-07T10:21:00Z UMLS:C4025785 Abnormal foot muscles human_phenotype HP:0001436 Abnormality of the foot musculature An anomaly of the musculature of foot. HPO:probinson Abnormal foot muscles ORCID:0000-0001-5208-3432 peter 2008-04-07T10:21:00Z UMLS:C4025784 human_phenotype HP:0001437 Abnormality of the musculature of the lower limbs A structural abnormality of the abdomen ('belly'), that is, the part of the body between the pelvis and the thorax. UMLS:C4020869 Abnormality of abdomen morphology Abnormality of abdomen structure Abnormality of the abdomen human_phenotype Abdomen abnormality HP:0001438 Abnormal abdomen morphology A structural abnormality of the abdomen ('belly'), that is, the part of the body between the pelvis and the thorax. HPO:probinson Abnormality of abdomen structure Abdomen abnormality peter 2008-04-07T10:27:00Z UMLS:C4025783 Abnormal thigh muscles human_phenotype HP:0001441 Abnormality of the musculature of the thigh Abnormal thigh muscles ORCID:0000-0001-5208-3432 peter 2008-04-07T10:31:00Z UMLS:C4025780 human_phenotype HP:0001445 Abnormality of the hip-girdle musculature peter 2008-04-07T10:40:00Z UMLS:C4025779 Abnormal upper limb muscles human_phenotype HP:0001446 Abnormality of the musculature of the upper limbs Abnormal upper limb muscles ORCID:0000-0001-5208-3432 peter 2008-04-17T02:37:00Z UMLS:C4025778 Duplication of long bones of foot human_phenotype HP:0001449 Duplication of metatarsal bones Duplication of long bones of foot ORCID:0000-0001-5208-3432 peter 2008-04-07T10:41:00Z UMLS:C4025776 human_phenotype HP:0001454 Abnormality of the upper arm peter 2008-04-07T10:42:00Z UMLS:C4025775 human_phenotype HP:0001457 Abnormality of the musculature of the upper arm Absence or underdevelopment of the musculature. peter 2008-04-07T10:46:00Z UMLS:C4025773 Absent/small skeletal muscles Absent/underdeveloped skeletal muscles human_phenotype HP:0001460 Aplasia/Hypoplasia involving the skeletal musculature Absence or underdevelopment of the musculature. HPO:curators Absent/small skeletal muscles ORCID:0000-0001-5208-3432 Absent/underdeveloped skeletal muscles ORCID:0000-0001-5208-3432 Absence or underdevelopment of the muscles of the shoulder. peter 2008-04-07T10:49:00Z UMLS:C4025772 Absent/small shoulder muscles Absent/underdeveloped shoulder muscles human_phenotype HP:0001464 Aplasia/Hypoplasia involving the shoulder musculature Absence or underdevelopment of the muscles of the shoulder. HPO:curators Absent/small shoulder muscles ORCID:0000-0001-5208-3432 Absent/underdeveloped shoulder muscles ORCID:0000-0001-5208-3432 Absence or underdevelopment of the musculature of the upper limbs. peter 2008-04-07T10:51:00Z UMLS:C4025770 Absent/small upper limb muscles Absent/underdeveloped upper limb muscles human_phenotype HP:0001467 Aplasia/Hypoplasia involving the musculature of the upper limbs Absence or underdevelopment of the musculature of the upper limbs. HPO:curators Absent/small upper limb muscles ORCID:0000-0001-5208-3432 Absent/underdeveloped upper limb muscles ORCID:0000-0001-5208-3432 Absence or underdevelopment of the muscles of the upper arm. peter 2008-04-07T10:52:00Z UMLS:C4025769 Absent/small upper arm muscles Absent/underdeveloped upper arm muscles human_phenotype HP:0001468 Aplasia/Hypoplasia involving the musculature of the upper arm Absence or underdevelopment of the muscles of the upper arm. HPO:curators Absent/small upper arm muscles ORCID:0000-0001-5208-3432 Absent/underdeveloped upper arm muscles ORCID:0000-0001-5208-3432 peter 2008-04-07T10:55:00Z UMLS:C4025768 Abnormality of the musculature of the pelvis human_phenotype HP:0001469 Abnormal morphology of the pelvis musculature peter 2008-04-07T10:56:00Z UMLS:C4025766 Absent/small pelvis muscles Absent/underdeveloped pelvis muscles human_phenotype HP:0001471 Aplasia/Hypoplasia of the musculature of the pelvis Absent/small pelvis muscles ORCID:0000-0001-5208-3432 Absent/underdeveloped pelvis muscles ORCID:0000-0001-5208-3432 Increased density of the bony tissue of the scapula. UMLS:C1849263 human_phenotype HP:0001474 Sclerotic scapulae Increased density of the bony tissue of the scapula. HPO:probinson Underdevelopment of one or more carpal bones. HP:0001209 HP:0006029 HP:0006072 HP:0006117 HP:0006130 HP:0006227 Small wrist bones UMLS:C1863749 UMLS:C4280594 Hypoplasia of carpal bones Hypoplastic carpal bones Small carpal bones Small carpals human_phenotype HP:0001498 Carpal bone hypoplasia Underdevelopment of one or more carpal bones. HPO:probinson Small wrist bones ORCID:0000-0001-5208-3432 Small carpal bones Small carpals HP:0008904 UMLS:C0262361 Abnormal growth Growth abnormality Growth issue human_phenotype HP:0001507 Growth abnormality Abnormal growth Growth abnormality Growth issue Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm. HP:0001535 HP:0008853 HP:0008878 HP:0008916 Undergrowth SNOMEDCT_US:36440009 SNOMEDCT_US:432788009 UMLS:C0231246 UMLS:C2315100 Faltering weight Postnatal failure to thrive Weight faltering human_phenotype Poor weight gain HP:0001508 Although there is no clear consensus on the exact definition of FTT, it is usually diagnoses in a child growing below the 3rd percentile or in a child whose decreased growth has cross two major growth percentiles (for example, from above the 75th percentile to below the 25th percentile). Failure to thrive Failure to thrive (FTT) refers to a child whose physical growth is substantially below the norm. HPO:probinson Undergrowth Faltering weight ORCID:0000-0001-5208-3432 Weight faltering ORCID:0000-0001-5208-3432 Poor weight gain A deficiency or slowing down of growth pre- and postnatally. HP:0001434 HP:0001512 HP:0001514 HP:0001517 HP:0001532 HP:0008847 HP:0008870 HP:0008886 HP:0008893 HP:0008926 SNOMEDCT_US:276617005 SNOMEDCT_US:444896005 SNOMEDCT_US:59576002 UMLS:C0151686 UMLS:C0456070 UMLS:C0878787 UMLS:C1837385 UMLS:C3552463 Delayed growth Growth deficiency Growth delay Growth failure Growth retardation Poor growth Retarded growth human_phenotype Very poor growth HP:0001510 Poor or abnormally slow gains in weight or height in a child. Growth delay A deficiency or slowing down of growth pre- and postnatally. HPO:probinson Delayed growth Growth deficiency Growth delay Growth failure Growth retardation Poor growth Retarded growth Very poor growth HPO:skoehler Accumulation of substantial excess body fat. MSH:D009765 SNOMEDCT_US:414915002 SNOMEDCT_US:414916001 UMLS:C0028754 Having too much body fat Obesity human_phenotype HP:0001513 Obesity Having too much body fat ORCID:0000-0002-6548-5200 Obesity Accumulation of fluid in the peritoneal cavity. MSH:D001201 SNOMEDCT_US:389026000 UMLS:C0003962 Accumulation of fluid in the abdomen human_phenotype HP:0001541 Ascites is commonly associated with liver disease that has resulted in portal hypertension and low serum albumin levels. Ascites Accumulation of fluid in the peritoneal cavity. HPO:probinson Accumulation of fluid in the abdomen A morphological anomaly of the rib cage. UMLS:C4025763 Abnormality of the rib cage HP:0001547 Abnormal rib cage morphology A morphological anomaly of the rib cage. HPO:probinson Abnormality of the rib cage Excessive postnatal growth which may comprise increased weight, increased length, and/or increased head circumference. UMLS:C1849265 UMLS:C1851731 UMLS:C3150281 General overgrowth human_phenotype Generalized overgrowth HP:0001548 Overgrowth Excessive postnatal growth which may comprise increased weight, increased length, and/or increased head circumference. HPO:probinson General overgrowth Generalized overgrowth HPO:skoehler peter 2008-02-20T11:05:00Z UMLS:C4025762 Abnormality of the ileum human_phenotype HP:0001549 Abnormal ileum morphology Increased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD above mean for age. Alternatively, an apparently increased maximum width of the tooth. Hyperplasia of tooth Hypertrophy of tooth Increased size of tooth Large tooth SNOMEDCT_US:71485000 UMLS:C0266036 UMLS:C4280590 UMLS:C4280591 UMLS:C4280592 Increased width of tooth Large teeth human_phenotype Tooth mass excess HP:0001572 The standard reference has means and standard deviations by gender [Moyers et al, 1976]. Although it is easy to measure the width of teeth, and the definition is made with reference to the width of teeth, macrodontia actually means that the overall size of the tooth is increased. Macrodontia Increased size of the teeth, which can be defined as a mesiodistal tooth diameter (width) more than 2 SD above mean for age. Alternatively, an apparently increased maximum width of the tooth. HPO:ibailleulforestier PMID:19125428 Hyperplasia of tooth ORCID:0000-0001-5889-4463 Hypertrophy of tooth ORCID:0000-0001-5889-4463 Increased size of tooth ORCID:0000-0001-5889-4463 Large tooth Increased width of tooth ORCID:0000-0001-5889-4463 Tooth mass excess ORCID:0000-0001-5889-4463 An abnormality of the integument, which consists of the skin and the superficial fascia. UMLS:C4025761 human_phenotype HP:0001574 Abnormality of skin, hair, or nails. Abnormality of the integument An abnormality of the integument, which consists of the skin and the superficial fascia. HPO:probinson An abnormality of the hair. UMLS:C0157733 UMLS:C2677869 Abnormality of the hair Hair abnormality Abnormality of the hair shaft HP:0001595 Abnormal hair morphology An abnormality of the hair. HPO:probinson Abnormality of the hair Hair abnormality Abnormality of the hair shaft ORCID:0000-0001-5889-4463 An abnormality of the larynx. UMLS:C4021777 Laryngeal abnormalities Laryngeal anomalies human_phenotype HP:0001600 Abnormality of the larynx An abnormality of the larynx. HPO:probinson Any abnormality of the cardiovascular system. MSH:D002318 MSH:D018376 SNOMEDCT_US:49601007 UMLS:C0007222 UMLS:C0243050 Abnormality of the cardiovascular system Cardiovascular abnormality human_phenotype Cardiovascular disease HP:0001626 The cardiovascular system consists of the heart, vasculature, and the lymphatic system. Abnormality of the cardiovascular system Any abnormality of the cardiovascular system. HPO:probinson Abnormality of the cardiovascular system Cardiovascular abnormality Cardiovascular disease Any structural anomaly of the heart. HP:3000001 MSH:D006330 SNOMEDCT_US:13213009 UMLS:C0018798 UMLS:C0152021 Abnormality of cardiac morphology Abnormality of the heart Abnormally shaped heart Cardiac abnormality Cardiac anomalies Cardiac anomaly Congenital heart defect Congenital heart defects Heart defect human_phenotype HP:0001627 Abnormal heart morphology Any structural anomaly of the heart. HPO:probinson Abnormality of the heart Abnormally shaped heart ORCID:0000-0001-5208-3432 Heart defect A hole between the two bottom chambers (ventricles) of the heart. The defect is centered around the most superior aspect of the ventricular septum. HP:0001652 Fyler:1300 MSH:D006345 SNOMEDCT_US:253549006 SNOMEDCT_US:30288003 UMLS:C0018818 Hole in heart wall separating two lower heart chambers VSD Ventricular septal defects Ventriculoseptal defect HP:0001629 Ventricular septal defect A hole between the two bottom chambers (ventricles) of the heart. The defect is centered around the most superior aspect of the ventricular septum. HPO:curators Hole in heart wall separating two lower heart chambers https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 VSD Atrial septal defect (ASD) is a congenital abnormality of the interatrial septum that enables blood flow between the left and right atria via the interatrial septum. HP:0001630 Fyler:2050 ICD-10:Q21.1 MSH:D006344 SNOMEDCT_US:253366007 SNOMEDCT_US:405752007 SNOMEDCT_US:70142008 UMLS:C0018817 ASD An opening in the wall separating the top two chambers of the heart Atria septal defect Atrial septum defect Defect in the atrial septum Hole in heart wall separating two upper heart chambers human_phenotype HP:0001631 Atrial septal defect Atrial septal defect (ASD) is a congenital abnormality of the interatrial septum that enables blood flow between the left and right atria via the interatrial septum. DDD:dbrown HPO:probinson ASD HPO:skoehler An opening in the wall separating the top two chambers of the heart orcid.org/0000-0002-6548-5200 Hole in heart wall separating two upper heart chambers https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 A structural anomaly of the muscle layer of the heart wall. UMLS:C4025758 Abnormality of the myocardium human_phenotype HP:0001637 Abnormal myocardium morphology Increased size of the heart. MSH:D006332 SNOMEDCT_US:8186001 UMLS:C0018800 Enlarged heart Increased heart size human_phenotype HP:0001640 Cardiomegaly Increased size of the heart. HPO:probinson Enlarged heart Increased heart size ORCID:0000-0001-5208-3432 In this case the right ventricle is more muscular than normal, causing a characteristic boot-shaped (coeur-en-sabot) appearance as seen on anterior- posterior chest x-rays. Right ventricular hypertrophy is commonly associated with any form of right ventricular outflow obstruction or pulmonary hypertension, which may in turn owe its origin to left-sided disease. The echocardiographic signs are thickening of the anterior right ventricular wall and the septum. Cavity size is usually normal, or slightly enlarged. In many cases there is associated volume overload present due to tricuspid regurgitation, in the absence of this, septal motion is normal. Fyler:3609 MSH:D017380 SNOMEDCT_US:89792004 UMLS:C0162770 Heart right ventricle hypertrophy human_phenotype HP:0001667 Right ventricular hypertrophy In this case the right ventricle is more muscular than normal, causing a characteristic boot-shaped (coeur-en-sabot) appearance as seen on anterior- posterior chest x-rays. Right ventricular hypertrophy is commonly associated with any form of right ventricular outflow obstruction or pulmonary hypertension, which may in turn owe its origin to left-sided disease. The echocardiographic signs are thickening of the anterior right ventricular wall and the septum. Cavity size is usually normal, or slightly enlarged. In many cases there is associated volume overload present due to tricuspid regurgitation, in the absence of this, septal motion is normal. HPO:probinson Heart right ventricle hypertrophy ORCID:0000-0001-5208-3432 An anomaly of the intra-atrial or intraventricular septum. HP:0001690 HP:0004760 MSH:D006343 SNOMEDCT_US:253273004 SNOMEDCT_US:396351009 SNOMEDCT_US:59494005 UMLS:C0018816 Abnormality of the cardiac septa Heart septal defect Septal defects human_phenotype HP:0001671 Abnormal cardiac septum morphology An anomaly of the intra-atrial or intraventricular septum. HPO:probinson Septal defects An abnormality of the aorta. HP:0030963 Fyler:1453 UMLS:C4025756 Abnormal aorta morphology Abnormality of the aorta human_phenotype HP:0001679 Abnormal aortic morphology An abnormality of the aorta. HPO:probinson PMID:24910511 Abnormal aorta morphology ORCID:0000-0001-5208-3432 An abnormality of the pericardium, i.e., of the fluid filled sac that surrounds the heart and the proximal ends of the aorta, vena cava, and the pulmonary artery. Fyler:1900 UMLS:C4025754 Abnormality of the pericardium human_phenotype HP:0001697 Abnormal pericardium morphology An abnormality of the pericardium, i.e., of the fluid filled sac that surrounds the heart and the proximal ends of the aorta, vena cava, and the pulmonary artery. HPO:probinson Inflammation of the sac-like covering around the heart (pericardium). MSH:D010493 SNOMEDCT_US:3238004 UMLS:C0031046 Swelling or irritation of membrane around heart human_phenotype HP:0001701 Pericarditis Inflammation of the sac-like covering around the heart (pericardium). HPO:probinson Swelling or irritation of membrane around heart ORCID:0000-0002-6548-5200 An abnormality of the right ventricle of the heart. Fyler:1820 SNOMEDCT_US:253516002 UMLS:C0344887 Abnormality of the right ventricle Right ventricular abnormality human_phenotype HP:0001707 The function of the right ventricle is to receive blood from the right atrium and to eject blood into the pulmonary artery. Abnormal right ventricle morphology An abnormality of the right ventricle of the heart. HPO:probinson Any structural abnormality of the left ventricle of the heart. Fyler:1810 SNOMEDCT_US:253535002 UMLS:C0344905 Abnormal heart left ventricle morphology Abnormality of the left ventricle Left ventricular abnormality human_phenotype HP:0001711 Abnormal left ventricle morphology Any structural abnormality of the left ventricle of the heart. HPO:probinson Abnormal heart left ventricle morphology ORCID:0000-0001-5208-3432 Enlargement or increased size of the heart left ventricle. HP:0005171 Fyler:3608 MSH:D017379 SNOMEDCT_US:55827005 UMLS:C0149721 Heart left ventricle hypertrophy Left ventricular wall hypertrophy human_phenotype HP:0001712 Left ventricular hypertrophy Enlargement or increased size of the heart left ventricle. MP:0002625 Heart left ventricle hypertrophy ORCID:0000-0001-5208-3432 An abnormality of a cardiac ventricle. UMLS:C4025752 Abnormality of cardiac ventricle human_phenotype HP:0001713 Abnormal cardiac ventricle morphology An abnormality of a cardiac ventricle. HPO:probinson Enlargement of the cardiac ventricular muscle tissue with increase in the width of the wall of the ventricle and loss of elasticity. Ventricular hypertrophy is clinically differentiated into left and right ventricular hypertrophy. HP:0005167 SNOMEDCT_US:266249003 UMLS:C0340279 human_phenotype HP:0001714 Ventricular hypertrophy Enlargement of the cardiac ventricular muscle tissue with increase in the width of the wall of the ventricle and loss of elasticity. Ventricular hypertrophy is clinically differentiated into left and right ventricular hypertrophy. HPO:probinson An abnormality of the pancreas. MSH:D010182 SNOMEDCT_US:3855007 UMLS:C0030286 UMLS:C4025751 Abnormality of the pancreas human_phenotype Pancreatic disease HP:0001732 Abnormality of the pancreas An abnormality of the pancreas. HPO:probinson Abnormality of the pancreas Pancreatic disease The presence of inflammation in the pancreas. MSH:D010195 SNOMEDCT_US:75694006 UMLS:C0030305 Pancreatic inflammation human_phenotype HP:0001733 Pancreatitis The presence of inflammation in the pancreas. HPO:probinson Pancreatic inflammation ORCID:0000-0001-5208-3432 A cyst of the pancreas that possess a lining of mucous epithelium. MSH:D010181 SNOMEDCT_US:31258000 UMLS:C0030283 UMLS:C1860394 Pancreatic cysts human_phenotype Multiple pancreatic cysts Pancreatic cyst HP:0001737 Pancreatic cysts are to be distinguished from pancreatic pseudocysts that do not possess a lining of mucous epithelium. Pancreatic cysts A cyst of the pancreas that possess a lining of mucous epithelium. HPO:probinson Pancreatic cysts Multiple pancreatic cysts Pancreatic cyst A structural anomaly of the nasopharynx. UMLS:C4025750 Abnormality of the nasopharynx HP:0001739 The nasopharynx (nasal part of the pharynx) lies behind the nose and above the level of the soft palate. Abnormal nasopharynx morphology An abnormality of the spleen. UMLS:C4025749 Abnormality of the spleen human_phenotype HP:0001743 The spleen is an abdominal organ that functions as a member of the hematopoietic system and of the immune system. Abnormality of the spleen An abnormality of the spleen. HPO:probinson Abnormality of the spleen Abnormal increased size of the spleen. HP:0001745 HP:0006269 MSH:D013163 SNOMEDCT_US:16294009 UMLS:C0038002 Increased spleen size human_phenotype HP:0001744 Splenomegaly Abnormal increased size of the spleen. HPO:probinson Increased spleen size ORCID:0000-0001-5208-3432 Absence (aplasia) of the spleen. Fyler:4771 SNOMEDCT_US:702624008 SNOMEDCT_US:707147002 SNOMEDCT_US:93030006 UMLS:C0600031 Absent spleen human_phenotype HP:0001746 Asplenia Absence (aplasia) of the spleen. HPO:curators Absent spleen ORCID:0000-0001-5208-3432 An abnormality of the skeleton of foot. HP:0010216 HP:0010611 MSH:D005530 SNOMEDCT_US:229844004 UMLS:C0016506 Abnormal feet structure Abnormality of the feet Abnormality of the foot Foot deformities Foot deformity HP:0001760 A disorder of the foot that can either be congenital or acquired. Such deformities can include hammer toe, club foot deformity, flat feet, pes cavus, congenital vertical talus (rocker bottom foot), and many others. Abnormal foot morphology An abnormality of the skeleton of foot. HPO:probinson Abnormal feet structure Abnormality of the feet Abnormality of the foot Foot deformities Foot deformity A measured foot length that is more than 2 SD below the mean for a newborn of 27 - 41 weeks gestation, or foot that is less than the 3rd centile for individuals from birth to 16 years of age (objective). Alternatively, a foot that appears disproportionately short (subjective). HP:0001764 HP:0001766 HP:0001778 HP:0008135 UMLS:C1848673 Hypoplastic feet Short feet Short foot Small feet human_phenotype HP:0001773 Short foot A measured foot length that is more than 2 SD below the mean for a newborn of 27 - 41 weeks gestation, or foot that is less than the 3rd centile for individuals from birth to 16 years of age (objective). Alternatively, a foot that appears disproportionately short (subjective). HPO:probinson PMID:19125433 Short feet Short foot Small feet An anomaly of a toe. UMLS:C2674738 Abnormalities of the toes Abnormality of toe human_phenotype HP:0001780 Abnormality of toe An anomaly of a toe. HPO:probinson Abnormalities of the toes Abnormality of toe Accumulation of fluid in the peritoneal cavity during the fetal period. SNOMEDCT_US:363125002 UMLS:C1285291 Foetal ascites human_phenotype HP:0001791 Fetal ascites Accumulation of fluid in the peritoneal cavity during the fetal period. HPO:probinson Foetal ascites Lateral deviation of the great toe (i.e., in the direction of the little toe). HP:0004682 MSH:D000071378 MSH:D006215 SNOMEDCT_US:122480009 SNOMEDCT_US:415692008 UMLS:C0006386 UMLS:C0018536 Bunion Lateral deviation of great toe Lateral deviation of halluces human_phenotype HP:0001822 Hallux valgus Lateral deviation of the great toe (i.e., in the direction of the little toe). HPO:curators Bunion ORCID:0000-0001-5208-3432 Reduction inexisting body weight. MSH:D015431 SNOMEDCT_US:161832001 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C1262477 human_phenotype HP:0001824 Weight loss Reduction inexisting body weight. HPO:probinson A kind of polydactyly characterized by the presence of a supernumerary toe or toes. HP:0009135 SNOMEDCT_US:62218008 UMLS:C0158734 Duplication of bones of the toes Polydactyly of feet Polydactyly of the foot human_phenotype HP:0001829 Foot polydactyly A kind of polydactyly characterized by the presence of a supernumerary toe or toes. HPO:probinson Duplication of bones of the toes Polydactyly of the foot most commonly refers to the presence of six toes on one foot. Postaxial polydactyly affects the lateral ray and the duplication may range from a well-formed articulated digit to a rudimentary digit. HP:0010346 UMLS:C2112129 UMLS:C4020865 Extra toe attached near the little toe Polydactyly affecting the 5th toe Postaxial polydactyly of feet Postaxial polydactyly of foot Posterior polydactyly of foot human_phenotype Fibular polydactyly HP:0001830 The modifier postaxial means that the supernumerary digit is not a hallux. Postaxial foot polydactyly Polydactyly of the foot most commonly refers to the presence of six toes on one foot. Postaxial polydactyly affects the lateral ray and the duplication may range from a well-formed articulated digit to a rudimentary digit. HPO:curators Extra toe attached near the little toe orcid.org/0000-0002-6548-5200 A toe that appears disproportionately short compared to the foot. HP:0001767 HP:0001781 HP:0001855 HP:0004701 HP:0005889 HP:0008099 UMLS:C1836195 Brachydactyly of the foot Hypoplasia of the toe Hypoplastic toes Short foot phalanges Short toe Short toes Stubby toes human_phenotype HP:0001831 This finding must be distinguished from digits that are of increased girth but of normal length and that of a long mid- and hind foot with normal digit lengths. The affected digits should be specified as described in the introductory comments. Note that we designate brachydactyly as a synonym, but this use of the term is distinct from the use of the same word in Bell's classification of brachdactyly. Short toe A toe that appears disproportionately short compared to the foot. HPO:probinson Short toe Short toes Stubby toes ORCID:0000-0001-5208-3432 Abnormalities of the metatarsal bones (i.e. of five tubular bones located between the tarsal bones of the hind- and mid-foot and the phalanges of the toes). UMLS:C4025745 Abnormality of the long bone of foot human_phenotype HP:0001832 Abnormal metatarsal morphology Abnormalities of the metatarsal bones (i.e. of five tubular bones located between the tarsal bones of the hind- and mid-foot and the phalanges of the toes). HPO:probinson Abnormality of the long bone of foot ORCID:0000-0001-5208-3432 Increased back to front length of the foot. HP:0008136 HP:0008143 SNOMEDCT_US:299462005 UMLS:C0576225 Disproportionately large feet Long foot large feet long feet human_phenotype HP:0001833 Long foot Increased back to front length of the foot. UHPO:probinson Disproportionately large feet Long foot large feet long feet Camptodactyly is a painless flexion contracture of the proximal interphalangeal (PIP) joint that is usually gradually progressive. This term refers to camptodactyly of one or more toes. UMLS:C4021774 Camptodactyly of feet human_phenotype HP:0001836 Camptodactyly of toe Camptodactyly is a painless flexion contracture of the proximal interphalangeal (PIP) joint that is usually gradually progressive. This term refers to camptodactyly of one or more toes. HPO:probinson Duplication of all or part of the first ray. HP:0009607 HP:0010050 MSH:C566632 UMLS:C1866339 UMLS:C2112942 Partial/complete duplication of the phalanges of the big toe Polydactyly affecting the hallux Preaxial hallucal polydactyly Preaxial polydactyly of feet Preaxial polydactyly of foot Preaxial polydactyly of the feet Preaxial polydactyly, feet human_phenotype HP:0001841 This term applies for a wide variety of partial and/or complete duplications of the phalanges of the big toe (sometimes including the 1st metatarsal). A partial duplication can present itself on x-rays as a notched phalanx, bifid phalanx or a broadened phalanx. Polydactyly affecting the big toe is called preaxial or hallucal polydactyly of the feet. Preaxial foot polydactyly Duplication of all or part of the first ray. HPO:probinson PMID:19125433 Partial/complete duplication of the phalanges of the big toe HPO:curators Preaxial polydactyly of the feet HPO:curators This term applies for all abnormalities of the big toe, also called hallux. UMLS:C4021773 Abnormalities of the hallux Abnormality of the big toe human_phenotype HP:0001844 Abnormality of the hallux This term applies for all abnormalities of the big toe, also called hallux. HPO:probinson Abnormality of the big toe ORCID:0000-0001-5208-3432 Increased length of the big toe. HP:0001867 UMLS:C1864375 Increased length of the hallux Large halluces Long big toe Long halluces human_phenotype HP:0001847 Long hallux Increased length of the big toe. HPO:probinson Long big toe ORCID:0000-0001-5208-3432 A developmental defect resulting in the presence of fewer than the normal number of toes. HP:0001777 SNOMEDCT_US:249820005 UMLS:C0426934 Missing toes Oligodactyly of feet human_phenotype HP:0001849 Foot oligodactyly A developmental defect resulting in the presence of fewer than the normal number of toes. HPO:probinson Missing toes An abnormality of the tarsus are the cluster of seven bones in the foot between the tibia and fibula and the metatarsus, including the calcaneus (heel) bone and the talus (ankle) bone. UMLS:C1862136 Abnormal ankle bones Abnormal tarsals human_phenotype HP:0001850 Abnormality of the tarsal bones An abnormality of the tarsus are the cluster of seven bones in the foot between the tibia and fibula and the metatarsus, including the calcaneus (heel) bone and the talus (ankle) bone. HPO:curators Abnormal ankle bones ORCID:0000-0001-5208-3432 HP:0005615 UMLS:C4021772 Bifid distal phalanges of toes Bifid terminal phalanx of toe Notched outermost bones of toes human_phenotype HP:0001853 Bifid distal phalanx of toe Notched outermost bones of toes ORCID:0000-0001-6908-9849 Short distance from the end of the toe to the most distal interphalangeal crease or distal interphalangeal joint flexion point, i.e., abnormally short distal phalanx of toe. UMLS:C4021771 Hypoplastic distal phalanges of feet Short outermost bone of toe human_phenotype HP:0001857 This term differs from Partial absence of the toe because in that term the phalanx must be missing, whereas here it may be small, but present. Relative shortening of the distal phalanges of the toes can be harder to assess than in the fingers, as they are normally quite short. Distal phalangeal lengths can be assessed subjectively by comparing that digit segment to the rest of the digit, to other normal digits in that patient, or to typical patients of that age or build. Short distal phalanx of toe Short distance from the end of the toe to the most distal interphalangeal crease or distal interphalangeal joint flexion point, i.e., abnormally short distal phalanx of toe. PMID:19125433 Short outermost bone of toe ORCID:0000-0001-5208-3432 An abnormality of the hematopoietic system. HP:0003135 MSH:D006402 SNOMEDCT_US:191124002 SNOMEDCT_US:34093004 UMLS:C0018939 UMLS:C0850715 UMLS:C4020864 Abnormality of blood and blood-forming tissues Abnormality of the hematopoietic system Hematological abnormality human_phenotype Abnormality of the haematopoietic system Hematologic disease HP:0001871 The hematopoietic system comprises the organs that are involved in the production of blood, primarily the bone marrow, spleen, tonsils, and lymph nodes. Abnormality of blood and blood-forming tissues An abnormality of the hematopoietic system. HPO:probinson Abnormality of blood and blood-forming tissues An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects. HP:0004830 HP:0004834 HP:0004849 HP:0004862 HP:0004865 HP:0008183 SNOMEDCT_US:248250000 SNOMEDCT_US:64779008 UMLS:C1458140 Bleeding diathesis Bleeding tendency Hemorrhagic diathesis human_phenotype HP:0001892 This term is kept for historical reasons. If possible, a more exact description of the phenotype (i.e., whether there is a vascular, platelet and coagulation defect) should be attempted. Abnormal bleeding An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects. HPO:probinson Bleeding tendency The formation of a blood clot inside a blood vessel that subsequently travels through the blood stream from the site where it formed to another location in the body, generally leading to vascular occlusion at the distant site. MSH:D013923 MSH:D016769 SNOMEDCT_US:13713005 SNOMEDCT_US:371039008 UMLS:C0040038 UMLS:C0085307 Blood clot in blood vessel Thromboembolic disease Thromboembolic events human_phenotype Embolism and thrombosis HP:0001907 Thromboembolism The formation of a blood clot inside a blood vessel that subsequently travels through the blood stream from the site where it formed to another location in the body, generally leading to vascular occlusion at the distant site. HPO:probinson Blood clot in blood vessel ORCID:0000-0002-6548-5200 HP:0002146 HP:0004355 HP:0004367 UMLS:C4021768 Laboratory abnormality Metabolism abnormality human_phenotype HP:0001939 Abnormality of metabolism/homeostasis Laboratory abnormality Metabolism abnormality Abnormal acid accumulation or depletion of base. HP:0001940 MSH:D000138 SNOMEDCT_US:51387008 UMLS:C0001122 human_phenotype HP:0001941 When describing acid-base abnormalities, acidosis and alkalosis refer to physiological processes that lower or raise the pH, respectively, while acidemia and alkalemia simply describe the state of an abnormal blood pH. This distinction is important: a patient with acidemia could have both a respiratory and metabolic acidosis as well as a concurrent metabolic alkalosis. Acidosis Abnormal acid accumulation or depletion of base. HPO:probinson PMID:24381489 A decreased concentration of glucose in the blood. HP:0003356 MSH:D007003 SNOMEDCT_US:237630007 SNOMEDCT_US:271327008 SNOMEDCT_US:302866003 UMLS:C0020615 Hypoglycaemia Low blood sugar human_phenotype HP:0001943 Hypoglycemia A decreased concentration of glucose in the blood. HPO:curators Low blood sugar ORCID:0000-0001-5208-3432 MSH:D003681 SNOMEDCT_US:34095006 UMLS:C0011175 Dehydration Exsiccosis HP:0001944 Dehydration Dehydration Elevated body temperature due to failed thermoregulation. MSH:D005334 SNOMEDCT_US:386661006 SNOMEDCT_US:50177009 UMLS:C0015967 Fever Hyperthermia Pyrexia human_phenotype HP:0001945 Hyperthermia is defined as a temperature greater than 37.5-38.3 degree celsius (100-101 degree Fahrenheit). Fever Elevated body temperature due to failed thermoregulation. HPO:sdoelken Fever Presence of elevated levels of ketone bodies in the body. HP:0003543 MSH:D007662 SNOMEDCT_US:213281004 SNOMEDCT_US:2538008 UMLS:C0022638 UMLS:C0235430 High levels of ketone bodies Hyperketosis human_phenotype HP:0001946 Ketone bodies are formed from acetyl-CoA in the liver by ketogenesis when the liver glycogen stores are depleted. Ketone bodies are acidic, and ketoacidosis ensues if the compensatory mechanisms are overloaded. The predominant ketones being acetoacetate, acetone, and beta-hydroxybutyrate. Ketosis Presence of elevated levels of ketone bodies in the body. HPO:probinson PMID:28278308 High levels of ketone bodies ORCID:0000-0001-5208-3432 Depletion of acid or accumulation base in the body fluids. MSH:D000471 SNOMEDCT_US:21420006 UMLS:C0002063 human_phenotype HP:0001948 When describing acid-base abnormalities, acidosis and alkalosis refer to physiological processes that lower or raise the pH, respectively, while acidemia and alkalemia simply describe the state of an abnormal blood pH. This distinction is important: a patient with acidemia could have both a respiratory and metabolic acidosis as well as a concurrent metabolic alkalosis. Alkalosis Depletion of acid or accumulation base in the body fluids. HPO:probinson PMID:24381489 Glucose intolerance (GI) can be defined as dysglycemia that comprises both prediabetes and diabetes. It includes the conditions of impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) and diabetes mellitus (DM). HP:0000833 Abnormal glucose tolerance UMLS:C0235401 Glucose intolerance human_phenotype HP:0001952 Glucose intolerance Glucose intolerance (GI) can be defined as dysglycemia that comprises both prediabetes and diabetes. It includes the conditions of impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) and diabetes mellitus (DM). PMID:29763085 Glucose intolerance Obesity located preferentially in the trunk of the body as opposed to the extremities. HP:0008885 MSH:D056128 SNOMEDCT_US:248311001 UMLS:C0311277 Centripetal obesity Truncal obesity human_phenotype HP:0001956 Truncal obesity Obesity located preferentially in the trunk of the body as opposed to the extremities. HPO:probinson Truncal obesity UMLS:C3151525 Small heart Underdeveloped heart human_phenotype HP:0001961 Hypoplastic heart Small heart ORCID:0000-0001-5208-3432 Underdeveloped heart ORCID:0000-0001-5208-3432 Absence or underdevelopment of the metatarsal bones. UMLS:C1860182 Absent or hypoplastic metatarsal Absent/hypoplastic metacarpals Absent/hypoplastic metatarsals Absent/small long bone of foot Absent/underdeveloped long bone of foot Aplastic/hypoplastic metatarsals human_phenotype HP:0001964 Aplasia/Hypoplasia of metatarsal bones Absence or underdevelopment of the metatarsal bones. HPO:curators Absent/small long bone of foot ORCID:0000-0001-5208-3432 Absent/underdeveloped long bone of foot ORCID:0000-0001-5208-3432 Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). UMLS:C4025731 Abnormal blood clot Abnormal blood clotting human_phenotype HP:0001977 Abnormal thrombosis Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). HPO:probinson Abnormal blood clot ORCID:0000-0001-6908-9849 An increased concentration of ammonia in the blood. HP:0008308 HP:0008334 MSH:D022124 SNOMEDCT_US:9360008 UMLS:C0220994 High blood ammonia levels human_phenotype HP:0001987 Hyperammonemia An increased concentration of ammonia in the blood. HPO:gcarletti High blood ammonia levels ORCID:0000-0001-5208-3432 Absence or hypoplasia of toes. UMLS:C3551148 Absent/small toe Absent/underdeveloped toe Aplastic/hypoplastic toe phalanges human_phenotype Absent/hypoplastic toes HP:0001991 Aplasia/Hypoplasia of toe Absence or hypoplasia of toes. HPO:probinson Absent/small toe ORCID:0000-0001-5208-3432 Absent/underdeveloped toe ORCID:0000-0001-5208-3432 Absent/hypoplastic toes HPO:skoehler Excretion of non-amino organic acids in urine. UMLS:C0241775 HP:0001992 Organic aciduria Excretion of non-amino organic acids in urine. HPO:probinson An abnormal morphology (form) of the face or its components. HP:0002004 HP:0002260 HP:0004643 HP:0004649 HP:0004652 HP:0004655 HP:0004675 HP:0005124 Deformity of face Malformation of face SNOMEDCT_US:248200007 SNOMEDCT_US:32003007 SNOMEDCT_US:398206004 SNOMEDCT_US:398302004 UMLS:C0266617 UMLS:C0424503 UMLS:C1385263 UMLS:C4072832 UMLS:C4072833 Abnormal facial shape Abnormal morphology of the face Distinctive facies Dysmorphic facial features Dysmorphic facies Facial dysmorphism Unusual facial appearance Unusual facies human_phenotype Distortion of face Funny looking face HP:0001999 This term now covers many of the historical inexact descriptions such as Bird-like facies that probably should be avoided in modern genetics. This portion of the Ontology should be revised. Abnormal facial shape An abnormal morphology (form) of the face or its components. DDD:jclayton-smith Deformity of face ORCID:0000-0001-5889-4463 Malformation of face ORCID:0000-0001-5889-4463 Abnormal facial shape Abnormal morphology of the face ORCID:0000-0001-5889-4463 Dysmorphic facies ORCID:0000-0001-5889-4463 Facial dysmorphism ORCID:0000-0001-5889-4463 Unusual facial appearance ORCID:0000-0001-5889-4463 Distortion of face ORCID:0000-0001-5889-4463 Funny looking face ORCID:0000-0001-5889-4463 A structural abnormality of the central nervous system. HP:0002405 HP:0002413 HP:0002481 HP:0007319 MSH:D002493 SNOMEDCT_US:23853001 UMLS:C0007682 UMLS:C4021765 Abnormality of the central nervous system Morphological abnormality of the CNS Morphological abnormality of the central nervous system Central nervous system disease HP:0002011 Morphological central nervous system abnormality A structural abnormality of the central nervous system. HPO:probinson Morphological abnormality of the CNS An abnormality of the viscera of the abdomen. UMLS:C4021764 Abnormality of the abdominal organs Gastrointestinal tract defects human_phenotype HP:0002012 The abdominal organs comprise the stomach, small and large intestines, liver, pancreas, bile tract, and spleen. Abnormality of the abdominal organs An abnormality of the viscera of the abdomen. HPO:probinson Abnormality of the abdominal organs Abnormally increased frequency of loose or watery bowel movements. MSH:D003967 SNOMEDCT_US:267060006 SNOMEDCT_US:62315008 UMLS:C0011991 Diarrhea Diarrhoea Watery stool human_phenotype HP:0002014 Diarrhea Abnormally increased frequency of loose or watery bowel movements. HPO:probinson Diarrhea Diarrhoea Watery stool Impaired ability to absorb one or more nutrients from the intestine. HP:0008270 UMLS:C3714745 Intestinal malabsorption Malabsorption human_phenotype HP:0002024 Malabsorption Impaired ability to absorb one or more nutrients from the intestine. HPO:probinson Intestinal malabsorption Malabsorption A structural abnormality of the esophagus. SNOMEDCT_US:69771008 UMLS:C0266126 Abnormal oesophagus morphology Abnormality of esophagus structure Anomaly of the esophagus HP:0002031 Abnormal esophagus morphology A structural abnormality of the esophagus. HPO:probinson Abnormal oesophagus morphology Abnormality of esophagus structure An abnormaltiy of the rectum, the final segment of the large intestine that stores solid waste until it passes through the anus. SNOMEDCT_US:86993003 UMLS:C0266210 Abnormality of the rectum Anomaly of the rectum HP:0002034 Abnormal rectum morphology An abnormaltiy of the rectum, the final segment of the large intestine that stores solid waste until it passes through the anus. HPO:probinson Abnormality of the rectum Anomaly of the rectum Inflammation, or an inflammatory state in the large intestine. MSH:D015212 SNOMEDCT_US:24526004 SNOMEDCT_US:302168000 UMLS:C0021390 UMLS:C0578878 Inflammation of the large intestine human_phenotype Inflammatory bowel disease HP:0002037 Inflammation of the large intestine Inflammation of the large intestine Inflammatory bowel disease Any structural abnormality of the telencephalon, which is also known as the cerebrum. UMLS:C4021762 Abnormality of the cerebrum Abnormality of the telencephalon human_phenotype HP:0002060 Abnormal cerebral morphology Any structural abnormality of the telencephalon, which is also known as the cerebrum. HPO:probinson An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. UMLS:C4018871 Respiratory abnormality human_phenotype HP:0002086 Abnormality of the respiratory system An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. HPO:probinson An abnormality of the upper respiratory tract. UMLS:C4025727 Abnormality of the upper respiratory tract Upper respiratory tract issues human_phenotype HP:0002087 Abnormality of the upper respiratory tract An abnormality of the upper respiratory tract. HPO:probinson Abnormality of the upper respiratory tract Upper respiratory tract issues Any structural anomaly of the lung. MSH:D008171 SNOMEDCT_US:19829001 UMLS:C0024115 UMLS:C4021760 Abnormality of lung structure Abnormality of the lungs Abnormally shaped lung Unusal lung shape Lung disease HP:0002088 Abnormal lung morphology Any structural anomaly of the lung. HPO:probinson Abnormality of lung structure Abnormality of the lungs Abnormally shaped lung Unusal lung shape Lung disease SNOMEDCT_US:80825009 UMLS:C0265783 Hypoplastic lung Hypoplastic lungs Lung hypoplasia Small lung Underdeveloped lung human_phenotype HP:0002089 Pulmonary hypoplasia Small lung ORCID:0000-0001-5208-3432 Underdeveloped lung ORCID:0000-0001-5208-3432 Inflammation of any part of the lung parenchyma. MSH:D011014 SNOMEDCT_US:233604007 UMLS:C0032285 Pneumonia human_phenotype HP:0002090 Pneumonia Inflammation of any part of the lung parenchyma. HPO:probinson Pneumonia Pulmonary hypertension is defined mean pulmonary artery pressure of 25mmHg or more and pulmonary capillary wedge pressure of 15mmHg or less when measured by right heart catheterisation at rest and in a supine position. HP:0006546 MSH:D006976 MSH:D065627 SNOMEDCT_US:11399002 SNOMEDCT_US:697898008 SNOMEDCT_US:70995007 UMLS:C0020542 UMLS:C2973725 UMLS:C3203102 Increased blood pressure in blood vessels of lungs Pulmonary artery hypertension Primary pulmonary hypertension HP:0002092 Pulmonary hypertension can be secondary to known cardiac, pulmonary, or hepatic disease. If no cause is identifiable, the term primary pulmonary hypertension is used. Pulmonary arterial hypertension Pulmonary hypertension is defined mean pulmonary artery pressure of 25mmHg or more and pulmonary capillary wedge pressure of 15mmHg or less when measured by right heart catheterisation at rest and in a supine position. HPO:probinson Increased blood pressure in blood vessels of lungs orcid.org/0000-0002-6548-5200 Primary pulmonary hypertension HPO:skoehler HP:0006534 MSH:D011656 SNOMEDCT_US:87433001 UMLS:C0034067 Pulmonary emphysema human_phenotype HP:0002097 Emphysema An abnormality of the pulmonary pleura, the thin, transparent membrane which covers the lungs and lines the inside of the chest walls. UMLS:C4025726 Abnormality of the pleura human_phenotype HP:0002103 Abnormal pleura morphology An abnormality of the pulmonary pleura, the thin, transparent membrane which covers the lungs and lines the inside of the chest walls. HPO:probinson Abnormality of the cerebral ventricles. UMLS:C4025724 human_phenotype HP:0002118 Abnormality of the cerebral ventricles Abnormality of the cerebral ventricles. HPO:probinson An increase in size of the ventricular system of the brain. HP:0002447 HP:0005691 HP:0007071 UMLS:C3278923 Cerebral ventricular dilatation Dilated cerebral ventricle Dilated cerebral ventricles Dilated ventricles Enlarged cerebral ventricles Enlarged ventricles Enlarged ventricular system Large cerebral ventricles and cisternae Ventricular dilatation human_phenotype HP:0002119 Ventriculomegaly An increase in size of the ventricular system of the brain. HPO:probinson An abnormality of the spinal cord (myelon). MSH:D013118 SNOMEDCT_US:48522003 UMLS:C0037928 UMLS:C4025722 Abnormality of the spinal cord human_phenotype Spinal cord disease Spinal cord pathology HP:0002143 Abnormality of the spinal cord An abnormality of the spinal cord (myelon). HPO:probinson Abnormality of the spinal cord Spinal cord disease An abnormally decreased phosphate concentration in the blood. MSH:D017674 SNOMEDCT_US:4996001 UMLS:C0085682 Hypophosphataemia Low blood phosphate level human_phenotype HP:0002148 Hypophosphatemia An abnormally decreased phosphate concentration in the blood. HPO:gcarletti Low blood phosphate level ORCID:0000-0001-5208-3432 MSH:D053565 SNOMEDCT_US:71938000 UMLS:C0020438 Elevated urine calcium levels Hypercalcinuria human_phenotype HP:0002150 Hypercalciuria Elevated urine calcium levels ORCID:0000-0001-5208-3432 An abnormally increased potassium concentration in the blood. MSH:D006947 SNOMEDCT_US:14140009 SNOMEDCT_US:166689004 SNOMEDCT_US:238142003 UMLS:C0020461 Elevated serum potassium levels human_phenotype HP:0002153 Hyperkalemia An abnormally increased potassium concentration in the blood. HPO:probinson Elevated serum potassium levels ORCID:0000-0001-5208-3432 An elevated concentration of glycine in the blood. SNOMEDCT_US:64654004 UMLS:C0268559 Elevated blood glycine levels Hyperglycinaemia human_phenotype HP:0002154 Normal blood glycine levels are around 200-250 micromole per liter. Hyperglycinemia An elevated concentration of glycine in the blood. HPO:gcarletti PMID:16902722 PMID:4696900 Elevated blood glycine levels ORCID:0000-0001-5208-3432 An abnormal increase in the level of triglycerides in the blood. HP:0003082 HP:0008174 HP:0008332 UMLS:C1522137 Increased circulating Tg levels Increased plasma Tg levels Increased plasma triglycerides Increased serum triglycerides Increased triglycerides human_phenotype HP:0002155 Hypertriglyceridemia An abnormal increase in the level of triglycerides in the blood. HPO:probinson Increased circulating Tg levels Increased plasma Tg levels Increased plasma triglycerides Increased serum triglycerides Increased triglycerides An increased concentration of nitrogen compounds in the blood. MSH:D053099 SNOMEDCT_US:445009001 UMLS:C0242528 Azotaemia human_phenotype HP:0002157 Abnormal levels of nitrogen-containing compounds, such as urea and creatinine. Azotemia An increased concentration of nitrogen compounds in the blood. HPO:gcarletti An increased concentration of lysine in the blood. MSH:D020167 SNOMEDCT_US:58558003 UMLS:C0268553 Elevated blood lysine human_phenotype HP:0002161 Normal blood lysine levels are around 180-200 micromole per liter. Hyperlysinemia An increased concentration of lysine in the blood. HPO:gcarletti PMID:4696900 Elevated blood lysine ORCID:0000-0001-5208-3432 Hemorrhage occurring within the skull. MSH:D020300 SNOMEDCT_US:1386000 UMLS:C0151699 Bleeding within the skull Intracranial haemorrhage human_phenotype HP:0002170 Intracranial hemorrhage Hemorrhage occurring within the skull. HPO:gcarletti Bleeding within the skull ORCID:0000-0001-5208-3432 Intracranial haemorrhage A cyst occurring within the choroid plexus within a cerebral ventricle. SNOMEDCT_US:230790004 UMLS:C0338597 human_phenotype HP:0002190 Choroid plexus cysts can be observed on prenatal ultrasound examinations and are associated with a weakly increased risk for fetal chromosome abnormalities such as trisomy 18. Choroid plexus cyst A cyst occurring within the choroid plexus within a cerebral ventricle. HPO:probinson An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery. MSH:D011655 SNOMEDCT_US:59282003 UMLS:C0034065 Blood clot in artery of lung human_phenotype HP:0002204 Pulmonary embolism Blood clot in artery of lung ORCID:0000-0002-6548-5200 Excessive, increased hair growth located in the facial region. MSH:C565029 UMLS:C1851400 Increased facial hair growth human_phenotype HP:0002219 Facial hypertrichosis Increased facial hair growth ORCID:0000-0001-5208-3432 Hemorrhage affecting the gastrointestinal tract. MSH:D006471 SNOMEDCT_US:74474003 UMLS:C0017181 GI hemorrhage Gastrointestinal bleeding Gastrointestinal haemorrhage human_phenotype HP:0002239 Gastrointestinal hemorrhage Hemorrhage affecting the gastrointestinal tract. HPO:probinson GI hemorrhage Gastrointestinal bleeding Gastrointestinal haemorrhage Abnormally increased size of the liver. HP:0001393 HP:0001398 MSH:D006529 SNOMEDCT_US:80515008 UMLS:C0019209 Enlarged liver human_phenotype HP:0002240 Hepatomegaly Abnormally increased size of the liver. HPO:probinson Enlarged liver An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine. HP:0002628 MSH:D007410 SNOMEDCT_US:85919009 UMLS:C0021831 Abnormality of the intestine Enteropathy human_phenotype HP:0002242 Abnormal intestine morphology An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine. HPO:probinson Abnormality of the intestine An abnormality of the small intestine. UMLS:C4025717 HP:0002244 Abnormality of the small intestine An abnormality of the small intestine. HPO:probinson Meckel's diverticulum is a congenital diverticulum located in the distal ileum. MEDDRA:10027055 MSH:D008467 SNOMEDCT_US:127962001 SNOMEDCT_US:37373007 UMLS:C0025037 human_phenotype HP:0002245 Meckel diverticulum Meckel's diverticulum is a congenital diverticulum located in the distal ileum. HPO:probinson MEDDRA:10027055 Meckel's diverticulum An abnormality of the duodenum, i.e., the first section of the small intestine. UMLS:C4025716 Abnormality of the duodenum HP:0002246 Abnormal duodenum morphology An abnormality of the duodenum, i.e., the first section of the small intestine. HPO:probinson The passage of blackish, tarry feces associated with gastrointestinal hemorrhage. Melena occurs if the blood remains in the colon long enough for it to be broken down by colonic bacteria. One degradation product, hematin, imbues the stool with a blackish color. Thus, melena generally occurs with bleeding from the upper gastrointestinal tract (e.g., stomach ulcers or duodenal ulcers), since the blood usually remains in the gut for a longer period of time than with lower gastrointestinal bleeding. MSH:D008551 SNOMEDCT_US:249627005 SNOMEDCT_US:267055007 SNOMEDCT_US:269899009 SNOMEDCT_US:2901004 SNOMEDCT_US:35064005 UMLS:C0025222 UMLS:C0474585 Black feces human_phenotype HP:0002249 Melena The passage of blackish, tarry feces associated with gastrointestinal hemorrhage. Melena occurs if the blood remains in the colon long enough for it to be broken down by colonic bacteria. One degradation product, hematin, imbues the stool with a blackish color. Thus, melena generally occurs with bleeding from the upper gastrointestinal tract (e.g., stomach ulcers or duodenal ulcers), since the blood usually remains in the gut for a longer period of time than with lower gastrointestinal bleeding. HPO:probinson Black feces ORCID:0000-0001-6908-9849 Any abnormality of the large intestine. UMLS:C4025715 Abnormality of the large intestine human_phenotype HP:0002250 The large intestine comprises the cecum and colon. Abnormal large intestine morphology Any abnormality of the large intestine. HPO:probinson Abnormality of the large intestine The presence of multiple diverticula of the colon. HP:0005860 MEDDRA:10009993 MSH:D004241 MSH:D043963 SNOMEDCT_US:398050005 UMLS:C0012811 UMLS:C0012819 Colonic diverticulosis human_phenotype Colon diverticula HP:0002253 Colonic diverticula The presence of multiple diverticula of the colon. HPO:probinson MEDDRA:10009993 Colonic diverticulosis MEDDRA:10013533 SNOMEDCT_US:8114009 UMLS:C0267498 human_phenotype HP:0002256 Small bowel diverticula MEDDRA:10013533 Diverticula of small intestine An abnormality of the autonomic nervous system. UMLS:C4025714 human_phenotype HP:0002270 The autonomic nervous system is the part of the peripheral nervous system that controls visceral functions such as heart rate and digestion and functions largely below the level of consciousness. Abnormality of the autonomic nervous system An abnormality of the autonomic nervous system. HPO:probinson HP:0004548 SNOMEDCT_US:297991008 UMLS:C0574763 Absent hair human_phenotype HP:0002298 Absent hair Absent hair An anomaly of the brainstem. UMLS:C1850601 Abnormal shape of brainstem Abnormality of the brainstem human_phenotype HP:0002363 Abnormality of brainstem morphology An anomaly of the brainstem. HPO:probinson Abnormal shape of brainstem ORCID:0000-0001-5208-3432 Underdevelopment of the brainstem. UMLS:C1842688 Brainstem hypoplasia Hypoplastic brain stem Hypoplastic brainstem Small brainstem Underdeveloped brainstem human_phenotype HP:0002365 This finding can be demonstrated by magnetic resonance imaging. Hypoplasia of the brainstem Underdevelopment of the brainstem. HPO:probinson Small brainstem Underdeveloped brainstem ORCID:0000-0001-5208-3432 An abnormality of the midbrain, which has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct. UMLS:C4021755 Abnormal shape of midbrain Abnormality of the mesencephalon Abnormality of the midbrain human_phenotype HP:0002418 Abnormality of midbrain morphology An abnormality of the midbrain, which has as its parts the tectum, cerebral peduncle, midbrain tegmentum and cerebral aqueduct. HPO:probinson Abnormal shape of midbrain ORCID:0000-0001-5208-3432 Abnormality of the midbrain UMLS:C4025708 human_phenotype HP:0002438 Cerebellar malformation Reduced size of the cerebral cortex. HP:0006791 HP:0007151 UMLS:C1837503 Decreased volume of cerebral cortex human_phenotype HP:0002472 Small cerebral cortex Reduced size of the cerebral cortex. HPO:probinson The presence of calcium deposition within brain structures. HP:0002502 HP:0005806 HP:0006848 SNOMEDCT_US:17944005 UMLS:C0270685 Abnormal deposits of calcium in the brain Brain calcification Intracerebral calcifications Intracranial calcification Intracranial calcifications human_phenotype HP:0002514 This finding can be demonstrated upon cerebral computer tomography, magnetic resonance imaging, or potentially by standard radiography of the skull. Cerebral calcification The presence of calcium deposition within brain structures. HPO:probinson Abnormal deposits of calcium in the brain orcid.org/0000-0002-6548-5200 An abnormality of the cerebral cortex. UMLS:C4025701 human_phenotype HP:0002538 Abnormality of the cerebral cortex An abnormality of the cerebral cortex. HPO:probinson The presence of developmental dysplasia of the cerebral cortex. HP:0007139 MSH:D054220 SNOMEDCT_US:253153000 UMLS:C0431380 Neocortical dysplasia human_phenotype HP:0002539 Cortical dysplasia The presence of developmental dysplasia of the cerebral cortex. HPO:probinson Absence of facial hair. UMLS:C1848192 Absent facial hair human_phenotype HP:0002550 Absent facial hair Absence of facial hair. HPO:probinson Absent facial hair Developmental dysplasia of the hair. HP:0004515 UMLS:C4020850 UMLS:C4025700 human_phenotype Generalized trichodysplasia HP:0002552 Trichodysplasia Developmental dysplasia of the hair. HPO:probinson Greater than normal amounts of fat in the feces. This is a result of malabsorption of lipids in the small intestine and results in frothy foul-smelling fecal matter that floats. MSH:D045602 SNOMEDCT_US:27868004 SNOMEDCT_US:66187002 UMLS:C0038238 Fat in feces human_phenotype HP:0002570 Steatorrhea Greater than normal amounts of fat in the feces. This is a result of malabsorption of lipids in the small intestine and results in frothy foul-smelling fecal matter that floats. HPO:probinson Fat in feces ORCID:0000-0002-6548-5200 An abnormality of the stomach. UMLS:C4025699 Abnormality of the stomach HP:0002577 The stomach is the hollow, muscular organ of the gastrointestinal tract between the esophagus and the small intestine. Abnormal stomach morphology An abnormality of the stomach. HPO:probinson Colitis refers to an inflammation of the colon and is often used to describe an inflammation of the large intestine (colon, cecum and rectum). Colitides may be acute and self-limited or chronic, and broadly fit into the category of digestive diseases. MSH:D003092 SNOMEDCT_US:64226004 UMLS:C0009319 HP:0002583 Colitis Colitis refers to an inflammation of the colon and is often used to describe an inflammation of the large intestine (colon, cecum and rectum). Colitides may be acute and self-limited or chronic, and broadly fit into the category of digestive diseases. HPO:sdoelken Bleeding from the intestines. SNOMEDCT_US:712510007 UMLS:C0267373 Intestinal bleeding Intestinal hemorrhage human_phenotype HP:0002584 Intestinal bleeding Bleeding from the intestines. DDD:akelly Intestinal bleeding An abnormality of the peritoneum. UMLS:C4025698 human_phenotype HP:0002585 The peritoneum is the thin tissue that lines the inner wall of the abdomen and covers most of the abdominal organs. Abnormality of the peritoneum An abnormality of the peritoneum. HPO:probinson Inflammation of the peritoneum. HP:0100591 MSH:D010538 SNOMEDCT_US:48661000 UMLS:C0031154 Inflammation of the peritoneum human_phenotype HP:0002586 Peritonitis Inflammation of the peritoneum. HPO:probinson Hypoplasia of the pancreas. HP:0005221 SNOMEDCT_US:68591005 UMLS:C0266267 Hypoplastic pancreas Underdeveloped pancreas human_phenotype HP:0002594 Hypoplasia is defined in MPATH as resulting in a small organ or structure owing to failure to develop to normal size. Pancreatic hypoplasia Hypoplasia of the pancreas. HPO:probinson Underdeveloped pancreas ORCID:0000-0001-5208-3432 An abnormality of the vasculature. UMLS:C0241657 Abnormality of blood vessels Abnormality of the vasculature Vascular abnormalities human_phenotype HP:0002597 Abnormality of the vasculature An abnormality of the vasculature. HPO:probinson Abnormality of blood vessels ORCID:0000-0001-5208-3432 Abnormality of the vasculature Vascular abnormalities Low Blood Pressure, vascular hypotension. HP:0005127 HP:0006701 MSH:D007022 SNOMEDCT_US:45007003 UMLS:C0020649 Arterial hypotension Low blood pressure human_phenotype HP:0002615 Hypotension Low Blood Pressure, vascular hypotension. HPO:probinson Low blood pressure Abnormal outpouching or sac-like dilatation in the wall of an atery, vein or the heart. Fyler:2399 MSH:D000783 SNOMEDCT_US:432119003 SNOMEDCT_US:85659009 UMLS:C0002940 UMLS:C4020848 Aneurysmal dilatation Wider than typical opening or gap Aneurysm Aneurysms Aneurysmal disease HP:0002617 Aneurysm is considered a severe form of dilatation. Vascular dilatation Abnormal outpouching or sac-like dilatation in the wall of an atery, vein or the heart. HPO:probinson PMID:30225143 Aneurysmal dilatation ORCID:0000-0001-5208-3432 Wider than typical opening or gap https://orcid.org/0000-0002-6548-5200 Aneurysm Aneurysms HPO:skoehler Aneurysmal disease An anomaly of vein. UMLS:C0241665 Abnormal vein Venous abnormality human_phenotype HP:0002624 Abnormal venous morphology An anomaly of vein. HPO:probinson Abnormal vein ORCID:0000-0001-5208-3432 Abnormality of the absorption of fat from the gastrointestinal tract. SNOMEDCT_US:197494007 UMLS:C0554103 human_phenotype HP:0002630 Fat malabsorption Abnormality of the absorption of fat from the gastrointestinal tract. HPO:probinson Sclerosis (hardening) of the arteries with increased thickness of the wall of arteries as well as increased stiffness and a loss of elasticity. Hardened artery wall MSH:D001161 SNOMEDCT_US:107671003 SNOMEDCT_US:28960008 SNOMEDCT_US:72092001 UMLS:C0003850 UMLS:C4280568 human_phenotype HP:0002634 Although arteriosclerosis and atherosclerosis are often used as if they were synonyms, they are not. Atherosclerosis is the most common type of arteriosclerosis, and is caused by plaque building up in the vessel, which in turn causes sclerosis, increased stiffness, and loss of elasticity of the affected arteries. Arteriosclerosis Sclerosis (hardening) of the arteries with increased thickness of the wall of arteries as well as increased stiffness and a loss of elasticity. HPO:probinson Hardened artery wall ORCID:0000-0001-5208-3432 An abnormality of the bony pelvic girdle, which is a ring of bones connecting the vertebral column to the femurs. UMLS:C4020847 Abnormal shape of pelvic girdle bone human_phenotype Abnormality of the pelvic girdle HP:0002644 Abnormality of pelvic girdle bone morphology An abnormality of the bony pelvic girdle, which is a ring of bones connecting the vertebral column to the femurs. HPO:probinson Abnormal shape of pelvic girdle bone ORCID:0000-0001-5208-3432 The presence of an abnormal shape of the calvaria (skullcap), that is, of that part of the skull that is made up of the superior portions of the frontal bone, occipital bone, and parietal bones and covers the cranial cavity that contains the brain. Abnormality of skull bone morphology Abnormality of the shape of skull bones UMLS:C4025692 UMLS:C4280260 Abnormal cranium morphology Abnormality of cranial bone morphology Abnormality of the shape of calvarium Abnormality of the shape of cranium Abnormally shaped skull human_phenotype HP:0002648 Abnormality of calvarial morphology The presence of an abnormal shape of the calvaria (skullcap), that is, of that part of the skull that is made up of the superior portions of the frontal bone, occipital bone, and parietal bones and covers the cranial cavity that contains the brain. DDD:awilkie HPO:probinson Abnormality of skull bone morphology ORCID:0000-0001-5889-4463 Abnormality of the shape of skull bones ORCID:0000-0001-5889-4463 Abnormality of cranial bone morphology ORCID:0000-0001-5889-4463 Abnormality of the shape of calvarium ORCID:0000-0001-5889-4463 Abnormality of the shape of cranium ORCID:0000-0001-5889-4463 Abnormally shaped skull ORCID:0000-0002-9353-5498 A general term describing features characterized by abnormal development of bones and connective tissues. HP:0005685 Abnormal skeletal development MSH:D010009 SNOMEDCT_US:105985007 SNOMEDCT_US:240190009 UMLS:C0029422 UMLS:C4280567 HP:0002652 The word skeletal dysplasia is most often used to describe a group of over 380 inherited conditions that involve abnormal development of bones and connective tissues. However, the word can also be used to describe the presence of congenital defects of bones or connective tissues that are found in one or more of the diseases, especially on prenatal ultrasound, i.e., a situation in which it is often not yet possible to make an exact etiological diagnosis. This is the sense of the phrase we use in the HPO. It is, however, preferable to annotate the observed abnormalities. Skeletal dysplasia A general term describing features characterized by abnormal development of bones and connective tissues. HPO:probinson Abnormal skeletal development ORCID:0000-0001-5208-3432 MSH:D010009 SNOMEDCT_US:59708000 UMLS:C0026760 human_phenotype HP:0002654 Multiple epiphyseal dysplasia Abnormal development of end part of bone SNOMEDCT_US:254080004 UMLS:C0392476 UMLS:C4280566 Abnormal development of the ends of long bones in arms and legs human_phenotype HP:0002656 Epiphyseal dysplasia Abnormal development of end part of bone ORCID:0000-0001-5208-3432 Abnormal development of the ends of long bones in arms and legs https://orcid.org/0000-0002-6548-5200 HP:0005862 UMLS:C1865200 UMLS:C4280565 Delayed epiphyseal maturation Delayed epiphyseal ossification Delayed opacification of the epiphyses Epiphyseal ossification delay human_phenotype Delayed maturation of end part of long bone HP:0002663 Delayed epiphyseal ossification Delayed maturation of end part of long bone ORCID:0000-0001-5208-3432 An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumour). HP:0003008 HP:0006741 Abnormal tissue mass MSH:D009369 NCIT:C3262 SNOMEDCT_US:108369006 SNOMEDCT_US:363346000 UMLS:C0006826 UMLS:C0027651 Neoplasia Oncological abnormality Tumor Tumour human_phenotype Cancer Oncology HP:0002664 The World Health Organization (WHO) classifies neoplasms into four main groups: (i) benign neoplasm, (ii) in situ neoplasm, (iii) malignant neoplasm, and (iv) neoplasm of uncertain or unknown behavior. A malignant neoplasm is also known as cancer. Neoplasm An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumour). HPO:probinson Abnormal tissue mass https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 Cancer Oncology HPO:probinson An abnormal narrowing of the foramen magnum. HP:0005468 SNOMEDCT_US:444879009 UMLS:C1535953 UMLS:C1861217 UMLS:C4072838 Foramen magnum stenosis Little foramen magnum Narrow foramen magnum Hypoplasia of foramen magnum Stenosis of foramen magnum human_phenotype HP:0002677 The foramen magnum is the aperture through which the medulla oblongata enters and exits the skull. Stenosis of the foramen magnum can represent a risk for compression to the spinal cord. Small foramen magnum An abnormal narrowing of the foramen magnum. HPO:probinson Little foramen magnum ORCID:0000-0001-5889-4463 Narrow foramen magnum ORCID:0000-0001-5889-4463 Hypoplasia of foramen magnum ORCID:0000-0001-5889-4463 Stenosis of foramen magnum ORCID:0000-0001-5889-4463 Abnormality of the calvaria, which is the roof of the skull formed by the frontal bone, parietal bones, and occipital bone. Abnormality of cranium UMLS:C4025691 UMLS:C4280561 Abnormality of calvarium Abnormality of cranial vault Abnormality of the skull cap Abnormality of the skullcap human_phenotype HP:0002683 The calvaria, or skull cap, is the upper part of the skull (cranium) and comprises the frontal, occipital and right and left parietal bones. Occasionally, calvaria is misspelled as 'calvarium' in the medical literature. Abnormality of the calvaria Abnormality of the calvaria, which is the roof of the skull formed by the frontal bone, parietal bones, and occipital bone. HPO:probinson Abnormality of cranium ORCID:0000-0001-5889-4463 Abnormality of calvarium ORCID:0000-0001-5889-4463 Abnormality of cranial vault ORCID:0000-0001-5889-4463 Abnormality of the skull cap ORCID:0000-0001-5889-4463 Abnormality of the skullcap ORCID:0000-0001-5208-3432 Hypoplasia of facial skeleton Small facial bones Small facial skeleton Underdevelopment of facial bones Underdevelopment of facial skeleton UMLS:C1846438 UMLS:C4229090 UMLS:C4280268 UMLS:C4280557 UMLS:C4280558 Decreased size of facial bones Decreased size of facial skeleton human_phenotype Flattening of facial bones Flattening of facial skeleton Hypotrophic facial bones Hypotrophic facial skeleton HP:0002692 Hypoplastic facial bones Hypoplasia of facial skeleton ORCID:0000-0001-5889-4463 Small facial bones ORCID:0000-0001-5889-4463 Small facial skeleton ORCID:0000-0001-5889-4463 Underdevelopment of facial bones ORCID:0000-0001-5889-4463 Underdevelopment of facial skeleton ORCID:0000-0001-5889-4463 Decreased size of facial bones ORCID:0000-0001-5889-4463 Decreased size of facial skeleton ORCID:0000-0001-5889-4463 Flattening of facial bones ORCID:0000-0001-5889-4463 Flattening of facial skeleton ORCID:0000-0001-5889-4463 Hypotrophic facial bones ORCID:0000-0001-5889-4463 Hypotrophic facial skeleton ORCID:0000-0001-5889-4463 An abnormality of the base of the skull, which forms the floor of the cranial cavity and separates the brain from other facial structures. The skull base is made up of five bones: the ethmoid, sphenoid, occipital, paired frontal, and paired parietal bones, and is subdivided into 3 regions: the anterior, middle, and posterior cranial fossae. The petro-occipital fissure subdivides the middle cranial fossa into 1 central component and 2 lateral components. UMLS:C4025688 Abnormality of cranial base Abnormality of the skull base human_phenotype HP:0002693 Abnormality of the skull base An abnormality of the base of the skull, which forms the floor of the cranial cavity and separates the brain from other facial structures. The skull base is made up of five bones: the ethmoid, sphenoid, occipital, paired frontal, and paired parietal bones, and is subdivided into 3 regions: the anterior, middle, and posterior cranial fossae. The petro-occipital fissure subdivides the middle cranial fossa into 1 central component and 2 lateral components. HPO:curators Abnormality of cranial base ORCID:0000-0001-5889-4463 Abnormality of the skull base Increased bone density of the skull base without significant changes in bony contour. HP:0005757 UMLS:C1851714 UMLS:C4072847 UMLS:C4072848 Dense bone of skull base HyperOssification of skull base HyperOstosis of skull base Marked sclerosis of skull base Sclerosis of cranial base Sclerosis of the skull base Sclerotic skull base HyperCalcification of skull base HyperMineralization of skull base human_phenotype HP:0002694 Sclerosis of skull base Increased bone density of the skull base without significant changes in bony contour. HPO:probinson Dense bone of skull base ORCID:0000-0001-5889-4463 HyperOssification of skull base ORCID:0000-0001-5889-4463 HyperOstosis of skull base ORCID:0000-0001-5889-4463 Sclerosis of cranial base ORCID:0000-0001-5889-4463 HyperCalcification of skull base ORCID:0000-0001-5889-4463 HyperMineralization of skull base ORCID:0000-0001-5889-4463 Any abnormality of the foramen magnum. UMLS:C4025687 human_phenotype HP:0002699 The foramen magnum is the aperture through which the medulla oblongata enters and exits the skull. Abnormality of the foramen magnum Any abnormality of the foramen magnum. HPO:probinson An abnormal increase in the size of the foramen magnum. UMLS:C1844508 UMLS:C4073291 UMLS:C4280554 UMLS:C4280555 Big foramen magnum Dilation of foramen magnum Wide foramen magnum enlarged foramen magnum Hyperplasia of foramen magnum Increased circumference of foramen magnum Increased diameter of foramen magnum human_phenotype HP:0002700 Large foramen magnum An abnormal increase in the size of the foramen magnum. HPO:curators Big foramen magnum ORCID:0000-0001-5889-4463 Dilation of foramen magnum ORCID:0000-0001-5889-4463 Wide foramen magnum ORCID:0000-0001-5889-4463 Hyperplasia of foramen magnum ORCID:0000-0001-5889-4463 Increased circumference of foramen magnum ORCID:0000-0001-5889-4463 Increased diameter of foramen magnum ORCID:0000-0001-5889-4463 An abnormality of the process of ossification of the skull. peter 2008-02-28T11:53:00Z Abnormality of skull bone formation UMLS:C4025686 UMLS:C4280550 UMLS:C4280551 UMLS:C4280552 UMLS:C4280553 Abnormality of ossification of calvarium Abnormality of ossification of cranium human_phenotype Abnormality of bone calcification of calvarium Abnormality of bone calcification of cranium Abnormality of bone calcification of skull Abnormality of bone formation of calvarium Abnormality of bone formation of cranium Abnormality of bone mineralization of calvarium Abnormality of bone mineralization of cranium Abnormality of bone mineralization of skull HP:0002703 The bones of the skull derive directly from mesenchyme cells by intramembranous ossification. Abnormality of skull ossification An abnormality of the process of ossification of the skull. HPO:probinson Abnormality of skull bone formation ORCID:0000-0001-5889-4463 Abnormality of ossification of calvarium ORCID:0000-0001-5889-4463 Abnormality of ossification of cranium ORCID:0000-0001-5889-4463 Abnormality of bone calcification of calvarium ORCID:0000-0001-5889-4463 Abnormality of bone calcification of cranium ORCID:0000-0001-5889-4463 Abnormality of bone calcification of skull ORCID:0000-0001-5889-4463 Abnormality of bone formation of calvarium ORCID:0000-0001-5889-4463 Abnormality of bone formation of cranium ORCID:0000-0001-5889-4463 Abnormality of bone mineralization of calvarium ORCID:0000-0001-5889-4463 Abnormality of bone mineralization of cranium ORCID:0000-0001-5889-4463 Abnormality of bone mineralization of skull ORCID:0000-0001-5889-4463 An abnormality of the immune system. HP:0003257 HP:0003346 HP:0010986 UMLS:C4021753 Abnormality of the immune system Immunological abnormality human_phenotype HP:0002715 The immune system is composed of organs and interdependent cell types that collectively protect the body from infections and from the growth of tumor cells. The organs of the immune system comprise the bone marrow, the spleen, the thymus,the lymph nodes, and the cell types comprise B cells, T cells, natural killer cells, granulocytes,dendritic cells, and macrophages. Abnormality of the immune system An abnormality of the immune system. HPO:probinson Abnormality of the immune system Immunological abnormality Underdevelopment of the lymph nodes. UMLS:C1865377 UMLS:C4025683 human_phenotype Small lymph nodes HP:0002732 Lymph node hypoplasia Underdevelopment of the lymph nodes. HPO:probinson Small lymph nodes A lymph node abnormality. HP:0008149 UMLS:C0149727 Abnormal lymph node histology Abnormality of the lymph nodes human_phenotype HP:0002733 Abnormality of the lymph nodes A lymph node abnormality. HPO:probinson Abnormal lymph node histology Abnormality of the lymph nodes Osteomyelitis is an inflammatory process accompanied by bone destruction and caused by an infecting microorganism. HP:0002755 HP:0005901 MSH:D010019 SNOMEDCT_US:111253001 SNOMEDCT_US:60168000 UMLS:C0029443 UMLS:C2242472 Bone infection human_phenotype HP:0002754 Osteomyelitis can be acute or chronic and can be caused by a variety of microbial agents. Osteomyelitis Osteomyelitis is an inflammatory process accompanied by bone destruction and caused by an infecting microorganism. HPO:probinson PMID:15276398 Bone infection ORCID:0000-0001-5208-3432 Any morphological abnormality of cartilage. HP:0410007 UMLS:C4025680 Abnormal shape of cartilage Abnormality of cartilage morphology human_phenotype HP:0002763 Abnormal cartilage morphology Any morphological abnormality of cartilage. HPO:probinson Abnormal shape of cartilage ORCID:0000-0001-5208-3432 UMLS:C3277114 Relatively short spine human_phenotype HP:0002766 Relatively short spine Relatively short spine A structural anomaly of the trachea. MSH:D014133 SNOMEDCT_US:47125007 UMLS:C0040580 UMLS:C4025678 Abnormality of the trachea human_phenotype Tracheal disease HP:0002778 Abnormal trachea morphology A structural anomaly of the trachea. HPO:probinson Calcification (abnormal deposits of calcium) in the tracheal tissues. SNOMEDCT_US:81089005 UMLS:C0264324 Calcification of the trachea Tracheal calcifications Tracheal ectopic calcification human_phenotype HP:0002787 Tracheal calcification Calcification (abnormal deposits of calcium) in the tracheal tissues. HPO:probinson PMID:18663210 Tracheal calcifications Fyler:4200 UMLS:C4025677 Abnormal respiration Functional respiratory abnormality human_phenotype Respiratory problem HP:0002795 This category describes not-primarily structural lesions. Functional respiratory abnormality Abnormal respiration ORCID:0000-0001-5208-3432 Functional respiratory abnormality Respiratory problem Any abnormality of bones of the arms or legs. UMLS:C4082761 Abnormal shape of limb bone Arm and/or leg bone differences Limb abnormality human_phenotype HP:0002813 Abnormality of limb bone morphology Any abnormality of bones of the arms or legs. HPO:probinson Abnormal shape of limb bone ORCID:0000-0001-5208-3432 Arm and/or leg bone differences Limb abnormality An abnormality of the leg. SNOMEDCT_US:449715001 UMLS:C1096086 Abnormality of the leg Abnormality of the lower limb Lower limb deformities human_phenotype HP:0002814 Abnormality of the lower limb An abnormality of the leg. HPO:probinson Abnormality of the lower limb Lower limb deformities An abnormality of the arm. HP:0003838 UMLS:C4020900 Abnormality of the arm Abnormality of the upper limb human_phenotype HP:0002817 Abnormality of the upper limb An abnormality of the arm. HPO:probinson Abnormality of the upper limb Any anomaly of the structure of the femur. HP:0001439 UMLS:C4021750 Abnormality of the femora Abnormality of the thighbone human_phenotype HP:0002823 The femur (plural: femora) is the thigh bone. Abnormality of femur morphology Any anomaly of the structure of the femur. HPO:probinson Abnormality of the thighbone ORCID:0000-0001-5208-3432 Inflammation of a lymph node. MSH:D008199 SNOMEDCT_US:19471005 UMLS:C0024205 Inflammation of the lymph nodes human_phenotype HP:0002840 Lymphadenitis Inflammation of a lymph node. HPO:probinson Inflammation of the lymph nodes ORCID:0000-0001-5208-3432 An abnormality of the ilium, the largest and uppermost bone of the pelvis. UMLS:C4021746 Iliac abnormalities human_phenotype HP:0002867 Abnormality of the ilium An abnormality of the ilium, the largest and uppermost bone of the pelvis. HPO:probinson An abnormally decreased potassium concentration in the blood. MSH:D007008 SNOMEDCT_US:166690008 SNOMEDCT_US:43339004 UMLS:C0020621 Low blood potassium levels human_phenotype HP:0002900 Hypokalemia An abnormally decreased potassium concentration in the blood. HPO:probinson Low blood potassium levels ORCID:0000-0001-6908-9849 An abnormally decreased calcium concentration in the blood. MSH:D006996 SNOMEDCT_US:5291005 UMLS:C0020598 Hypocalcaemia Low blood calcium levels human_phenotype HP:0002901 Hypocalcemia An abnormally decreased calcium concentration in the blood. HPO:curators Low blood calcium levels ORCID:0000-0001-6908-9849 An abnormally decreased sodium concentration in the blood. MSH:D007010 SNOMEDCT_US:89627008 UMLS:C0020625 Low blood sodium levels human_phenotype HP:0002902 Hyponatremia An abnormally decreased sodium concentration in the blood. HPO:probinson Low blood sodium levels ORCID:0000-0001-6908-9849 An abnormally increased phosphate concentration in the blood. MSH:D054559 SNOMEDCT_US:20165001 UMLS:C0085681 UMLS:C0553706 High blood phosphate levels human_phenotype HP:0002905 Hyperphosphatemia An abnormally increased phosphate concentration in the blood. HPO:gcarletti High blood phosphate levels ORCID:0000-0001-5208-3432 An abnormally decreased magnesium concentration in the blood. HP:0003284 SNOMEDCT_US:190855004 UMLS:C0151723 Low blood Mg levels Low blood magnesium levels human_phenotype HP:0002917 Hypomagnesemia An abnormally decreased magnesium concentration in the blood. HPO:probinson Low blood Mg levels Low blood magnesium levels ORCID:0000-0001-6908-9849 An abnormally increased magnesium concentration in the blood. SNOMEDCT_US:66978005 UMLS:C0151714 High blood Mg levels High blood magnesium levels human_phenotype HP:0002918 Hypermagnesemia An abnormally increased magnesium concentration in the blood. HPO:probinson High blood Mg levels High blood magnesium levels ORCID:0000-0001-6908-9849 An abnormality of the cerebrospinal fluid (CSF). UMLS:C0151583 Abnormal CSF findings Abnormality of the CSF human_phenotype HP:0002921 The cerebrospinal fluid (CSF) is secreted by the choroid plexus, and flows uninterrupted throughout the central nervous system (the central cerebrospinal canal of the spinal cord and through the four interconnected cerebral ventricles in the brain). Abnormality of the cerebrospinal fluid An abnormality of the cerebrospinal fluid (CSF). HPO:probinson Abnormal CSF findings Abnormality of the CSF An abnormal functionality of the thyroid gland. UMLS:C0857576 Abnormal thyroid function human_phenotype HP:0002926 Abnormality of thyroid physiology An abnormal functionality of the thyroid gland. HPO:probinson Abnormal thyroid function HPO:skoehler Decreased height of the intervertebral disk. SNOMEDCT_US:11301007 UMLS:C0263870 Narrow intervertebral disc spaces Narrow intervertebral spaces human_phenotype HP:0002945 A decrease in the height of the intervertebral disks is usually observed as a narrowing of the space between the vertebrae on X-ray examination. Intervertebral space narrowing Decreased height of the intervertebral disk. HPO:probinson SNOMEDCT_US:87294007 UMLS:C0265681 human_phenotype HP:0002946 Supernumerary vertebrae An abnormality of the lower arm. UMLS:C4025666 Abnormality of the forearm human_phenotype HP:0002973 Abnormality of the forearm An abnormality of the lower arm. HPO:probinson Abnormality of the forearm Absence or underdevelopment of tissue in the central nervous system. peter 2008-03-31T05:13:00Z HP:0001323 UMLS:C4025665 Absent/underdeveloped central nervous system tissue Aplasia/Hypoplasia involving the CNS human_phenotype HP:0002977 Aplasia/Hypoplasia involving the central nervous system Absence or underdevelopment of tissue in the central nervous system. HPO:probinson Absent/underdeveloped central nervous system tissue ORCID:0000-0001-5208-3432 Aplasia/Hypoplasia involving the CNS An abnormality of the calf, i.e. of the posterior part of the lower leg. UMLS:C4021832 Abnormality of the calf human_phenotype HP:0002981 Abnormality of the calf An abnormality of the calf, i.e. of the posterior part of the lower leg. HPO:probinson Abnormality of the calf The presence of abnormally small extremities. HP:0003030 HP:0005753 MEDDRA:10027546 SNOMEDCT_US:74370006 UMLS:C0025995 Smaller or shorter than typical limbs human_phenotype HP:0002983 Micromelia The presence of abnormally small extremities. HPO:probinson MEDDRA:10027546 Micromelia Smaller or shorter than typical limbs https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 A chronic loss of elbow joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevent normal movement of the joints of the elbow. HP:0003937 HP:0004984 HP:0005654 SNOMEDCT_US:202271004 UMLS:C0409338 Contracture of elbow joint Contractures of elbows Contractures of the elbows Elbow contracture Elbow contractures Elbow flexion contractures Elbow flexion deformity Fixed flexion at the elbow joint human_phenotype HP:0002987 Elbow flexion contracture A chronic loss of elbow joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevent normal movement of the joints of the elbow. HPO:probinson Contractures of elbows Elbow contracture Elbow contractures HP:0006395 UMLS:C1849955 Decreased elbow mobility Limited elbow mobility Limited elbow movement Restricted elbow motion human_phenotype HP:0002996 Limited elbow movement Decreased elbow mobility Limited elbow mobility Limited elbow movement Restricted elbow motion Abnormality originating in one or more muscles, i.e., of the set of muscles of body. HP:0003197 HP:0003708 HP:0040290 UMLS:C4021745 Muscular abnormality human_phenotype HP:0003011 Abnormality of the musculature Abnormality originating in one or more muscles, i.e., of the set of muscles of body. HPO:probinson Muscular abnormality Abnormality of the wrist, the structure connecting the hand and the forearm. HP:0001224 UMLS:C4021744 Abnormalities of the wrists Abnormality of the wrist human_phenotype HP:0003019 Abnormality of the wrist Abnormality of the wrist, the structure connecting the hand and the forearm. HPO:probinson Abnormalities of the wrists Abnormality of the wrist One or more abnormally short long bone. HP:0000949 HP:0004983 HP:0004988 HP:0005000 HP:0005029 HP:0005044 HP:0005052 HP:0005077 HP:0005083 HP:0005647 HP:0005822 HP:0006382 HP:0006457 HP:0006472 UMLS:C1854912 Long bone shortening Short long bone Short tubular bones shortened long tubular bones human_phenotype HP:0003026 Long bones are also known as tubular bones. Short long bone One or more abnormally short long bone. HPO:probinson Long bone shortening Short long bone UMLS:C4025660 Abnormality of the ankles human_phenotype HP:0003028 Abnormality of the ankles Abnormality of the ankles UMLS:C1838664 Enlargement of the ankles human_phenotype HP:0003029 Enlargement of the ankles Enlargement of the ankles An elevation in bone density in one or more diaphyses. Sclerosis is normally detected on a radiograph as an area of increased opacity. HP:0005611 MSH:D003966 SNOMEDCT_US:318761000119105 SNOMEDCT_US:34643004 UMLS:C0011989 Craniodiaphyseal osteosclerosis Diaphyseal osteosclerosis Increased bone density in shaft of long bone human_phenotype HP:0003034 Diaphyseal sclerosis An elevation in bone density in one or more diaphyses. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in shaft of long bone ORCID:0000-0001-5208-3432 Increase in size of one or more joints. UMLS:C1859111 Enlarged joints human_phenotype Prominent joints HP:0003037 Enlarged joints Increase in size of one or more joints. HPO:probinson Enlarged joints An abnormality of the shoulder, which is defined as the structures surrounding the shoulder joint where the humerus attaches to the scapula. UMLS:C4025659 Abnormality of the shoulder HP:0003043 Abnormal shoulder morphology An abnormality of the shoulder, which is defined as the structures surrounding the shoulder joint where the humerus attaches to the scapula. HPO:probinson Abnormality of the shoulder Chronic reduction in active and passive mobility of the shoulder joint due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement. SNOMEDCT_US:202265005 UMLS:C0409336 human_phenotype HP:0003044 Shoulder flexion contracture Chronic reduction in active and passive mobility of the shoulder joint due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement. HPO:probinson SNOMEDCT_US:43689004 UMLS:C0231678 Ulnar deviation of wrists human_phenotype HP:0003049 Ulnar deviation of the wrist Abnormal increase in size of one or more metaphyses. HP:0005018 UMLS:C1855544 Enlarged wide portion of a long bone human_phenotype HP:0003051 Enlarged metaphyses Abnormal increase in size of one or more metaphyses. HPO:probinson Enlarged wide portion of a long bone ORCID:0000-0001-5889-4463 An abnormality of the humerus (i.e., upper arm bone). HP:0002988 UMLS:C4021742 Abnormality of the humeri human_phenotype HP:0003063 Abnormality of the humerus An abnormality of the humerus (i.e., upper arm bone). HPO:curators An abnormally increased calcium concentration in the blood. MSH:D006934 SNOMEDCT_US:166702002 SNOMEDCT_US:66931009 UMLS:C0020437 High blood calcium levels Hypercalcaemia Increased calcium in blood human_phenotype HP:0003072 Hypercalcemia An abnormally increased calcium concentration in the blood. HPO:curators High blood calcium levels ORCID:0000-0001-6908-9849 Increased calcium in blood ORCID:0000-0001-5208-3432 An increased concentration of glucose in the blood. MSH:D006943 SNOMEDCT_US:237598005 SNOMEDCT_US:80394007 UMLS:C0020456 High blood glucose High blood sugar human_phenotype HP:0003074 Hyperglycemia An increased concentration of glucose in the blood. HPO:probinson High blood glucose ORCID:0000-0001-6908-9849 High blood sugar ORCID:0000-0001-6908-9849 An increased concentration of glucose in the urine. HP:0003122 MSH:D006029 SNOMEDCT_US:45154002 UMLS:C0017979 Glucose in urine Glucosuria human_phenotype HP:0003076 Glycosuria, the excretion of abnormal amounts of glucose in the urine, generally results in osmotic diuresis. Glycosuria An increased concentration of glucose in the urine. HPO:gcarletti Glucose in urine https://orcid.org/0000-0002-6548-5200 An elevated lipid concentration in the blood. HP:0008159 HP:0008356 MSH:D006949 SNOMEDCT_US:55822004 UMLS:C0020473 Elevated lipids in blood human_phenotype HP:0003077 Hyperlipidemia is an elevation of the blood levels of lipids including primarily cholesterol, phospholipids and triglycerides and cholesterol esters. The lipids are transported on lipoproteins some of which are commonly used for clinical measurements, including chylomicrons, very-low density lipoproteins (VLDL), intermediate-density lipoproteins (IDL), low-density lipoproteins, and high-density lipoproteins (HDL). Hyperlipidemia An elevated lipid concentration in the blood. HPO:probinson Elevated lipids in blood https://orcid.org/0000-0002-6548-5200 An increased concentration of potassium(1+) in the urine. UMLS:C1846351 Hyperkaliuresis Increased urinary K Increased urinary potassium human_phenotype HP:0003081 Increased urinary potassium An increased concentration of potassium(1+) in the urine. HPO:probinson Increased urinary K Increased urinary potassium Underdevelopment of the proximal epiphysis of the femur. HP:0003374 HP:0008791 HP:0008792 UMLS:C1839254 Small capital femoral epiphyses Small femoral capital epiphyses Small innermost thighbone end part Small proximal femoral epiphyses Underdevelopment of the innermost thighbone end part human_phenotype HP:0003090 Hypoplasia of the capital femoral epiphysis Underdevelopment of the proximal epiphysis of the femur. HPO:probinson Small innermost thighbone end part ORCID:0000-0001-5208-3432 Underdevelopment of the innermost thighbone end part ORCID:0000-0001-5208-3432 An abnormal shortening of the femur. HP:0009749 SNOMEDCT_US:93255008 UMLS:C0345375 Femoral hypoplasia Hypoplasia of the femora Short femurs Short thighbone human_phenotype HP:0003097 Short femur An abnormal shortening of the femur. HPO:probinson Short thighbone ORCID:0000-0001-5208-3432 Any deviation from the normal concentration of cholesterol in the blood circulation. peter 2008-03-17T01:02:00Z HP:0003464 UMLS:C4025656 Abnormal cholesterol homeostasis Abnormality of cholesterol metabolism human_phenotype HP:0003107 Abnormal circulating cholesterol concentration Abnormality of cholesterol metabolism An increased concentration of glycine in the urine. HP:0002931 MSH:C563009 SNOMEDCT_US:236477004 UMLS:C0341706 UMLS:C0543541 Glycinuria High urine glycine levels human_phenotype HP:0003108 Normal urinary glycine total (free and combined form) excretion is around 450 mg per 24 hours. Hyperglycinuria An increased concentration of glycine in the urine. HPO:gcarletti PMID:18901181 PMID:20240447 High urine glycine levels ORCID:0000-0001-5208-3432 An increased excretion of phosphates in the urine. HP:0003266 SNOMEDCT_US:22450000 UMLS:C0268079 UMLS:C0948023 High urine phosphate levels Phosphaturia human_phenotype HP:0003109 Hyperphosphaturia An increased excretion of phosphates in the urine. HPO:curators High urine phosphate levels ORCID:0000-0001-5208-3432 An abnormality of the composition of urine or the levels of its components. HP:0011865 HP:0011866 UMLS:C4025655 Pee issues Urine issues HP:0003110 Abnormality of urine homeostasis An abnormality of the composition of urine or the levels of its components. HPO:probinson Pee issues Urine issues Abnormality of the homeostasis (concentration) of a monoatomic ion. HP:0003253 SNOMEDCT_US:237840007 UMLS:C1704431 UMLS:C4025654 Abnormality of ion homeostasis Electrolyte disorders human_phenotype HP:0003111 Abnormal blood ion concentration Abnormality of the homeostasis (concentration) of a monoatomic ion. HPO:probinson Electrolyte disorders The presence of an abnormal decrease or increase of one or more amino acids in the blood circulation. UMLS:C4025653 Abnormality of serum amino acid level Abnormality of serum amino acid levels HP:0003112 Abnormal circulating amino acid concentration The presence of an abnormal decrease or increase of one or more amino acids in the blood circulation. HPO:curators Abnormality of serum amino acid levels An abnormal concentration of a hormone in the blood. UMLS:C4025652 Abnormality of circulating hormone level human_phenotype HP:0003117 Abnormal circulating hormone level An abnormal concentration of a hormone in the blood. HPO:probinson Abnormality of circulating hormone level Any deviation from the normal concentration of a lipid in the blood circulation. HP:0003611 MSH:D050171 SNOMEDCT_US:370992007 UMLS:C0242339 UMLS:C4025650 Dyslipidemia HP:0003119 According to CHEBI:18059 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. Abnormal circulating lipid concentration Any deviation from the normal concentration of a lipid in the blood circulation. HPO:probinson A contrqacture (chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin) that prevent normal movement of one or more joints of the limbs. HP:0005631 HP:0005839 UMLS:C1969879 Limb contractures human_phenotype HP:0003121 Limb joint contracture A contrqacture (chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin) that prevent normal movement of one or more joints of the limbs. HPO:probinson Limb contractures An increased concentration of cholesterol in the blood. HP:0008154 HP:0008173 HP:0008359 High cholesterol MSH:D006937 SNOMEDCT_US:13644009 SNOMEDCT_US:166830008 UMLS:C0020443 UMLS:C0595929 Elevated serum cholesterol Elevated total cholesterol Increased total cholesterol human_phenotype HP:0003124 Hypercholesterolemia An increased concentration of cholesterol in the blood. HPO:gcarletti High cholesterol Elevated serum cholesterol Elevated total cholesterol Increased total cholesterol An abnormally decreased calcium concentration in the urine. SNOMEDCT_US:86353007 UMLS:C0020599 Low urine calcium levels human_phenotype HP:0003127 Hypocalciuria An abnormally decreased calcium concentration in the urine. HPO:probinson Low urine calcium levels ORCID:0000-0001-5208-3432 An decreased concentration of cholesterol in the blood. SNOMEDCT_US:61336008 UMLS:C0151718 Decreased circulating cholesterol level human_phenotype HP:0003146 Hypocholesterolemia An decreased concentration of cholesterol in the blood. HPO:gcarletti Decreased circulating cholesterol level ORCID:0000-0001-5208-3432 Increased excretion of oxalates in the urine. MSH:D006959 SNOMEDCT_US:367621000119107 UMLS:C0020500 High urine oxalate levels Increased level of oxalate in urine human_phenotype HP:0003159 Hyperoxaluria Increased excretion of oxalates in the urine. HPO:probinson High urine oxalate levels ORCID:0000-0001-5208-3432 Increased level of oxalate in urine ORCID:0000-0001-5208-3432 ORCID:0000-0001-9969-8610 PMID:11135054 An abnormality of the acetabulum, i.e., the Acetabular part of hip bone, which together with the head of the femur forms the hip joint. UMLS:C4021739 Abnormality of the hipbone socket Acetabular abnormality human_phenotype HP:0003170 Abnormality of the acetabulum An abnormality of the acetabulum, i.e., the Acetabular part of hip bone, which together with the head of the femur forms the hip joint. HPO:probinson Abnormality of the hipbone socket ORCID:0000-0001-5208-3432 Underdevelopment of the breast. HP:0000784 SNOMEDCT_US:8915006 UMLS:C0266013 Underdeveloped breasts human_phenotype HP:0003187 Breast hypoplasia Underdevelopment of the breast. HPO:probinson Underdeveloped breasts Distance from nasion to subnasale more than two standard deviations above the mean, or alternatively, an apparently increased length from the nasal root to the nasal base. HP:0005283 HP:0200142 UMLS:C1839798 Elongated nose Increased height of nose Increased length of nose Increased nasal height Increased nasal length Long nose Nasal elongation human_phenotype HP:0003189 Long nose Distance from nasion to subnasale more than two standard deviations above the mean, or alternatively, an apparently increased length from the nasal root to the nasal base. PMID:19152422 Elongated nose ORCID:0000-0001-5889-4463 Increased height of nose ORCID:0000-0001-5889-4463 Increased length of nose ORCID:0000-0001-5889-4463 Increased nasal height ORCID:0000-0001-5889-4463 Increased nasal length ORCID:0000-0001-5889-4463 Long nose Nasal elongation ORCID:0000-0001-5889-4463 Distance from nasion to subnasale more than two standard deviations below the mean, or alternatively, an apparently decreased length from the nasal root to the nasal tip. HP:0000440 HP:0000449 HP:0000450 HP:0003192 HP:0003195 HP:0005270 HP:0200092 SNOMEDCT_US:249310005 UMLS:C0426414 UMLS:C1854114 Decreased length of nose Hypoplastic nose Nasal hypoplasia Short nose Shortened nose human_phenotype Small nose HP:0003196 Note: a small nose has both decreased height and a decreased width. These should be coded separately. Short nose Distance from nasion to subnasale more than two standard deviations below the mean, or alternatively, an apparently decreased length from the nasal root to the nasal tip. HPO:probinson PMID:19152422 Decreased length of nose ORCID:0000-0001-5889-4463 Short nose Shortened nose HPO:skoehler Small nose Pathological deposition of calcium salts in one or more arteries. peter 2008-03-26T04:05:00Z HP:0012455 UMLS:C1168153 human_phenotype HP:0003207 Most individuals aged over 60 years have progressively enlarging deposits of calcium mineral in their major arteries. This vascular calcification reduces aortic and arterial elastance, which impairs cardiovascular hemodynamics, resulting in substantial morbidity and mortality in the form of hypertension, aortic stenosis, cardiac hypertrophy, myocardial and lower-limb ischemia, congestive heart failure, and compromised structural integrity.The severity and extent of mineralization reflect atherosclerotic plaque burden and strongly and independently predict cardiovascular morbidity and mortality. (From PMID:18519861). Arterial calcification Pathological deposition of calcium salts in one or more arteries. HPO:probinson PMID:18519861 An increased concentration of dicarboxylic acid in the urine. UMLS:C1856432 HP:0003215 Dicarboxylic aciduria occurs during increased mobilization or inhibited beta-oxidation of fatty acids, where a number of 3-hydroxydicarboxylic acids are excreted in the urine. Dicarboxylic aciduria An increased concentration of dicarboxylic acid in the urine. HPO:gcarletti Decreased concentration of methylcobalamin. Methylcobalamin is a form of vitamin B12. HP:0008287 UMLS:C4021736 Methylcobalamin deficiency human_phenotype HP:0003223 Decreased methylcobalamin Decreased concentration of methylcobalamin. Methylcobalamin is a form of vitamin B12. HPO:probinson An abnormally increased sodium concentration in the blood. MSH:D006955 SNOMEDCT_US:286926003 SNOMEDCT_US:39355002 UMLS:C0020488 High blood sodium levels human_phenotype HP:0003228 Hypernatremia An abnormally increased sodium concentration in the blood. HPO:probinson High blood sodium levels ORCID:0000-0001-5208-3432 An increased concentration of tyrosine in the blood. SNOMEDCT_US:56595005 UMLS:C1879362 Increased tyrosine in blood Tyrosinemia human_phenotype HP:0003231 Defect in fumarylacetoacetase. Hypertyrosinemia An increased concentration of tyrosine in the blood. HPO:probinson Increased tyrosine in blood ORCID:0000-0001-5208-3432 A decreased concentration of carnitine in the blood. SNOMEDCT_US:421784001 UMLS:C1142132 Decreased plasma carnitine human_phenotype Carnitine deficiency HP:0003234 Carnitine is responsible for the transport of fatty acids from the cytosol into the mitochondria. Decreased plasma carnitine A decreased concentration of carnitine in the blood. HPO:gcarletti Decreased plasma carnitine Carnitine deficiency An increased concentration of methionine in the blood. MSH:C564683 SNOMEDCT_US:124283007 SNOMEDCT_US:43123004 SNOMEDCT_US:57835009 UMLS:C0268621 Increased methionine in blood Methioninemia human_phenotype HP:0003235 Elevated blood methionine levels in the range of 500-2000 micromolar. Hypermethioninemia An increased concentration of methionine in the blood. HPO:gcarletti Increased methionine in blood ORCID:0000-0001-5208-3432 Underdevelopment of part or all of the external reproductive organs. HP:0000788 HP:0003245 UMLS:C1855333 Hypogenitalism Small genitalia Underdevelopment of external reproductive organs human_phenotype HP:0003241 Partial or complete failure of the genitalia to develop, often as a consequence of hypogonadism. External genital hypoplasia Underdevelopment of part or all of the external reproductive organs. HPO:probinson Underdevelopment of external reproductive organs https://orcid.org/0000-0002-6548-5200 UMLS:C1851722 Overgrowth of external genitalia human_phenotype HP:0003247 Overgrowth of external genitalia Overgrowth of external genitalia Aplasia of the vagina. HP:0008709 MSH:C536523 SNOMEDCT_US:248871003 SNOMEDCT_US:87380008 UMLS:C0220763 UMLS:C1321884 UMLS:C1841990 Absent vagina Congenital absence of the vagina human_phenotype HP:0003250 Aplasia of the vagina Aplasia of the vagina. HPO:probinson Absent vagina A increased concentration of arginine in the urine. UMLS:C4025635 High urine arginine levels human_phenotype HP:0003268 Normal urinary arginine total (free and combined form) excretion is around 30 mg per 24 hours. Argininuria A increased concentration of arginine in the urine. HPO:probinson PMID:18901181 PMID:20240447 High urine arginine levels ORCID:0000-0001-5208-3432 Abnormal increased size of the viscera of the abdomen. SNOMEDCT_US:28543008 UMLS:C0042782 human_phenotype HP:0003271 Visceromegaly is enlargement of the internal organs in the abdomen, including liver, spleen, stomach, kidneys, or pancreas. Visceromegaly Abnormal increased size of the viscera of the abdomen. HPO:probinson An abnormality of the hip bone. UMLS:C4021735 Abnormality of the hip bone Abnormality of the hips human_phenotype HP:0003272 The hip region comprises the vasculature of hip, skin of hip, superficial fascia of hip, the hip bone, hip joint, and musculature of hip. The hip is part of the pelvic girdle. Abnormality of the hip bone An abnormality of the hip bone. HPO:probinson Abnormality of the hip bone Abnormality of the hips SNOMEDCT_US:202283002 UMLS:C0409354 Flexion contracture of hips Flexion contractures of hips Hip contractures Hip flexion contractures human_phenotype HP:0003273 Hip contracture Underdeveloped acetabulae. UMLS:C1846442 Acetabular hypoplasia Hypoplastic acetabula human_phenotype HP:0003274 Hypoplastic acetabulae Underdeveloped acetabulae. HPO:probinson A functional anomaly of mitochondria. UMLS:C4021734 Mitochondrial dysfunction human_phenotype HP:0003287 Abnormality of mitochondrial metabolism A functional anomaly of mitochondria. ORCID:0000-0001-5208-3432 An increased concentration of lysine in the urine. HP:0002158 UMLS:C4021733 High urine lysine levels Lysinuria human_phenotype HP:0003297 Normal urinary lysine total (free and combined form) excretion is around 80 mg per 24 hours. Hyperlysinuria An increased concentration of lysine in the urine. HPO:probinson PMID:18901181 PMID:20240447 High urine lysine levels ORCID:0000-0001-5208-3432 Abnormal morphology of vertebral body. UMLS:C1839326 Abnormally shaped vertebrae human_phenotype HP:0003312 Abnormal form of the vertebral bodies SNOMEDCT_US:298186005 UMLS:C0574967 human_phenotype HP:0003318 Cervical spine hypermobility Any abnormality of the cervical vertebral column. HP:0004587 UMLS:C1852464 Abnormal cervical spine Abnormality of cervical vertebra Abnormality of the cervical vertebrae Cervical spine abnormalities Cervical vertebral abnormalities Disorder of cervical vertebra human_phenotype Cervical vertebral anomalies HP:0003319 Abnormality of the cervical spine Any abnormality of the cervical vertebral column. HPO:probinson Abnormal cervical spine Abnormality of cervical vertebra https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0001-5889-4463 Abnormality of the cervical vertebrae https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0001-5889-4463 Cervical vertebral anomalies HPO:skoehler Any anomaly in the composite material or the layered arrangement of the bony skeleton. UMLS:C4025630 human_phenotype HP:0003330 Abnormal bone structure Any anomaly in the composite material or the layered arrangement of the bony skeleton. HPO:probinson An abnormality of the process of endochondral ossification, which is a type of replacement ossification in which bone tissue replaces cartilage. HP:0003331 UMLS:C4025628 human_phenotype HP:0003336 This term is intended to describe histological abnormalities of enchondral ossification observed upon bone biopsy. Abnormal enchondral ossification An abnormality of the process of endochondral ossification, which is a type of replacement ossification in which bone tissue replaces cartilage. HPO:probinson An increased concentration of an amino acid in the urine. HP:0002903 HP:0008335 HP:0200014 SNOMEDCT_US:35912001 UMLS:C0238621 UMLS:C4020843 High urine amino acid levels Hyperaminoaciduria Increased levels of animo acids in urine Abnormal urinary amino-acid findings HP:0003355 Aminoaciduria An increased concentration of an amino acid in the urine. HPO:SKOEHLER High urine amino acid levels orcid.org/0000-0001-5208-3432 Increased levels of animo acids in urine orcid.org/0000-0002-6548-5200 Abnormal urinary amino-acid findings UMLS:C4025622 Abnormal neck or head of thigh bone Abnormality of the femoral neck or head region HP:0003366 Abnormal femoral neck/head morphology Abnormal neck or head of thigh bone ORCID:0000-0001-5208-3432 An abnormality of the femoral neck (which is the process of bone, connecting the femoral head with the femoral shaft). UMLS:C4025621 Abnormal neck of thigh bone Abnormality of the femoral neck HP:0003367 Abnormal femoral neck morphology An abnormality of the femoral neck (which is the process of bone, connecting the femoral head with the femoral shaft). HPO:probinson Abnormal neck of thigh bone ORCID:0000-0001-5208-3432 An abnormality of the femoral head. UMLS:C4025620 Abnormal head of thigh bone Abnormality of the femoral head human_phenotype HP:0003368 Abnormal femoral head morphology An abnormality of the femoral head. HPO:probinson Abnormal head of thigh bone ORCID:0000-0001-5208-3432 An abnormal enlargement of the proximal epiphysis of the femur. UMLS:C1859697 Enlarged capital femoral epiphyses Enlarged end part of innermost thighbone human_phenotype HP:0003371 Enlargement of the proximal femoral epiphysis An abnormal enlargement of the proximal epiphysis of the femur. HPO:probinson Enlarged end part of innermost thighbone ORCID:0000-0001-5208-3432 SNOMEDCT_US:165624002 UMLS:C0151900 human_phenotype HP:0003452 Increased serum iron Increased concentration of long-chain fatty acids in the blood circulation. HP:0008333 HP:0045016 UMLS:C1859241 Elevated long chain fatty acids Elevated serum long-chain fatty acids Increased serum long-chain fatty acids human_phenotype HP:0003455 This feature can be measured in plasma, as well as in cultured fibroblasts of amniocytes. Elevated circulating long chain fatty acid concentration Increased concentration of long-chain fatty acids in the blood circulation. HPO:probinson An abnormality of one or more of the vertebrae. HP:0005719 Fyler:4108 SNOMEDCT_US:205043005 SNOMEDCT_US:74877002 UMLS:C0158775 UMLS:C4020839 UMLS:C4020840 Abnormal vertebrae Abnormality of the vertebrae Vertebral anomalies human_phenotype Abnormal vertebral bodies Multiple vertebral anomalies HP:0003468 A vertebra is one of 33 bony segments that form the spinal column of humans. There are 7 cervical, 12 thoracic, 5 lumbar, 5 sacral and 4 coccygeal vertebrae (the coccygeal vertebrae are fused into one coccyx bone). Abnormal vertebral morphology An abnormality of one or more of the vertebrae. HPO:probinson Multiple vertebral anomalies HPO:skoehler A kind of short stature in which different regions of the body are shortened to differing extents. HP:0008895 HP:0008900 UMLS:C0878659 UMLS:C1846797 Short stature, disproportionate human_phenotype Short stature, severe disproportionate HP:0003498 Disproportionate short stature A kind of short stature in which different regions of the body are shortened to differing extents. HPO:probinson Short stature, severe disproportionate HPO:skoehler A type of disproportionate short stature characterized by a short trunk but a average-sized limbs. HP:0001524 HP:0003500 HP:0008923 UMLS:C1846435 Disproportionate short-trunked dwarfism Disproportionate short-trunked short stature Short-trunked dwarfism human_phenotype HP:0003521 Disproportionate short-trunk short stature A type of disproportionate short stature characterized by a short trunk but a average-sized limbs. HPO:probinson Disproportionate short-trunked dwarfism Disproportionate short-trunked short stature Short-trunked dwarfism A reduction in methionine synthase activity. UMLS:C1848580 Decreased activity of methionine synthase Methionine synthase activity decreased Methionine synthase deficiency Reduced methionine synthase activity human_phenotype HP:0003524 Cobalamin-dependent methionine synthase catalyzes the transfer of a methyl group from N5-methyltetrahydrofolate to homocysteine, producing tetrahydrofolate and methionine, i.e., (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine. Decreased methionine synthase activity A reduction in methionine synthase activity. HPO:probins An increased concentration of ornithine in the urine. UMLS:C4025602 human_phenotype HP:0003532 Ornithinuria An increased concentration of ornithine in the urine. HPO:probinson Any abnormality of the soft tissues, including both connective tissue (tendons, ligaments, fascia, fibrous tissues, and fat). UMLS:C4025596 human_phenotype HP:0003549 Abnormality of connective tissue Any abnormality of the soft tissues, including both connective tissue (tendons, ligaments, fascia, fibrous tissues, and fat). HPO:curators A decreased concentration of citrulline in the blood. UMLS:C1839532 human_phenotype HP:0003572 Low plasma citrulline A decreased concentration of citrulline in the blood. HPO:gcarletti An abnormally increased sodium concentration in the cytosol. UMLS:C4025593 High intracellular Na Increased intracellular Na+ levels human_phenotype HP:0003575 Increased intracellular sodium An abnormally increased sodium concentration in the cytosol. HPO:gcarletti Increased concentration of trimethylamine in the urine. MSH:C536561 SNOMEDCT_US:237959005 UMLS:C0342739 High urine trimethylamine levels human_phenotype HP:0003614 Increased concentration of trimethylamine, an organic amino compound with an oder characterized as that of rotting fish, in the urine. Trimethylaminuria is generally caused by impaired oxidation of trimethylamine into the odorless compound trimethylamine N-oxide. Trimethylaminuria Increased concentration of trimethylamine in the urine. HPO:probinson High urine trimethylamine levels ORCID:0000-0001-5208-3432 Loss (disappearance) of previously present subcutaneous fat tissue in arm or leg. HP:0003757 UMLS:C1837764 Loss of fat tissue below the skin in limbs Loss of subcutaneous adipose tissue from extremities human_phenotype HP:0003635 Loss of subcutaneous adipose tissue in limbs Loss (disappearance) of previously present subcutaneous fat tissue in arm or leg. HPO:probinson Loss of fat tissue below the skin in limbs ORCID:0000-0001-5208-3432 A decreased concentration of methionine in the blood. UMLS:C1848555 Decreased plasma methionine Decreased serum methionine human_phenotype HP:0003658 Normal methionine blood levels are around 30 micromole per liter. Hypomethioninemia A decreased concentration of methionine in the blood. HPO:gcarletti Decreased plasma methionine Decreased serum methionine Absence of the epiphysis located at the proximal end of the distal phalanx of the 5th finger. peter 2008-12-22T01:37:43Z UMLS:C4025577 Absent end part of the outermost bone of the little finger Absent end part of the outermost bone of the pinkie finger Absent end part of the outermost bone of the pinky finger human_phenotype HP:0003696 Absent epiphysis of the distal phalanx of the 5th finger Absence of the epiphysis located at the proximal end of the distal phalanx of the 5th finger. HPO:curators Absent end part of the outermost bone of the little finger ORCID:0000-0001-5208-3432 Absent end part of the outermost bone of the pinkie finger ORCID:0000-0001-5208-3432 Absent end part of the outermost bone of the pinky finger ORCID:0000-0001-5208-3432 Hypertrophy (increase in size) of muscle cells (as opposed to hyperplasia, which refers to an increase in the number of muscle cells). UMLS:C2265792 Hypertrophic muscles Increased skeletal muscle cells Muscle hypertrophy Muscular hypertrophy human_phenotype HP:0003712 Increased muscle bulk based on clinical observation. Skeletal muscle hypertrophy Hypertrophy (increase in size) of muscle cells (as opposed to hyperplasia, which refers to an increase in the number of muscle cells). HPO:curators Increased skeletal muscle cells ORCID:0000-0001-5208-3432 UMLS:C1859442 Minimal fat below the skin human_phenotype HP:0003717 Minimal subcutaneous fat Minimal fat below the skin ORCID:0000-0001-5208-3432 Muscle hypertrophy affecting the thighs. UMLS:C1846674 Increased thigh size human_phenotype HP:0003733 Proximal lower limb hypertrophy Thigh hypertrophy Muscle hypertrophy affecting the thighs. HPO:probinson Increased thigh size ORCID:0000-0001-5208-3432 A reduced amount of fat tissue in the lowest layer of the integument. This feature can be appreciated by a reduced skinfold thickness. HP:0001002 HP:0007409 SNOMEDCT_US:248316006 UMLS:C0424631 UMLS:C1857657 Decreased subcutaneous adipose tissue Decreased subcutaneous fat Reduced fat tissue below the skin Reduced subcutaneous fat Scanty adipose tissue human_phenotype HP:0003758 Reduced subcutaneous adipose tissue Reduced fat tissue below the skin ORCID:0000-0001-5208-3432 Congenital underdevelopment of lymph vessels. UMLS:C4025570 Underdeveloped lymphatic vessels human_phenotype HP:0003759 This feature can be demonstrated by lymphography. Hypoplasia of lymphatic vessels Congenital underdevelopment of lymph vessels. HPO:probinson Underdeveloped lymphatic vessels ORCID:0000-0001-5208-3432 A nevus is a type of hamartoma that is a circumscribed stable malformation of the skin. MSH:D009506 MSH:D009508 SNOMEDCT_US:21119008 SNOMEDCT_US:400096001 SNOMEDCT_US:51697005 UMLS:C0027960 UMLS:C0027962 Mole Naevus human_phenotype Naevi Nevi HP:0003764 The word Nevus derives from the Latin word Knee-vus meaning birthmark or mole. Nevus A nevus is a type of hamartoma that is a circumscribed stable malformation of the skin. HPO:probinson Mole ORCID:0000-0001-6908-9849 Developmental hypoplasia (shortening) of middle phalanx of toe. UMLS:C4021723 Short middle bones (feet) Short middle phalanges of toes human_phenotype HP:0003795 Short middle phalanx of toe Developmental hypoplasia (shortening) of middle phalanx of toe. HPO:probinson Short middle bones (feet) ORCID:0000-0001-5208-3432 HP:0003845 UMLS:C4021722 Abnormal shape of end part of upper limb long bones Abnormality involving the epiphyses of the upper limbs Epihyseal plate abnormality of the upper limbs human_phenotype HP:0003839 Abnormality of upper limb epiphysis morphology Abnormal shape of end part of upper limb long bones ORCID:0000-0001-5208-3432 A delay in the process of formation and maturation of the epiphysis of one or more long bones of the upper limbs. UMLS:C4025560 UMLS:C4280544 human_phenotype Delayed maturation fo the end part of the upper limb bone HP:0003840 Delayed upper limb epiphyseal ossification A delay in the process of formation and maturation of the epiphysis of one or more long bones of the upper limbs. HPO:probinson Delayed maturation fo the end part of the upper limb bone ORCID:0000-0001-5208-3432 UMLS:C4025556 Small end part of upper limb bones human_phenotype HP:0003844 Small epiphyses of the upper limbs Small end part of upper limb bones ORCID:0000-0001-5208-3432 An elevation in bone density in one or more diaphyses of the arms. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4025547 Increased bone density in central part of long bone of upper limbs human_phenotype HP:0003860 Diaphyseal sclerosis of the upper limbs An elevation in bone density in one or more diaphyses of the arms. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in central part of long bone of upper limbs ORCID:0000-0001-5208-3432 Clefting affecting the humerus. UMLS:C4025545 Notched long bone in upper arm human_phenotype HP:0003864 Bifid humerus Clefting affecting the humerus. HPO:curators Notched long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4025539 Deformed long bone in upper arm human_phenotype HP:0003871 Deformed humerus Deformed long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4021716 Increased bone density in long bone of upper arm Sclerosis of humerus human_phenotype HP:0003881 Humeral sclerosis Increased bone density in long bone of upper arm ORCID:0000-0001-5208-3432 UMLS:C4025530 Triangular long bone of upper arm human_phenotype HP:0003884 Triangular humerus Triangular long bone of upper arm ORCID:0000-0001-5208-3432 An anomaly of the humeral epiphysis. UMLS:C4021714 Abnormality of end part of the long bone of the upper arm Abnormality of the humeral epiphyses human_phenotype HP:0003891 Abnormality of the humeral epiphysis An anomaly of the humeral epiphysis. HPO:probinson Abnormality of end part of the long bone of the upper arm ORCID:0000-0001-5208-3432 Lack of formation of bone in the epiphysis of the humerus. UMLS:C4021713 Absent maturation of end part of long bone in upper arm Absent ossification of the humeral epiphyses human_phenotype HP:0003892 Normally, the proximal humeral epiphysis can be visualized at about 40 weeks of gestation. Absent humeral epiphyseal ossification Lack of formation of bone in the epiphysis of the humerus. HPO:probinson Absent maturation of end part of long bone in upper arm ORCID:0000-0001-5208-3432 A delay in the process of formation and maturation of the humeral epiphysis. UMLS:C4021712 UMLS:C4280543 Delayed maturation/delayed ossification of the humeral epiphyses human_phenotype Delayed maturation of the end part of the long bone in upper arm HP:0003894 Delayed humeral epiphyseal ossification A delay in the process of formation and maturation of the humeral epiphysis. HPO:probinson Delayed maturation of the end part of the long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4025523 UMLS:C4280542 human_phenotype Irregular maturation of the end part of the long bone in upper arm HP:0003897 Irregular ossification of the humeral epiphyses Irregular maturation of the end part of the long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4025522 Large end part of long bone in upper arm human_phenotype HP:0003898 Large humeral epiphyses Large end part of long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4025520 Small end part of long bone in upper arm human_phenotype HP:0003900 Small humeral epiphyses Small end part of long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4025517 Abnormality of the wide portion of the long bone in upper arm human_phenotype HP:0003907 Abnormality of the humeral metaphyses Abnormality of the wide portion of the long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4025513 Irregular bone maturation of the wide portion of the long bone in upper arm human_phenotype HP:0003914 Irregular ossification of humeral metaphyses Irregular bone maturation of the wide portion of the long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4025509 Hardening of wide portion of long bone of upper arm Stiffening of wide portion of long bone of upper arm human_phenotype HP:0003918 Sclerotic humeral metaphysis Hardening of wide portion of long bone of upper arm ORCID:0000-0001-5208-3432 Stiffening of wide portion of long bone of upper arm ORCID:0000-0001-5208-3432 An anomaly of the humeral diaphysis. UMLS:C4025502 Abnormality of shaft of long bone in upper arm human_phenotype HP:0003926 Abnormality of the humeral diaphysis An anomaly of the humeral diaphysis. HPO:probinson Abnormality of shaft of long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4025496 Increased bone density in shaft of long bone in upper arm human_phenotype HP:0003933 Sclerosis of humeral diaphysis Increased bone density in shaft of long bone in upper arm ORCID:0000-0001-5208-3432 UMLS:C4025491 Abnormality of the joint spaces of the elbow human_phenotype HP:0003943 Abnormality of the joint spaces of the elbow Abnormality of the joint spaces of the elbow UMLS:C4025488 Abnormality of end part of the elbow bone human_phenotype HP:0003946 Abnormality of the epiphyses of the elbow Abnormality of end part of the elbow bone ORCID:0000-0001-5208-3432 A delay in the process of formation and maturation of the epiphysis of one or more long bones that are part of the elbow. UMLS:C4025487 Delayed maturation of the end part of the elbow bone human_phenotype HP:0003947 Delayed elbow epiphyseal ossification A delay in the process of formation and maturation of the epiphysis of one or more long bones that are part of the elbow. HPO:probinson Delayed maturation of the end part of the elbow bone ORCID:0000-0001-5208-3432 UMLS:C4025485 Abnormal wide portion of elbow bone human_phenotype HP:0003949 Abnormality of the elbow metaphyses Abnormal wide portion of elbow bone ORCID:0000-0001-5208-3432 Absence of one or more forearm bones associated with congenital failure of development. UMLS:C4021701 Absent forearm bone Aplasia of the forearm bones human_phenotype HP:0003953 Absent forearm bone Absence of one or more forearm bones associated with congenital failure of development. HPO:probinson Absent forearm bone UMLS:C4025479 Deformed forearm bones human_phenotype HP:0003959 Deformed forearm bones Deformed forearm bones UMLS:C4025472 Increased bone density of forearm bones human_phenotype HP:0003967 Sclerotic forearm bones Increased bone density of forearm bones ORCID:0000-0001-5208-3432 The total absence of the hand, with no bony elements distal to the radius or ulna. SNOMEDCT_US:371199008 UMLS:C0265594 Absent hand Acheiria human_phenotype HP:0004050 Absent hand The total absence of the hand, with no bony elements distal to the radius or ulna. PMID:19125433 Absent hand Ossification of hand bones is less advanced than would be expected according to age-adjusted norms. UMLS:C4020833 UMLS:C4021686 Delay maturation/delayed ossification of the hand human_phenotype Delayed maturation of the hand bones HP:0004052 Delayed ossification of the hand bones Ossification of hand bones is less advanced than would be expected according to age-adjusted norms. HPO:probinson Delayed maturation of the hand bones Osteosclerosis affecting one or more bones of the hand. HP:0004055 UMLS:C4021684 Generalized sclerosis of hand bones Hand bone sclerosis Increased bone density in hand bone Increased bone density in hand bones human_phenotype HP:0004054 Sclerosis of hand bone Osteosclerosis affecting one or more bones of the hand. HPO:probinson Increased bone density in hand bone ORCID:0000-0001-5208-3432 Deviated fingers is a term that should be used if one or more fingers of the hand are deviated from their normal position, either to the radial or ulnar side. A deviation of a finger can be caused by an abnormal form of one or more of the phalanges of the affected finger, or by a deviation or displacement of one or more phalanges. HP:0006229 SNOMEDCT_US:203556007 SNOMEDCT_US:26517000 UMLS:C0410740 Atypical position of finger Deviated fingers Finger pointing in a different direction than usual human_phenotype HP:0004097 Deviation of finger Deviated fingers is a term that should be used if one or more fingers of the hand are deviated from their normal position, either to the radial or ulnar side. A deviation of a finger can be caused by an abnormal form of one or more of the phalanges of the affected finger, or by a deviation or displacement of one or more phalanges. HPO:curators Atypical position of finger https://orcid.org/0000-0002-6548-5200 Finger pointing in a different direction than usual Significant increase in the length and girth of most or all of a digit compared to its contralateral digit (if unaffected) or compared to what would be expected for age/body build. The increased girth is accompanied by an increase in the dorso-ventral dimension AND the lateral dimension of the digit. MEDDRA:10025386 MSH:C562546 SNOMEDCT_US:48449000 UMLS:C0265552 Finger overgrowth Megalodactyly human_phenotype HP:0004099 There are no recognized standards for the girth of digits and this finding can vary substantially in the population. This assessment relies on the judgment of the examiner to recognize when the difference between the expected and the observed is significant. The affected digits should be specified. The definition does not mandate the component of the increased size (bone, connective tissue, etc.), but should exclude edema. The requirement that the girth is most, or all, of the digit is intended to distinguish this from broad fingertips. This should be distinguished from Broad fingers or Broad fingertips as the girth is circumferential in macrodactyly, which is not the case for broad fingers or broad fingertips, which are increased only (or predominantly) in their lateral (A/P) width. Macrodactyly Significant increase in the length and girth of most or all of a digit compared to its contralateral digit (if unaffected) or compared to what would be expected for age/body build. The increased girth is accompanied by an increase in the dorso-ventral dimension AND the lateral dimension of the digit. PMID:19125433 MEDDRA:10025386 Macrodactyly Finger overgrowth HPO:sdoelken This term groups together three conditions that presumably represent different degrees of severity of a midline defect of the nose or nasal tip. peter 2009-01-21T04:59:54Z HP:0003190 UMLS:C4025411 UMLS:C4280539 Central defect of nose Central nasal defect Midline defect of the nose Midline nasal defect human_phenotype Central cleft of nose Midline cleft of nose HP:0004122 Midline defect of the nose This term groups together three conditions that presumably represent different degrees of severity of a midline defect of the nose or nasal tip. HPO:sdoelken Central defect of nose ORCID:0000-0001-5889-4463 Central nasal defect ORCID:0000-0001-5889-4463 Midline defect of the nose Midline nasal defect ORCID:0000-0001-5889-4463 Central cleft of nose ORCID:0000-0001-5889-4463 Midline cleft of nose ORCID:0000-0001-5889-4463 An abnormality affecting one or both 5th fingers. UMLS:C4021678 Abnormality of the 5th finger Abnormality of the little finger Abnormality of the pinkie finger Abnormality of the pinky finger human_phenotype HP:0004207 Abnormal 5th finger morphology An abnormality affecting one or both 5th fingers. HPO:sdoelken Abnormality of the little finger Abnormality of the pinkie finger ORCID:0000-0001-5208-3432 Abnormality of the pinky finger ORCID:0000-0001-5208-3432 Abnormality of the phalanges of the 5th (little) finger. UMLS:C4025408 Abnormality of the little finger bone Abnormality of the phalanges of the 5th finger Abnormality of the pinkie finger bone Abnormality of the pinky finger bone human_phenotype HP:0004213 Abnormal 5th finger phalanx morphology Abnormality of the phalanges of the 5th (little) finger. HPO:sdoelken Abnormality of the little finger bone ORCID:0000-0001-5208-3432 Abnormality of the pinkie finger bone ORCID:0000-0001-5208-3432 Abnormality of the pinky finger bone ORCID:0000-0001-5208-3432 UMLS:C4025406 Abnormality of the middle bone of little finger Abnormality of the middle bone of pinkie finger Abnormality of the middle bone of pinky finger human_phenotype HP:0004219 Abnormality of the middle phalanx of the 5th finger Abnormality of the middle bone of little finger ORCID:0000-0001-5208-3432 Abnormality of the middle bone of pinkie finger ORCID:0000-0001-6908-9849 Abnormality of the middle bone of pinky finger ORCID:0000-0001-5208-3432 Hypoplastic/small middle phalanx of the fifth finger. HP:0001243 HP:0003069 HP:0004221 HP:0005649 HP:0005706 HP:0005734 HP:0005813 UMLS:C1834060 5th finger middle phalangeal hypoplasia Brachymesophalangism V Fifth finger mid-phalanx hypoplasia Hypoplastic fifth finger middle phalanx Hypoplastic middle phalanx of the 5th finger Hypoplastic/small middle phalanx of the 5th finger Hypoplastic/small middle phalanx of the little finger Short middle bone of the little finger Short middle bone of the pinkie finger Short middle bone of the pinky finger Short middle phalanx of the little finger Type A3 brachydactyly human_phenotype HP:0004220 Brachymesophalangia-V, a short and broad middle phalanx of the fifth digit, is the most common of all skeletal anomalies of the hand. When this feature appears alone, it is clinically known as brachydactyly type A3 (BDA3). Short middle phalanx of the 5th finger Hypoplastic/small middle phalanx of the fifth finger. HPO:skoehler PMID:18494372 Short middle bone of the little finger ORCID:0000-0001-5208-3432 Short middle bone of the pinkie finger ORCID:0000-0001-5208-3432 Short middle bone of the pinky finger ORCID:0000-0001-5208-3432 Abnormality of the epiphysis of the middle phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. UMLS:C4025405 Abnormality of the end part of middle little finger bone Abnormality of the end part of middle pinkie finger bone Abnormality of the end part of middle pinky finger bone human_phenotype HP:0004224 Abnormality of the epiphysis of the middle phalanx of the 5th finger Abnormality of the epiphysis of the middle phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. HPO:curators Abnormality of the end part of middle little finger bone ORCID:0000-0001-5208-3432 Abnormality of the end part of middle pinkie finger bone ORCID:0000-0001-5208-3432 Abnormality of the end part of middle pinky finger bone ORCID:0000-0001-5208-3432 Abnormality of the distal phalanx of the 5th (little) finger. UMLS:C4021673 Abnormality of the distal phalanx of the little finger Abnormality of the outermost little finger bone Abnormality of the outermost pinkie finger bone Abnormality of the outermost pinky finger bone Abnormality of the terminal phalanx of the little finger human_phenotype HP:0004225 Abnormality of the distal phalanx of the 5th finger Abnormality of the distal phalanx of the 5th (little) finger. HPO:curators Abnormality of the outermost little finger bone ORCID:0000-0001-5208-3432 Abnormality of the outermost pinkie finger bone ORCID:0000-0001-5208-3432 Abnormality of the outermost pinky finger bone ORCID:0000-0001-5208-3432 Hypoplastic/small distal phalanx of the fifth finger. HP:0006171 UMLS:C1836674 Brachytelophalangism V Fifth digit distal phalangeal hypoplasia Hypoplastic/small terminal phalanx of the little finger Short distal phalanx of the fifth finger Short outermost little finger bone Short outermost pinkie finger bone Short outermost pinky finger bone human_phenotype HP:0004227 Short distal phalanx of the 5th finger Hypoplastic/small distal phalanx of the fifth finger. HPO:sdoelken Short outermost little finger bone ORCID:0000-0001-5208-3432 Short outermost pinkie finger bone ORCID:0000-0001-5208-3432 Short outermost pinky finger bone ORCID:0000-0001-5208-3432 The presence of more than the normal number of carpal bones. Extra wrist bones SNOMEDCT_US:20136007 SNOMEDCT_US:9181003 UMLS:C0265609 Supernumerary carpal bones human_phenotype HP:0004232 Accessory carpal bones The presence of more than the normal number of carpal bones. HPO:curators Extra wrist bones ORCID:0000-0001-5208-3432 Increased size of carpal bones. Large wrist bones UMLS:C4021671 Large carpals human_phenotype HP:0004237 Large carpal bones Increased size of carpal bones. HPO:probinson Large wrist bones ORCID:0000-0001-5208-3432 UMLS:C4025376 UMLS:C4280534 human_phenotype Deficient maturation of hand bones HP:0004274 Deficient ossification of hand bones Deficient maturation of hand bones ORCID:0000-0001-5208-3432 UMLS:C3276746 Duplication of hand bones human_phenotype HP:0004275 Duplication of hand bones Duplication of hand bones UMLS:C4025374 human_phenotype Irregular maturation of hand bones HP:0004280 Irregular ossification of hand bones Irregular maturation of hand bones ORCID:0000-0001-5208-3432 UMLS:C4025373 human_phenotype HP:0004281 Irregular sclerosis of hand bones UMLS:C4025368 human_phenotype HP:0004288 Pseudoepiphyses of hand bones An abnormality of the gastric mucous membrane. peter 2008-02-20T11:12:00Z UMLS:C4025362 Abnormality of the mucous membrane layer of stomach human_phenotype HP:0004295 Abnormality of the gastric mucosa An abnormality of the gastric mucous membrane. HPO:probinson Abnormality of the mucous membrane layer of stomach ORCID:0000-0001-5208-3432 peter 2008-02-20T11:24:00Z UMLS:C4025361 Abnormality of GI blood vessels Abnormality of GI vasculature human_phenotype HP:0004296 Abnormality of gastrointestinal vasculature Abnormality of GI blood vessels ORCID:0000-0001-5208-3432 Abnormality of GI vasculature An abnormality of the biliary system. peter 2008-02-20T11:34:00Z UMLS:C0940767 human_phenotype HP:0004297 Abnormality of the biliary system An abnormality of the biliary system. HPO:probinson The presence of any abnormality affecting the abdominal wall. peter 2008-02-20T11:40:00Z HP:0001462 UMLS:C4021664 Abnormality of external features of the abdomen Abnormality of the abdominal wall human_phenotype HP:0004298 Abnormality of the abdominal wall The presence of any abnormality affecting the abdominal wall. HPO:probinson Abnormality of the abdominal wall Any abnormality of the skeletal muscle cell. Muscle fibers are subdivided into two types. Type I fibers are fatigue-resistant and rich in oxidative enzymes (they stain light with the myosin ATPase reaction), and type II fibers are fast-contracting, fatigue-prone, and rich in glycolytic enzymes (these fibers stain darkly). Normal muscle tissue has a random distribution of type I and type II fibers. peter 2008-02-20T12:04:00Z HP:0003706 HP:0011806 UMLS:C4021663 Abnormal muscle fibre morphology Abnormal skeletal muscle fiber morphology Abnormality of muscle fibers human_phenotype HP:0004303 Normal human muscle is composed of many individual muscle fibers bundled together by layers of connective tissue that are arranged in a nesting-doll like fashion. The inner most structure, the single muscle fiber, is covered by a thin layer of primarily reticular fibers called the endomysium. The endomysium is quite inconspicuous and muscle fibers appear to be in direct contact with each other. The finest capillaries, nerve twigs and lymphatic capillaries are found within the endomysium. Groups of muscle fibers are bound together by the thicker perimysium, forming structures called fascicles. Capillaries, nerve fibers and lymphatic vessels also track in the perimyseum. Bundles of fascicles are encased within the dense irregular connective tissue of the epimysium. These connective tissue layers provide mechanical protection for the muscle fibers and increase the tensile strength of the muscle. The layers are continuous with the tendon, which provides attachment to bone. Individual muscle fibers are syncytia, formed by embryonic fusion of many myoblasts or later, myosatellite cells. Each muscle fiber contains many nuclei, peripherally positioned immediately adjacent to the sarcolemmal membrane. In healthy muscle only 3-5 percent of fibers contain nuclei that are located internally, within the cell, but many disease processes lead to internal nuclei. Each nucleus provides a segment of the cell with needed translated protein products. Abnormal muscle fiber morphology Any abnormality of the skeletal muscle cell. Muscle fibers are subdivided into two types. Type I fibers are fatigue-resistant and rich in oxidative enzymes (they stain light with the myosin ATPase reaction), and type II fibers are fast-contracting, fatigue-prone, and rich in glycolytic enzymes (these fibers stain darkly). Normal muscle tissue has a random distribution of type I and type II fibers. HPO:probinson PMID:22938878 Abnormal muscle fibre morphology An abnormality of the endocardium. peter 2008-02-20T01:23:00Z HP:0005260 UMLS:C4021662 Abnormality of the endocardium Abnormality of the endomycoardium human_phenotype HP:0004306 Abnormal endocardium morphology An abnormality of the endocardium. HPO:probinson Thickening of the left ventricle wall with congenital onset. peter 2008-02-20T01:23:00Z UMLS:C4025359 human_phenotype HP:0004307 Abnormal anatomic location of the heart Thickening of the left ventricle wall with congenital onset. PMID:154915 A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms). peter 2008-02-27T03:19:00Z HP:0001509 HP:0003501 HP:0003507 HP:0003512 HP:0003518 HP:0003519 HP:0008871 HP:0008882 HP:0008888 HP:0008913 SNOMEDCT_US:237836003 UMLS:C0349588 Decreased body height Height less than 3rd percentile Short stature Small stature Stature below 3rd percentile human_phenotype HP:0004322 Short stature A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms). HPO:curators Decreased body height Short stature Small stature An abnormal increase or decrease of weight or an abnormal distribution of mass in the body. peter 2008-02-27T03:21:00Z HP:0010718 UMLS:C0878621 UMLS:C4025357 Abnormality of body weight human_phenotype Abnormality of habitus HP:0004323 Abnormality of body weight An abnormal increase or decrease of weight or an abnormal distribution of mass in the body. HPO:probinson Abnormality of body weight Abnormally increased body weight. peter 2008-02-27T03:21:00Z HP:0045083 MSH:D015430 SNOMEDCT_US:161831008 SNOMEDCT_US:262286000 SNOMEDCT_US:8943002 UMLS:C0043094 Increased body weight human_phenotype Weight gain HP:0004324 Increased body weight Increased body weight Weight gain Abnormally low body weight. peter 2008-02-27T03:22:00Z HP:0001823 HP:0001826 MSH:D013851 MSH:D015431 SNOMEDCT_US:161832001 SNOMEDCT_US:248342006 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C0041667 UMLS:C1262477 UMLS:C1844806 Decreased body weight Decreased weight Low body weight Low weight Weight less than 3rd percentile human_phenotype HP:0004325 Decreased body weight Decreased body weight Decreased weight Low body weight Low weight Weight less than 3rd percentile Severe weight loss, wasting of muscle, loss of appetite, and general debility related to a chronic disease. peter 2008-02-27T03:23:00Z MSH:D002100 SNOMEDCT_US:238108007 SNOMEDCT_US:285384003 UMLS:C0006625 Wasting syndrome human_phenotype HP:0004326 Cachexia Severe weight loss, wasting of muscle, loss of appetite, and general debility related to a chronic disease. HPO:probinson Wasting syndrome ORCID:0000-0001-5208-3432 Any structural anomaly of the vitreous body. peter 2008-02-27T04:20:00Z UMLS:C4025356 Abnormal vitreous humour morphology human_phenotype HP:0004327 The vitreous humor is the clear gel that fills the space between the lens and the retina. Abnormal vitreous humor morphology Any structural anomaly of the vitreous body. HPO:probinson Abnormal vitreous humour morphology An abnormality of the anterior segment of the eyeball (which comprises the structures in front of the vitreous humour: the cornea, iris, ciliary body, and lens). peter 2008-02-27T04:23:00Z UMLS:C4025355 Abnormal anterior segment morphology Abnormality of the anterior segment of the eye Abnormality of the anterior segment of the eyeball Abnormality of the anterior segment of the globe human_phenotype HP:0004328 The anterior segment comprises the structures in front of the vitreous humour: the cornea, iris, ciliary body, and lens. Abnormal anterior eye segment morphology An abnormality of the anterior segment of the eyeball (which comprises the structures in front of the vitreous humour: the cornea, iris, ciliary body, and lens). HPO:probinson peter 2008-02-27T04:25:00Z UMLS:C4025354 Abnormal morphology of the posterior segment of the globe Abnormality of the posterior segment of the eye Abnormality of the posterior segment of the eyeball Abnormality of the posterior segment of the globe human_phenotype HP:0004329 The posterior segment comprises the anterior hyaloid membrane and all of the optical structures behind it: the vitreous humor, retina, choroid, and optic nerve. Abnormal posterior eye segment morphology An increase in the magnitude or amount of ossification of the skull. peter 2008-02-28T11:54:00Z SNOMEDCT_US:17401000119104 UMLS:C0020496 UMLS:C4072850 UMLS:C4072851 Hyperossification of skull Hyperostosis of skull Sclerosis of bones of skull Sclerosis of skull human_phenotype Increased Mineralization of skull Increased calcification of skull HP:0004330 Increased skull ossification An increase in the magnitude or amount of ossification of the skull. HPO:probinson Hyperossification of skull ORCID:0000-0001-5889-4463 Hyperostosis of skull ORCID:0000-0001-5889-4463 Sclerosis of bones of skull ORCID:0000-0001-5889-4463 Sclerosis of skull ORCID:0000-0001-5889-4463 Increased Mineralization of skull ORCID:0000-0001-5889-4463 Increased calcification of skull ORCID:0000-0001-5889-4463 A reduction in the magnitude or amount of ossification of the skull. peter 2008-02-28T11:54:00Z HP:0003780 SNOMEDCT_US:253980008 UMLS:C0432073 UMLS:C4280533 Decreased bone formation of skull Deficient skull ossification Hypoossification of skull Ossification defect of skull Poorly mineralized skull Poorly ossified skull Poorly ossified skull bones human_phenotype Decreased calcification of skull Decreased mineralization of skull HP:0004331 Decreased skull ossification A reduction in the magnitude or amount of ossification of the skull. HPO:probinson Decreased bone formation of skull https://orcid.org/0000-0002-6548-5200 Hypoossification of skull ORCID:0000-0001-5889-4463 Ossification defect of skull ORCID:0000-0001-5889-4463 Poorly ossified skull ORCID:0000-0001-5889-4463 Decreased calcification of skull ORCID:0000-0001-5889-4463 Decreased mineralization of skull ORCID:0000-0001-5889-4463 Abnormality of an amino acid metabolic process. peter 2008-03-08T07:53:00Z UMLS:C1328440 human_phenotype Amino acid levels abnormal HP:0004337 Abnormality of amino acid metabolism Abnormality of an amino acid metabolic process. HPO:probinson Any deviation from the normal concentration of a aromatic amino acid in the blood circulation. peter 2008-03-08T07:55:00Z UMLS:C4025352 Abnormality of aromatic amino acid family metabolism human_phenotype HP:0004338 Abnormal circulating aromatic amino acid concentration Any deviation from the normal concentration of a aromatic amino acid in the blood circulation. HPO:probinson Any deviation from the normal concentration of a sulfur amino acid in the blood circulation. peter 2008-03-08T08:01:00Z UMLS:C4021660 Abnormal circulating sulphur amino acid concentration Abnormality of sulfur-containing amino acids human_phenotype HP:0004339 Cysteine and methionine contain a sulfur atom. Abnormal circulating sulfur amino acid concentration Any deviation from the normal concentration of a sulfur amino acid in the blood circulation. HPO:gcarletti Abnormal circulating sulphur amino acid concentration peter 2008-03-08T08:08:00Z UMLS:C4021659 Abnormality of B-vitamin metabolism human_phenotype HP:0004340 Abnormality of vitamin B metabolism peter 2008-03-08T08:09:00Z UMLS:C4021658 Abnormality of the vitamin B12 metabolism human_phenotype HP:0004341 Abnormality of vitamin B12 metabolism This term applies to all changes in bone mineral density which (depending on severity) can be seen on x-rays as a change in density and or structure of the bone. Changes may affect all bones of the organism, just certain bones or only parts of bones and include decreased mineralisation as may be seen in osteoporosis or increased mineralisation and or ossification as in osteopetrosis, exostoses or any kind of atopic calicfications of different origin and distribution. The overall amount of mineralization of the bone-organ can be measured as the amount of matter per cubic centimeter of bones, usually measured by densitometry of the lumbar spine or hip. The measurements are usually reported as g/cm3 or as a Z-score (the number of standard deviations above or below the mean for the patient's age and sex). Note that measurement with this method does not reflect local changes in other bones, and as such might not be correct with regard the hole bone-organ. peter 2008-03-11T08:10:00Z UMLS:C4021657 Abnormality of bone mineralisation and ossification human_phenotype HP:0004348 Abnormality of bone mineral density This term applies to all changes in bone mineral density which (depending on severity) can be seen on x-rays as a change in density and or structure of the bone. Changes may affect all bones of the organism, just certain bones or only parts of bones and include decreased mineralisation as may be seen in osteoporosis or increased mineralisation and or ossification as in osteopetrosis, exostoses or any kind of atopic calicfications of different origin and distribution. The overall amount of mineralization of the bone-organ can be measured as the amount of matter per cubic centimeter of bones, usually measured by densitometry of the lumbar spine or hip. The measurements are usually reported as g/cm3 or as a Z-score (the number of standard deviations above or below the mean for the patient's age and sex). Note that measurement with this method does not reflect local changes in other bones, and as such might not be correct with regard the hole bone-organ. HPO:probinson A reduction of bone mineral density, that is, of the amount of matter per cubic centimeter of bones. peter 2008-03-11T08:10:00Z UMLS:C2674432 Decreased bone mineral density Decreased bone mineral density Z score Low solidness and mass of the bones human_phenotype HP:0004349 Reduced bone mineral density A reduction of bone mineral density, that is, of the amount of matter per cubic centimeter of bones. HPO:sdoelken Decreased bone mineral density HPO:skoehler Low solidness and mass of the bones https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 Any deviation from the normal concentration of a purine in the blood circulation. peter 2008-03-17T01:04:00Z UMLS:C4025346 Abnormal circulating purine level HP:0004352 Purines are nitrogenous bases including the two nucleotide bases deoxyadenosine and deoxyguanosine. Abnormal circulating purine concentration Any deviation from the normal concentration of a carboxylic acid in the blood circulation. peter 2008-03-17T01:11:00Z UMLS:C4025344 human_phenotype HP:0004354 Carboxylic acid refers to an organic compound that contains a carboxyl group (-COOH). Abnormal circulating carboxylic acid concentration Any deviation from the normal concentration of a carboxylic acid in the blood circulation. HPO:gcarletti Any deviation from the normal circulation of leucine in the blood circulation. peter 2008-03-17T03:02:00Z UMLS:C4025341 human_phenotype HP:0004357 Abnormal circulating leucine concentration Any deviation from the normal circulation of leucine in the blood circulation. HPO:probinson A deviation from the normal concentration of a fatty acid in the blood circulation. peter 2008-03-17T03:28:00Z UMLS:C4020830 UMLS:C4021656 Abnormality of fatty acid metabolism human_phenotype Fatty acids abnormal HP:0004359 A fatty acid is an aliphatic monocarboxylic acid derived from or contained in esterified form. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. R-COOH. Fatty acids are usually derived from triglycerides or phospholipids. Abnormal circulating fatty-acid concentration A deviation from the normal concentration of a fatty acid in the blood circulation. HPO:probinson An abnormality of the balance or maintenance of the balance of acids and bases in bodily fluids, resulting in an abnormal pH. peter 2008-03-17T03:35:00Z MSH:D000137 UMLS:C0001118 human_phenotype Acid base imbalance HP:0004360 Abnormality of acid-base homeostasis An abnormality of the balance or maintenance of the balance of acids and bases in bodily fluids, resulting in an abnormal pH. HPO:probinson Any deviation from the normal concentration of calcium in the blood circulation. peter 2008-03-17T04:15:00Z HP:0040077 Abnormal blood calcium concentration Abnormal blood calcium levels Abnormal circulating Ca concentration Abnormal circulating Ca2+ concentration HP:0004363 Abnormal circulating calcium concentration Any deviation from the normal concentration of calcium in the blood circulation. HPO:probinson Abnormal blood calcium concentration https://orcid.org/0000-0001-7941-2961 Abnormal blood calcium levels ORCID:0000-0001-5208-3432 Abnormal circulating Ca concentration https://orcid.org/0000-0001-7941-2961 Abnormal circulating Ca2+ concentration https://orcid.org/0000-0001-7941-2961 Any deviation from the normal concentration of a nitrogen compound in the blood circulation. peter 2008-03-17T04:51:00Z UMLS:C4025336 human_phenotype HP:0004364 Ammonia (NH3), one of the most clinically important nitrogen compounds in human metabolism, is a substance containing nitrogen resulting from the catabolism of protein. It is converted to the less toxic substance urea prior to excretion in urine. Abnormal circulating nitrogen compound concentration Any deviation from the normal concentration of a nitrogen compound in the blood circulation. HPO:gcarletti Abnormally elevated concentration of a purine compound. Purine compounds are aromatic heterocyclic compounds containing a purine moiety, which is formed a pyrimidine-ring ring fused to an imidazole ring. peter 2008-03-18T06:31:00Z UMLS:C4025332 Increased purine level Increased purine levels HP:0004368 Increased circulating purine concentration Increased purine levels Abnormally reduced concentration of a purine compound. Purine compounds are aromatic heterocyclic compounds containing a purine moiety, which is formed a pyrimidine-ring ring fused to an imidazole ring. peter 2008-03-18T06:32:00Z UMLS:C4025331 Decreased purine level Decreased purine levels HP:0004369 Decreased circulating purine concentration Decreased purine levels An abnormality of temperature homeostasis. peter 2008-03-18T06:34:00Z MSH:D001832 UMLS:C0005904 UMLS:C1832160 Abnormality of temperature regulation Poor temperature regulation human_phenotype Body temperature changes HP:0004370 Abnormality of temperature regulation An abnormality of temperature homeostasis. HPO:probinson Abnormality of temperature regulation Poor temperature regulation Body temperature changes Abnormality of the anal canal. peter 2008-03-18T08:11:00Z UMLS:C4025329 Abnormality of the anus human_phenotype HP:0004378 The anal canal is continuous proximally with the rectum and distally terminates with the anus. Abnormality of the anus Abnormality of the anal canal. HPO:probinson Abnormality of the anus Underdevelopment of the left side of the heart. May include atresia of the aortic or mitral orifice and hypoplasia of the ascending aorta. peter 2008-03-18T08:56:00Z MSH:D018636 SNOMEDCT_US:62067003 UMLS:C0152101 Heart left ventricle hypoplasia Left ventricular hypoplasia Underdeveloped left heart human_phenotype HP:0004383 Hypoplastic left heart syndrome is an unsatisfactory term describing lethal underdevelopment of the left ventricle (LV). It represents the more severe end of a spectrum of LV hypoplasia, mandating single-ventricle palliation or cardiac transplantation. Less severe borderline ventricular hypoplasia may instead allow various biventricular therapeutic strategies and better long-term outcomes. Hypoplastic left heart Underdevelopment of the left side of the heart. May include atresia of the aortic or mitral orifice and hypoplasia of the ascending aorta. HPO:probinson PMID:22192721 Underdeveloped left heart ORCID:0000-0001-5208-3432 Inflammation of the alimentary part of the gastrointestinal system. peter 2008-03-18T09:01:00Z UMLS:C1535950 GI inflammation Gastrointestinal inflammation human_phenotype HP:0004386 Gastrointestinal inflammation GI inflammation Gastrointestinal inflammation A colon of abnormally small caliber. peter 2008-03-18T09:02:00Z MSH:C562563 SNOMEDCT_US:18389004 UMLS:C0266200 UMLS:C3553395 human_phenotype Microcolon on contrast enema HP:0004388 Microcolon A colon of abnormally small caliber. PMID:3484569 Microcolon on contrast enema HPO:skoehler An abnormality of the pylorus. peter 2008-03-18T09:15:00Z UMLS:C4025326 human_phenotype HP:0004400 Abnormality of the pylorus An abnormality of the pylorus. HPO:probinson An abnormality of the pulmonary artery. peter 2008-03-18T09:28:00Z SNOMEDCT_US:128588008 SNOMEDCT_US:198914002 SNOMEDCT_US:36110001 UMLS:C0009681 Abnormality of lung artery human_phenotype HP:0004414 Abnormality of the pulmonary artery An abnormality of the pulmonary artery. HPO:probinson Abnormality of lung artery ORCID:0000-0001-5208-3432 The formation of a blood clot inside an artery. peter 2008-03-18T09:32:00Z SNOMEDCT_US:65198009 UMLS:C0151942 Blood clot in artery human_phenotype HP:0004420 Arterial thrombosis The formation of a blood clot inside an artery. HPO:probinson Blood clot in artery ORCID:0000-0001-6908-9849 An abnormality of the cheek- one of two bilateral soft tissue facial structures in the region of the face inferior to the eyes and between the nose and the ear. "Buccal" means relating to the cheek. The cheek is part of the midface peter 2008-03-18T09:42:00Z UMLS:C4025324 Abnormality of the cheek Abnormality of the cheeks Anomaly of the cheeks Deformity of the cheeks Malformation of the cheeks human_phenotype HP:0004426 Abnormality of the cheek Abnormality of the cheek Abnormality of the cheeks ORCID:0000-0001-5208-3432 ORCID:0000-0001-5889-4463 Anomaly of the cheeks Deformity of the cheeks ORCID:0000-0001-5889-4463 Malformation of the cheeks ORCID:0000-0001-5889-4463 Excessive growth of the bones of cranium, i.e., of the skull. peter 2008-03-18T09:57:00Z HP:0002698 Enlargement of skull bones Excessive growth of skull bones Hypertrophy of cranial bones Overgrowth of skull bones Thick skull bones UMLS:C1832451 UMLS:C4280528 UMLS:C4280529 UMLS:C4280530 UMLS:C4280531 Hyperostosis of cranial bones Hyperostosis of cranial vault Increased ossification of cranial bones human_phenotype HP:0004437 Cranial hyperostosis Excessive growth of the bones of cranium, i.e., of the skull. HPO:probinson Enlargement of skull bones ORCID:0000-0001-5889-4463 Excessive growth of skull bones ORCID:0000-0001-5889-4463 Hypertrophy of cranial bones ORCID:0000-0001-5889-4463 Overgrowth of skull bones ORCID:0000-0001-5889-4463 Thick skull bones ORCID:0000-0001-5889-4463 Hyperostosis of cranial bones ORCID:0000-0001-5889-4463 Increased ossification of cranial bones ORCID:0000-0001-5889-4463 An abnormality of the middle-ear ossicles (three small bones called malleus, incus, and stapes) that are contained within the middle ear and serve to transmit sounds from the air to the fluid-filled labyrinth (cochlea). HP:0001759 UMLS:C1836678 Malformed ossicles Ossicular malformation human_phenotype HP:0004452 Abnormality of the middle ear ossicles An abnormality of the middle-ear ossicles (three small bones called malleus, incus, and stapes) that are contained within the middle ear and serve to transmit sounds from the air to the fluid-filled labyrinth (cochlea). HPO:probinson The progressive development of an abnormally large skull. HP:0000261 UMLS:C1859896 Macrocephaly, progressive Progressively abnormally enlarging cranium Progressively abnormally enlarging skull human_phenotype HP:0004481 Progressive macrocephaly The progressive development of an abnormally large skull. HPO:probinson Progressively abnormally enlarging cranium ORCID:0000-0001-5889-4463 Progressively abnormally enlarging skull ORCID:0000-0001-5889-4463 Excessive growth of the calvaria. Enlargement of calvarial bones Excessive growth of calvarial bones Hypertrophy of calvarial bones Overgrowth of calvarial bones Thick calvarial bones MSH:C537963 UMLS:C1863351 UMLS:C4280519 UMLS:C4280520 Hyperostosis of calvarial bones Increased ossification of calvarial bones Overgrowth of skullcap human_phenotype HP:0004490 The calvaria (skull cap) is made up of the frontal, occipital, right and left parietal, right and left temporal, sphenoid, and ethmoid bones, and thus comprises the upper dome-like part of the skull and does not include the lower jaw. Calvarial hyperostosis Excessive growth of the calvaria. HPO:probinson Enlargement of calvarial bones ORCID:0000-0001-5889-4463 Excessive growth of calvarial bones ORCID:0000-0001-5889-4463 Hypertrophy of calvarial bones ORCID:0000-0001-5889-4463 Overgrowth of calvarial bones ORCID:0000-0001-5889-4463 Thick calvarial bones ORCID:0000-0001-5889-4463 Hyperostosis of calvarial bones ORCID:0000-0001-5889-4463 Increased ossification of calvarial bones ORCID:0000-0001-5889-4463 Overgrowth of skullcap ORCID:0000-0001-5889-4463 Excessive growth of the craniofacial bones. Enlargement of craniofacial bones Excessive growth of craniofacial bones Hypertrophy of craniofacial bones Overgrowth of craniofacial bones Thick craniofacial bones UMLS:C1868085 UMLS:C4280516 UMLS:C4280517 UMLS:C4280518 Excessive bone growth of the skull and face Hyperostosis of craniofacial bones Increased ossification of craniofacial bones human_phenotype HP:0004493 Craniofacial hyperostosis Excessive growth of the craniofacial bones. HPO:probinson Enlargement of craniofacial bones ORCID:0000-0001-5889-4463 Excessive growth of craniofacial bones ORCID:0000-0001-5889-4463 Hypertrophy of craniofacial bones ORCID:0000-0001-5889-4463 Overgrowth of craniofacial bones ORCID:0000-0001-5889-4463 Thick craniofacial bones ORCID:0000-0001-5889-4463 Excessive bone growth of the skull and face orcid.org/0000-0002-6548-5200 Hyperostosis of craniofacial bones ORCID:0000-0001-5889-4463 Increased ossification of craniofacial bones ORCID:0000-0001-5889-4463 Hyperplasia of the islets of Langerhans, i.e., of the regions of the pancreas that contain its endocrine cells. HP:0001736 HP:0006275 UMLS:C0597167 Hyperplastic islets of langerhans Hypertrophic pancreatic islets Islet of Langerhans hyperplasia Islets of langerhans hypertrophy Pancreatic islet-cell hypertrophy human_phenotype HP:0004510 The islets of Langerhans contain the alpha cells (producing glucagon), beta cells (insulin and amylin), delta cells (somatostatin),PP cells (pancreatic polypeptide), and the epsilon cells (ghrelin). Pancreatic islet-cell hyperplasia Hyperplasia of the islets of Langerhans, i.e., of the regions of the pancreas that contain its endocrine cells. HPO:probinson Increased bone density affecting the bones of the spine (vertebral column). UMLS:C4020828 UMLS:C4280254 UMLS:C4280513 UMLS:C4280514 UMLS:C4280515 Increased density of spinal bone Ivory spinal bone human_phenotype Compact spinal bone Concrete spinal bone Dense spinal bone Eburnation of spinal bone Sclerosis of spinal bone increased spinal bone density Z HP:0004563 Increased spinal bone density Increased bone density affecting the bones of the spine (vertebral column). HPO:curators Increased density of spinal bone ORCID:0000-0001-5889-4463 Ivory spinal bone ORCID:0000-0001-5889-4463 Compact spinal bone ORCID:0000-0001-5889-4463 Concrete spinal bone ORCID:0000-0001-5889-4463 Dense spinal bone ORCID:0000-0001-5889-4463 Eburnation of spinal bone ORCID:0000-0001-5889-4463 Sclerosis of spinal bone ORCID:0000-0001-5889-4463 Increased top to bottom height of vertebral bodies. HP:0005693 UMLS:C1864853 Tall vertebral bodies human_phenotype HP:0004570 Increased vertebral height Increased top to bottom height of vertebral bodies. HPO:probinson UMLS:C4025311 human_phenotype HP:0004582 Irregularity of vertebral bodies UMLS:C1832983 human_phenotype HP:0004599 Absent or minimally ossified vertebral bodies A lack of ossification of the vertebral bodies. HP:0008427 UMLS:C1860202 human_phenotype HP:0004606 Unossified vertebral bodies HPO:skoehler A lack of ossification of the vertebral bodies. HPO:probinson Reduced size of cervical vertebrae. HP:0008429 UMLS:C1851130 Small cervical vertebrae human_phenotype HP:0004629 Small cervical vertebral bodies Reduced size of cervical vertebrae. HPO:probinson Underdevelopment of one or more muscles innervated by the facial nerve (the seventh cranial nerve). Small facial muscles UMLS:C1834042 UMLS:C4280509 UMLS:C4280510 UMLS:C4280511 Decreased size of facial muscles Deficiency of facial musculature Underdevelopment of facial muscles human_phenotype Atrophy of facial musculature Hypotrophic facial musculature HP:0004660 Hypoplasia of facial musculature Underdevelopment of one or more muscles innervated by the facial nerve (the seventh cranial nerve). HPO:probinson Small facial muscles ORCID:0000-0001-5889-4463 Decreased size of facial muscles ORCID:0000-0001-5889-4463 Deficiency of facial musculature ORCID:0000-0001-5889-4463 Underdevelopment of facial muscles ORCID:0000-0001-5889-4463 Atrophy of facial musculature ORCID:0000-0001-5889-4463 Hypotrophic facial musculature ORCID:0000-0001-5889-4463 UMLS:C1859116 Large ankle bones human_phenotype HP:0004679 Large tarsal bones Large ankle bones ORCID:0000-0001-6908-9849 Short (hypoplastic) fifth metatarsal bone. HP:0004702 HP:0010671 UMLS:C4021649 Hypoplasia of the fifth metatarsal bone Short 5th long bone of foot human_phenotype HP:0004704 Short fifth metatarsal Short (hypoplastic) fifth metatarsal bone. HPO:probinson Short 5th long bone of foot ORCID:0000-0001-5208-3432 An abnormality of the renal collecting system. HP:0004731 UMLS:C1851303 Abnormal collecting system Abnormality of the renal collecting system Renal collecting system anomalies human_phenotype HP:0004742 Abnormal renal collecting system morphology An abnormality of the renal collecting system. HPO:probinson Underdevelopment or reduced size of the heart right ventricle, often due to a reduced number of cells. HP:0004951 Fyler:1821 UMLS:C4082954 Heart right ventricle hypoplasia Small right heart chamber Underdeveloped right heart chamber human_phenotype HP:0004762 Hypoplasia of right ventricle Underdevelopment or reduced size of the heart right ventricle, often due to a reduced number of cells. MP:0010422 Heart right ventricle hypoplasia ORCID:0000-0001-5208-3432 Small right heart chamber ORCID:0000-0001-6908-9849 Underdeveloped right heart chamber ORCID:0000-0001-6908-9849 Underdevelopment of the small intestine. UMLS:C4025291 Underdeveloped small intestine human_phenotype HP:0004790 Hypoplasia of the small intestine Underdevelopment of the small intestine. HPO:probinson Underdeveloped small intestine ORCID:0000-0001-6908-9849 An abnormally elevated blood pressure in the circulation of the pulmonary artery. HP:0004958 UMLS:C3805917 Elevated lung artery pressure increased pulmonary artery pressure HP:0004890 Elevated pulmonary artery pressure An abnormally elevated blood pressure in the circulation of the pulmonary artery. HPO:probinson increased pulmonary artery pressure ORCID:0000-0001-5208-3432 An abnormality of magnesium ion homeostasis. HP:0008274 UMLS:C4020826 UMLS:C4025274 Abnormal Mg concentration Abnormality of magnesium homeostasis human_phenotype Abnormal magnesium metabolism HP:0004921 Abnormal magnesium concentration An abnormality of magnesium ion homeostasis. HPO:probinson Abnormal Mg concentration An increased concentration of L-phenylalanine in the blood. MSH:D010661 SNOMEDCT_US:68528007 UMLS:C0751435 human_phenotype HP:0004923 Hyperphenylalaninemia An increased concentration of L-phenylalanine in the blood. HPO:probinson peter 2008-03-26T04:07:00Z UMLS:C4025271 Abnormality of the lung blood vessels human_phenotype HP:0004930 Abnormality of the pulmonary vasculature Abnormality of the lung blood vessels ORCID:0000-0001-5208-3432 Abnormal calcification of the vasculature. MSH:D061205 SNOMEDCT_US:237897009 UMLS:C0342649 human_phenotype HP:0004934 Vascular calcification Abnormal calcification of the vasculature. HPO:probinson Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow. MSH:D020246 SNOMEDCT_US:111293003 UMLS:C0042487 Blood clot in vein human_phenotype HP:0004936 Venous thrombosis Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow. HPO:probinson Blood clot in vein ORCID:0000-0001-6908-9849 A congenital defect with aplasia (absence) of one of the right or left pulmonary artery. SNOMEDCT_US:86252004 UMLS:C0265905 Absent lung artery Missing pulmonary artery human_phenotype HP:0004960 This is a rare feature that has been observed in recessive lethal osteogenesis imperfecta with mutation in CRTAP. Absent pulmonary artery A congenital defect with aplasia (absence) of one of the right or left pulmonary artery. HPO:probinson PMID:17192541 Absent lung artery ORCID:0000-0001-5208-3432 Missing pulmonary artery ORCID:0000-0001-6908-9849 An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in the thoracic aorta. UMLS:C1969292 human_phenotype HP:0004962 Thoracic aorta calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in the thoracic aorta. HPO:probinson Calcification, that is, pathological deposition of calcium salts in the aorta. UMLS:C1096249 human_phenotype HP:0004963 Note that the phrase "aortic calcification" is mainly used to describe calcification of the aortic valve rather than of the aorta itself. Calcification of the aorta Calcification, that is, pathological deposition of calcium salts in the aorta. HPO:probinson Underdevelopment of the pulmonary artery. Fyler:2966 SNOMEDCT_US:54682008 UMLS:C0265910 Underdeveloped lung artery Underdeveloped pulmonary artery human_phenotype HP:0004971 Pulmonary artery hypoplasia Underdevelopment of the pulmonary artery. HPO:probinson Underdeveloped lung artery ORCID:0000-0001-5208-3432 Underdeveloped pulmonary artery ORCID:0000-0001-6908-9849 Abnormally increased density of metaphyseal bone. UMLS:C3552526 Increased bone density in wide portion of long bone Sclerotic metaphyses human_phenotype HP:0004979 Metaphyseal sclerosis Abnormally increased density of metaphyseal bone. HPO:probinson Increased bone density in wide portion of long bone ORCID:0000-0001-5208-3432 UMLS:C1857192 human_phenotype HP:0004997 Multicentric ossification of proximal humeral epiphyses Absence or underdevelopment of the proximal epiphysis of the femur. UMLS:C4025261 Absent/small end part of innermost thighbone Absent/underdeveloped end part of innermost thighbone human_phenotype HP:0005003 Aplasia/Hypoplasia of the capital femoral epiphysis Absence or underdevelopment of the proximal epiphysis of the femur. HPO:probinson Absent/small end part of innermost thighbone ORCID:0000-0001-5208-3432 Absent/underdeveloped end part of innermost thighbone ORCID:0000-0001-5208-3432 Developmental hypoplasia (shortening) of all phalanges of the foot. UMLS:C4025257 Short toe bones human_phenotype HP:0005035 Shortening of all phalanges of the toes Developmental hypoplasia (shortening) of all phalanges of the foot. HPO:probinson Short toe bones ORCID:0000-0001-5208-3432 Ossification affecting the external ear cartilage. peter 2008-03-25T05:09:00Z HP:0008549 UMLS:C1408806 Cartilaginous ossification of pinnae Ossification of pinnae Petrified ear human_phenotype Ear cartilage calcification HP:0005103 Calcification of the auricular cartilage Ossification affecting the external ear cartilage. HPO:probinson PMID:15523361 PMID:23259082 peter 2008-03-25T05:21:00Z Fyler:4870 UMLS:C4025252 Abnormal nose morphology Abnormal of morphology of nose Abnormal of nasal shape Abnormal of shape of nose human_phenotype HP:0005105 This is a category for overall abnormal morphology that may be replaced later with more exact descriptions. Abnormal nasal morphology Abnormal nose morphology ORCID:0000-0001-5208-3432 Abnormal of morphology of nose ORCID:0000-0001-5889-4463 Abnormal of nasal shape ORCID:0000-0001-5889-4463 Abnormal of shape of nose ORCID:0000-0001-5889-4463 An abnormality of the intervertebral disk. peter 2008-03-25T06:05:00Z UMLS:C4025249 Abnormality of the intervertebral disc human_phenotype HP:0005108 Any abnormality of the fibrocartilaginous structures that are located between adjacent vertebral bodies. Abnormality of the intervertebral disk An abnormality of the intervertebral disk. HPO:probinson Abnormality of the intervertebral disc Any structural abnormality of a cardiac atrium. peter 2008-03-26T04:12:00Z UMLS:C4025246 Abnormality of cardiac atrium morphology Abnormality of heart atrium human_phenotype HP:0005120 Abnormal cardiac atrium morphology Any structural abnormality of a cardiac atrium. HPO:probinson Abnormality of heart atrium ORCID:0000-0001-5208-3432 Underdeveloped, small left heart atrium Fyler:3040 UMLS:C1970625 Left atrium hypoplasia Underdeveloped left heart atrium human_phenotype HP:0005156 Hypoplastic left atrium MSH:D013585 SNOMEDCT_US:240206002 UMLS:C0410574 human_phenotype HP:0005186 Synovial hypertrophy Absence of the abdominal musculature. UMLS:C3149223 Absent abdominal musculature human_phenotype HP:0005199 Aplasia of the abdominal wall musculature Absence of the abdominal musculature. HPO:probinson Hypertrophy of the stomach. Increased stomach size UMLS:C1834341 UMLS:C4280502 human_phenotype HP:0005207 Gastric hypertrophy Hypertrophy of the stomach. HPO:probinson Increased stomach size ORCID:0000-0001-5208-3432 Underdevelopment of the colon. UMLS:C1392839 Hypoplasia of the colon Underdeveloped colon human_phenotype HP:0005210 Hypoplastic colon Underdevelopment of the colon. HPO:probinson Underdeveloped colon ORCID:0000-0001-5208-3432 The presence of abnormal calcium deposition lesions in the pancreas. UMLS:C1842406 Pancreatic calcifications human_phenotype HP:0005213 Pancreatic calcification The presence of abnormal calcium deposition lesions in the pancreas. HPO:probinson Pancreatic calcifications The presence of multiple diverticula of the intestine. UMLS:C1394691 UMLS:C1395674 human_phenotype Bowel diverticula HP:0005222 Bowel diverticulosis The presence of multiple diverticula of the intestine. HPO:probinson UMLS:C1850328 human_phenotype HP:0005223 Duplicated colon A collection of pus in the area of the rectum. HP:0002567 SNOMEDCT_US:197166005 SNOMEDCT_US:91669008 UMLS:C0149770 UMLS:C0267566 Perirectal abscess HP:0005224 Rectal abscess A collection of pus in the area of the rectum. HPO:probinson The presence of developmental dysplasia of the pancreas. UMLS:C4019084 human_phenotype HP:0005232 Dysplasia is defined in MPATH as a distortion or deficiency of the tissue or cellular architecture. Pancreatic dysplasia The presence of developmental dysplasia of the pancreas. HPO:probinson The presence of a hypoplastic gallbladder. SNOMEDCT_US:93259002 UMLS:C0345282 Hypoplastic gallbladder human_phenotype HP:0005233 Hypoplasia of the gallbladder The presence of a hypoplastic gallbladder. HPO:probinson Developmental hypoplasia of the intestine. UMLS:C4021640 Hypoplastic intestines Underdeveloped instestine human_phenotype HP:0005245 Intestinal hypoplasia Developmental hypoplasia of the intestine. HPO:probinson Underdeveloped instestine ORCID:0000-0001-5208-3432 Underdevelopment of the abdominal musculature. UMLS:C3279407 Abdominal muscular hypoplasia human_phenotype HP:0005247 Hypoplasia of the abdominal wall musculature Underdevelopment of the abdominal musculature. HPO:probinson HP:0001590 UMLS:C1837482 Small chest Small thorax human_phenotype HP:0005257 Thoracic hypoplasia Small chest Small thorax Hemorrhage occurring within a joint. peter 2008-03-26T04:27:00Z HP:0001391 HP:0005196 MSH:D006395 SNOMEDCT_US:81808003 UMLS:C0018924 Bleeding within a joint Hemarthroses Hemarthrosis Joint haemorrhage Spontaneous joint hemorrhage human_phenotype HP:0005261 Joint hemorrhage Hemorrhage occurring within a joint. HPO:gcarletti Bleeding within a joint ORCID:0000-0001-5208-3432 Hemarthrosis peter 2008-03-26T04:27:00Z UMLS:C4025225 human_phenotype HP:0005262 Abnormality of the synovia The presence of inflammation of the gastric mucous membrane. peter 2008-03-26T04:32:00Z MEDDRA:10017853 MSH:D005756 SNOMEDCT_US:4556007 UMLS:C0017152 Stomach inflammation human_phenotype HP:0005263 Gastritis The presence of inflammation of the gastric mucous membrane. HPO:probinson MEDDRA:10017853 Gastritis Stomach inflammation ORCID:0000-0001-5208-3432 An abnormality of the gallbladder. peter 2008-03-26T04:40:00Z SNOMEDCT_US:253803008 SNOMEDCT_US:49714001 UMLS:C0266249 Abnormality of the gallbladder Anomaly of the gallbladder human_phenotype HP:0005264 Abnormality of the gallbladder An abnormality of the gallbladder. HPO:probinson Abnormality of the gallbladder A discrete abnormal tissue mass that protrudes into the lumen of the intestine and is attached to the intestinal wall either by a stalk, pedunculus, or a broad base. peter 2008-03-26T04:46:00Z MSH:D007417 SNOMEDCT_US:254588001 UMLS:C0021846 human_phenotype Intestinal polyps HP:0005266 Intestinal polyp A discrete abnormal tissue mass that protrudes into the lumen of the intestine and is attached to the intestinal wall either by a stalk, pedunculus, or a broad base. HPO:probinson UMLS:C1855616 Cartilaginous nasal ossification human_phenotype HP:0005275 Cartilaginous ossification of nose Cartilaginous nasal ossification ORCID:0000-0001-5889-4463 UMLS:C1844731 UMLS:C4280496 UMLS:C4280497 Decreased size of nasal tip Decreased size of tip of nose Hypoplasia of tip of nose Small nasal tip Small tip of nose Underdevelopment of nasal tip Underdevelopment of tip of nose Aplasia of nasal tip human_phenotype Deficient nasal tip Hypotrophic nasal tip Hypotrophic tip of nose HP:0005278 Hypoplastic nasal tip Decreased size of nasal tip ORCID:0000-0001-5889-4463 Decreased size of tip of nose ORCID:0000-0001-5889-4463 Hypoplasia of tip of nose ORCID:0000-0001-5889-4463 Small nasal tip ORCID:0000-0001-5889-4463 Small tip of nose ORCID:0000-0001-5889-4463 Underdevelopment of nasal tip ORCID:0000-0001-5889-4463 Underdevelopment of tip of nose ORCID:0000-0001-5889-4463 Aplasia of nasal tip ORCID:0000-0001-5889-4463 Deficient nasal tip ORCID:0000-0001-5889-4463 Hypotrophic nasal tip ORCID:0000-0001-5889-4463 Hypotrophic tip of nose ORCID:0000-0001-5889-4463 Abnormality of the nostril. peter 2008-03-26T06:04:00Z UMLS:C4021637 Abnormality of the nostrils Anomaly of the nares Deformity of the nares Deformity of the nostrils Malformation of the nares Malformation of the nostrils human_phenotype HP:0005288 Abnormality of the nares Abnormality of the nostril. HPO:curators Abnormality of the nostrils Anomaly of the nares ORCID:0000-0001-5889-4463 Deformity of the nares ORCID:0000-0001-5889-4463 Deformity of the nostrils ORCID:0000-0001-5889-4463 Malformation of the nares ORCID:0000-0001-5889-4463 Malformation of the nostrils ORCID:0000-0001-5889-4463 UMLS:C1855736 UMLS:C4280491 UMLS:C4280492 UMLS:C4280493 Decreased size of internal carotid artery Small internal carotid artery Aplasia of internal carotid artery human_phenotype Deficiency of internal carotid artery Hypotrophic internal carotid artery HP:0005290 Internal carotid artery hypoplasia Decreased size of internal carotid artery ORCID:0000-0001-5889-4463 Small internal carotid artery ORCID:0000-0001-5889-4463 Aplasia of internal carotid artery ORCID:0000-0001-5889-4463 Deficiency of internal carotid artery ORCID:0000-0001-5889-4463 Hypotrophic internal carotid artery ORCID:0000-0001-5889-4463 UMLS:C1970501 Underdeveloped lung veins human_phenotype HP:0005304 Hypoplastic pulmonary veins Underdeveloped lung veins ORCID:0000-0001-5208-3432 Formation of a blood clot (thrombus) inside a cerebral vein, causing the obstruction of blood flow. SNOMEDCT_US:95455008 UMLS:C0151945 Blood clot in cerebral vein Cerebral thrombosis Cerebral vein thrombosis human_phenotype HP:0005305 Cerebral venous thrombosis Formation of a blood clot (thrombus) inside a cerebral vein, causing the obstruction of blood flow. HPO:probinson Blood clot in cerebral vein ORCID:0000-0001-6908-9849 UMLS:C1970630 Absent lung vessels human_phenotype HP:0005311 Agenesis of pulmonary vessels Absent lung vessels ORCID:0000-0001-5208-3432 UMLS:C3277426 Lack of facial fat below the skin human_phenotype HP:0005320 Lack of facial subcutaneous fat Lack of facial fat below the skin ORCID:0000-0001-5889-4463 Underdevelopment of the urinary bladder. HP:0005342 UMLS:C1855335 Hypoplastic bladder Underdeveloped bladder human_phenotype HP:0005343 Hypoplasia of the bladder Underdevelopment of the urinary bladder. HPO:probinson Underdeveloped bladder ORCID:0000-0001-5208-3432 Any structural abnormality of the carotid arteries, including the common carotid artery and its' arterial branches. peter 2008-03-26T06:37:00Z UMLS:C4025211 Abnormality of the carotid arteries human_phenotype HP:0005344 Abnormal carotid artery morphology An abnormality of the structure of the veins that return deoxygenated blood from the body into the heart, i.e., the superior vena cava and the inferior vena cava. peter 2008-03-26T06:40:00Z HP:0030971 UMLS:C4025210 human_phenotype Abnormality of the vena cava HP:0005345 Abnormal vena cava morphology An increased density in the cranial sutures following obliteration. UMLS:C4025195 human_phenotype HP:0005441 Sclerotic cranial sutures An increased density in the cranial sutures following obliteration. HPO:curators An increase in bone density affecting the calvaria (roof of the skull). UMLS:C1855657 human_phenotype HP:0005450 Calvarial osteosclerosis An increase in bone density affecting the calvaria (roof of the skull). HPO:curators UMLS:C1835442 human_phenotype HP:0005451 Decreased cranial base ossification Normally, the posterior and lateral fontanelles are obliterated by about six months after birth, the anterior fontanelle closes by about the middle of the second year. This term refers to the situation in which the fontanelles close at an inappropriately early time point. Early closure of the cranial sutures Premature closure of the cranial sutures MSH:D003398 SNOMEDCT_US:1667003 SNOMEDCT_US:57219006 UMLS:C0010278 UMLS:C0277827 UMLS:C4072853 Early closure of the fontanelles Obliterated fontanelles Early closure of the bregma sutures Premature closure of the bregma sutures human_phenotype HP:0005458 Premature closure of fontanelles Normally, the posterior and lateral fontanelles are obliterated by about six months after birth, the anterior fontanelle closes by about the middle of the second year. This term refers to the situation in which the fontanelles close at an inappropriately early time point. DDD:awilkie HPO:probinson Early closure of the cranial sutures ORCID:0000-0001-5889-4463 Premature closure of the cranial sutures ORCID:0000-0001-5889-4463 Early closure of the fontanelles ORCID:0000-0001-5889-4463 Early closure of the bregma sutures ORCID:0000-0001-5889-4463 Premature closure of the bregma sutures ORCID:0000-0001-5889-4463 Abnormally increased density of craniofacial bone tissue. UMLS:C1845805 UMLS:C4025193 human_phenotype Cranial sclerosis HP:0005464 Craniofacial osteosclerosis Abnormally increased density of craniofacial bone tissue. HPO:probinson Abnormal reduction in ossification of the calvaria (roof of the skull consisting of the frontal bone, parietal bones, temporal bones, and occipital bone). HP:0002701 HP:0002702 HP:0005454 HP:0005471 UMLS:C1833762 Poorly ossified calvaria Poorly ossified calvarium Soft calvaria Soft skullcap Undermineralized calvarium human_phenotype Skull soft on palpation HP:0005474 Decreased calvarial ossification Abnormal reduction in ossification of the calvaria (roof of the skull consisting of the frontal bone, parietal bones, temporal bones, and occipital bone). DDD:awilkie HPO:probinson Soft skullcap ORCID:0000-0001-5889-4463 Progressively increasing bone density of the skull base without significant changes in bony contour. UMLS:C1835470 human_phenotype HP:0005477 Progressive sclerosis of skull base Progressively increasing bone density of the skull base without significant changes in bony contour. HPO:probinson Head circumference which falls below 2 standard deviations below the mean for age and gender because of insufficient head growth after birth. HP:0000241 HP:0000259 HP:0005499 Development of small head that was not present at birth UMLS:C1847514 Acquired microcephaly Deceleration of head growth Microcephaly, acquired Microcephaly, postnatal Postnatal deceleration of head circumference Secondary microcephaly human_phenotype HP:0005484 Postnatal microcephaly Head circumference which falls below 2 standard deviations below the mean for age and gender because of insufficient head growth after birth. HPO:probinson Development of small head that was not present at birth ORCID:0000-0001-5889-4463 Acquired microcephaly ORCID:0000-0001-5889-4463 A fontanelle that is small for age. Little cranial sutures Small cranial sutures SNOMEDCT_US:276710001 UMLS:C0456133 UMLS:C4072854 UMLS:C4072855 Little fontanelle Microfontanelle Small soft spot Small bregma sutures human_phenotype HP:0005486 Small fontanelle A fontanelle that is small for age. HPO:probinson PMID:12825844 Little cranial sutures ORCID:0000-0001-5889-4463 Small cranial sutures ORCID:0000-0001-5889-4463 Little fontanelle ORCID:0000-0001-5889-4463 Microfontanelle ORCID:0000-0001-5889-4463 Small soft spot ORCID:0000-0001-5889-4463 Small bregma sutures ORCID:0000-0001-5889-4463 An anomaly of the form or number of cells in the bone marrow. peter 2008-03-27T10:46:00Z MSH:D001855 SNOMEDCT_US:127035006 UMLS:C0005956 UMLS:C4021634 Anomaly of the bone marrow cells human_phenotype Bone marrow disease HP:0005561 Abnormality of bone marrow cell morphology An anomaly of the form or number of cells in the bone marrow. DDD:wouwehand HPO:probinson Bone marrow disease A reduction in the count of nephrons per kidney. UMLS:C1841994 UMLS:C2673888 Oligonephronia human_phenotype Decreased numbers of glomeruli HP:0005563 Decreased numbers of nephrons A reduction in the count of nephrons per kidney. Eurenomics:ewuehl A duplication of the renal pelvis. UMLS:C1839269 human_phenotype HP:0005580 Duplication of renal pelvis A duplication of the renal pelvis. HPO:probinson UMLS:C3278401 Hair hypopigmentation Loss of hair color human_phenotype HP:0005599 Hypopigmentation of hair Loss of hair color https://orcid.org/0000-0002-6548-5200 UMLS:C3805692 human_phenotype HP:0005606 Hyperpigmented nevi and streak peter 2008-03-28T09:03:00Z HP:0005940 Fyler:4232 UMLS:C4021631 Tracheobronchial anomalies human_phenotype HP:0005607 Abnormal tracheobronchial morphology Absence or underdevelopment of the femur. HP:0006396 HP:0006425 UMLS:C1851310 Absent/small thighbone Absent/underdeveloped thighbone Hypoplastic to absent femora Hypoplastic/aplastic femora human_phenotype HP:0005613 Aplasia/hypoplasia of the femur Absence or underdevelopment of the femur. HPO:probinson Absent/small thighbone ORCID:0000-0001-5208-3432 Absent/underdeveloped thighbone ORCID:0000-0001-5208-3432 The ability of the interphalangeal joints to move beyond their normal range of motion. UMLS:C4025172 Increased mobility of hinge joints human_phenotype HP:0005620 Hypermobility of interphalangeal joints The ability of the interphalangeal joints to move beyond their normal range of motion. HPO:curators Increased mobility of hinge joints ORCID:0000-0001-5208-3432 Absent ossification of the calvaria (vault of the skull). UMLS:C4021629 Absent bone maturation of skullcap Absent ossification of skull vault human_phenotype HP:0005623 Absent ossification of calvaria Absent ossification of the calvaria (vault of the skull). HPO:probinson Absent bone maturation of skullcap ORCID:0000-0001-5889-4463 UMLS:C1408532 Absent forearm human_phenotype Absent forearms HP:0005632 Absent forearm Absent forearm Absent forearms HPO:skoehler The presence of abnormal calcium deposition of the intervertebral disk. SNOMEDCT_US:240211000 UMLS:C0410607 Intervertebral disc calcification Multiple intervertebral disk calcifications human_phenotype HP:0005645 Intervertebral disk calcification The presence of abnormal calcium deposition of the intervertebral disk. HPO:probinson Intervertebral disc calcification An increase in bone density affecting the basicranium (base of the skull). UMLS:C4021624 Osteosclerosis of the skull base human_phenotype HP:0005746 Bundled term. Consider obsoleting it and splitting of osteosclerosis of base of skull. Osteosclerosis of the base of the skull An increase in bone density affecting the basicranium (base of the skull). HPO:probinson UMLS:C1859523 Contractures, lower limbs human_phenotype HP:0005750 Contractures of the joints of the lower limbs Underdevelopment of both forearm bones, the ulna and the radius, resulting in a shortened forearm. UMLS:C1855299 Short forearm human_phenotype HP:0005773 Short forearm Underdevelopment of both forearm bones, the ulna and the radius, resulting in a shortened forearm. HPO:probinson Short forearm Underdevelopment of the humerus. HP:0002989 HP:0003014 HP:0003064 HP:0006419 HP:0006464 HP:0006468 UMLS:C1832117 Humeral hypoplasia Humeral shortening Hypoplastic humerus Short humeri Short humerus Short long bone of upper arm Short upper arms human_phenotype HP:0005792 Short humerus Underdevelopment of the humerus. HPO:probinson Short humerus Short long bone of upper arm ORCID:0000-0001-6908-9849 Short upper arms Aplasia (absence) of the distal phalanges. UMLS:C1861339 Absent outermost digital bones human_phenotype HP:0005807 Absent distal phalanges Aplasia (absence) of the distal phalanges. HPO:curators Absent outermost digital bones ORCID:0000-0001-5208-3432 The presence of more than 12 rib pairs. HP:0000901 SNOMEDCT_US:205460009 UMLS:C0345397 Extra ribs human_phenotype HP:0005815 Supernumerary ribs The presence of more than 12 rib pairs. HPO:probinson Extra ribs Short (hypoplastic) middle phalanx of finger, affecting one or more fingers. HP:0001208 HP:0006068 HP:0006081 HP:0010240 UMLS:C1846950 Brachymesophalangy Disproportionately short middle phalanges Hypoplasia of the middle phalanges of the hand Hypoplastic middle phalanges Hypoplastic middle phalanx Midphalangeal hypoplasia Short middle bone of finger Short middle phalanges Shortened middle finger bones human_phenotype HP:0005819 Short middle phalanx of finger Short (hypoplastic) middle phalanx of finger, affecting one or more fingers. HPO:probinson Short middle bone of finger ORCID:0000-0001-5208-3432 UMLS:C4025128 human_phenotype HP:0005825 Mixed sclerosis of humeral metaphyses One or more bent (flexed) toe joints that cannot be straightened actively or passively. HP:0001860 HP:0008128 HP:0008367 HP:0200027 UMLS:C1406835 Contractures involving the toes Contractures of the toes Toe contractures human_phenotype HP:0005830 Flexion contracture of toe One or more bent (flexed) toe joints that cannot be straightened actively or passively. HPO:probinson A lack of bone mineralization of one or more body of cervical vertebra. UMLS:C4025115 human_phenotype HP:0005885 Absent ossification of cervical vertebral bodies HPO:skoehler A lack of bone mineralization of one or more body of cervical vertebra. HPO:probinson peter 2008-03-27T02:13:00Z UMLS:C4025110 Abnormality of end part of long bone of hand human_phenotype HP:0005913 Abnormality of metacarpal epiphyses Abnormality of end part of long bone of hand ORCID:0000-0001-5208-3432 Aplasia or Hypoplasia affecting the metacarpal bones. peter 2008-03-27T02:14:00Z HP:0006007 UMLS:C1836192 Absent or hypoplastic metacarpals Absent/small long bones of hand Absent/underdeveloped long bones of hand Aplastic/hypoplastic metacarpals Hypoplastic metacarpals Hypoplastic/absent metacarpal bones Hypoplastic/absent metacarpals Metacarpal aplasia/hypoplasia human_phenotype HP:0005914 Aplasia/Hypoplasia involving the metacarpal bones Aplasia or Hypoplasia affecting the metacarpal bones. HPO:curators Absent/small long bones of hand ORCID:0000-0001-5208-3432 Absent/underdeveloped long bones of hand ORCID:0000-0001-5208-3432 Irregularly shaped metacarpal bones of varying degree. peter 2008-03-27T02:17:00Z HP:0010556 UMLS:C4021615 Abnormal shape of long bones of hand Abnormal shape of metacarpal bones human_phenotype HP:0005916 Abnormal metacarpal morphology Irregularly shaped metacarpal bones of varying degree. HPO:curators Abnormal shape of long bones of hand ORCID:0000-0001-5208-3432 The presence of more than the normal number of metacarpal bones. peter 2008-03-27T02:18:00Z SNOMEDCT_US:91846008 UMLS:C0545617 Extra long bones of hand human_phenotype HP:0005917 Supernumerary metacarpal bones The presence of more than the normal number of metacarpal bones. HPO:curators Extra long bones of hand ORCID:0000-0001-5208-3432 Abnormalities affecting the phalanx of finger. peter 2008-03-27T02:19:00Z HP:0005786 HP:0006259 UMLS:C4021614 Abnormal form of phalanges of the hand Abnormality of phalanx of finger Abnormality of the finger bones Abnormality of the phalanges Abnormality of the phalanges of the hand human_phenotype HP:0005918 This category is a supercategory for abnormalties affect phalanges of the hand. Abnormal finger phalanx morphology Abnormalities affecting the phalanx of finger. HPO:probinson Abnormality of the finger bones ORCID:0000-0001-5208-3432 Abnormality of one or all of the epiphyses of the phalanges of the hand. Note that this includes the epiphysis of the 1st metacarpal. In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). peter 2008-03-27T02:21:00Z HP:0009151 UMLS:C4021613 human_phenotype HP:0005920 Abnormal epiphysis morphology of the phalanges of the hand Abnormality of one or all of the epiphyses of the phalanges of the hand. Note that this includes the epiphysis of the 1st metacarpal. In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). HPO:curators Any structural anomaly of the hand. peter 2008-03-27T02:25:00Z HP:0003098 UMLS:C4025109 Abnormal shape of hand human_phenotype HP:0005922 This is a category to be used for general descriptions of hand dysmorphology. In time, it should be replaced by more accurate descriptions. Abnormal hand morphology Any structural anomaly of the hand. HPO:probinson Abnormal shape of hand ORCID:0000-0001-5208-3432 peter 2008-03-27T02:27:00Z UMLS:C4025108 Abnormality of the wide portion of the hand bone human_phenotype HP:0005923 Abnormalities of the metaphyses of the hand Abnormality of the wide portion of the hand bone ORCID:0000-0001-5208-3432 Any abnormality of the epiphyses of the phalanges or metacarpal bones. peter 2008-03-27T02:28:00Z UMLS:C4025107 Abnormality of the end part of the hand bone Abnormality of the end part of the hand bones Abnormality of the epiphyses of the fingers Abnormality of the epiphyses of the phalanges of the hand human_phenotype HP:0005924 Abnormality of the epiphyses of the hand Any abnormality of the epiphyses of the phalanges or metacarpal bones. HPO:curators Abnormality of the end part of the hand bone ORCID:0000-0001-5208-3432 peter 2008-03-27T02:28:00Z UMLS:C4025106 Abnormalities of shaft of long bone of the hand human_phenotype HP:0005925 Abnormalities of the diaphyses of the hand Abnormalities of shaft of long bone of the hand ORCID:0000-0001-5208-3432 Absence (due to failure to form) or underdevelopment of the bones of the hand. peter 2008-03-27T02:29:00Z UMLS:C4021612 Absent/small hand bones Absent/underdeveloped hand bones Hypoplasia/absence of hand bones human_phenotype HP:0005927 Aplasia/hypoplasia involving bones of the hand Absence (due to failure to form) or underdevelopment of the bones of the hand. HPO:probinson Absent/small hand bones ORCID:0000-0001-5208-3432 Absent/underdeveloped hand bones ORCID:0000-0001-5208-3432 An anomaly of epiphysis, which is the expanded articular end of a long bone that developes from a secondary ossification center, and which during the period of growth is either entirely cartilaginous or is separated from the shaft by a cartilaginous disk. peter 2008-03-27T03:00:00Z HP:0000936 UMLS:C4021611 Abnormal shape of end part of bone Abnormality of the epiphyses Anomaly of the epiphyses Epiphyseal abnormality human_phenotype HP:0005930 Abnormality of epiphysis morphology An anomaly of epiphysis, which is the expanded articular end of a long bone that developes from a secondary ossification center, and which during the period of growth is either entirely cartilaginous or is separated from the shaft by a cartilaginous disk. HPO:probinson Abnormal shape of end part of bone ORCID:0000-0001-5208-3432 A decreased concentration of arginine in the blood. UMLS:C1859735 UMLS:C4025095 Low blood arginine levels human_phenotype Arginine deficiency HP:0005961 Hypoargininemia A decreased concentration of arginine in the blood. HPO:gcarletti Low blood arginine levels ORCID:0000-0001-5208-3432 Developmental hypoplasia of the thyroid gland. MSH:D050033 SNOMEDCT_US:367524008 UMLS:C0151516 Hypoplastic thyroid Small thyroid gland human_phenotype HP:0005990 Thyroid hypoplasia Developmental hypoplasia of the thyroid gland. HPO:probinson Small thyroid gland Reduced amount of adipose tissue in the region of the neck. UMLS:C1837763 Loss of adipose tissue around the neck Loss of fat around neck human_phenotype HP:0005995 Decreased adipose tissue around neck Reduced amount of adipose tissue in the region of the neck. HPO:probinson Loss of fat around neck ORCID:0000-0001-6908-9849 UMLS:C1860111 Abnormally shaped wrist bones human_phenotype HP:0006014 Abnormally shaped carpal bones Abnormally shaped wrist bones ORCID:0000-0001-5208-3432 Delay in the process of formation and maturation of the epiphysis of one or more phalanx. UMLS:C4021609 Delayed phalangeal epiphyseal bone maturation human_phenotype Delayed bone maturation of end part of digital bone HP:0006016 Delayed phalangeal epiphyseal ossification Delay in the process of formation and maturation of the epiphysis of one or more phalanx. HPO:probinson Delayed bone maturation of end part of digital bone ORCID:0000-0001-5208-3432 A delay in the process of formation and maturation of the epiphysis of one or more long bones. UMLS:C1835573 Multiple carpal ossification centres human_phenotype HP:0006067 Multiple carpal ossification centers A delay in the process of formation and maturation of the epiphysis of one or more long bones. HPO:probinson Multiple carpal ossification centres SNOMEDCT_US:298193009 UMLS:C0574974 Increased mobility in finger joint human_phenotype HP:0006094 Finger joint hypermobility Increased mobility in finger joint ORCID:0000-0001-5208-3432 Increased length of the proximal phalanx of finger. UMLS:C4025090 Long innermost finger bone human_phenotype HP:0006127 Long proximal phalanx of finger Increased length of the proximal phalanx of finger. HPO:probinson Long innermost finger bone ORCID:0000-0001-5208-3432 Abnormally large size of the metaphyseal epiphyses. UMLS:C1865035 Enlarged end part of long bone of hand human_phenotype HP:0006134 Enlarged metacarpal epiphyses Abnormally large size of the metaphyseal epiphyses. HPO:curators Enlarged end part of long bone of hand ORCID:0000-0001-5208-3432 Increased length of multiple or a single phalanx of finger. UMLS:C4025087 Long finger bone human_phenotype HP:0006155 Long phalanx of finger Increased length of multiple or a single phalanx of finger. HPO:probinson Long finger bone ORCID:0000-0001-5208-3432 Bending or curvature of a thumb towards the ulnar side (towards the ring finger). Curved thumb deviated towards palm SNOMEDCT_US:299137000 UMLS:C0575904 UMLS:C4280465 Ulnar deviation of the 1st finger human_phenotype HP:0006156 Ulnar deviation of thumb Bending or curvature of a thumb towards the ulnar side (towards the ring finger). HPO:probinson PMID:10955488 Curved thumb deviated towards palm ORCID:0000-0001-5208-3432 UMLS:C1859700 human_phenotype HP:0006163 Enlarged metacarpophalangeal joints UMLS:C1839285 Two carpal ossification centres present at birth human_phenotype HP:0006176 Two carpal ossification centers present at birth Two carpal ossification centres present at birth UMLS:C1861350 Enlarged innermost hinge joint human_phenotype HP:0006185 Enlarged proximal interphalangeal joints Enlarged innermost hinge joint ORCID:0000-0001-5208-3432 UMLS:C1851811 Increased mobility of outermost hinge joint human_phenotype HP:0006201 Hypermobility of distal interphalangeal joints Increased mobility of outermost hinge joint ORCID:0000-0001-5208-3432 UMLS:C1859701 Enlarged hinge joints human_phenotype HP:0006247 Enlarged interphalangeal joints Enlarged hinge joints ORCID:0000-0001-5208-3432 peter 2008-03-28T10:14:00Z UMLS:C4025076 Abnormality of hand joint mobility human_phenotype HP:0006256 Abnormality of hand joint mobility Abnormality of hand joint mobility peter 2008-03-28T02:29:00Z UMLS:C4025075 Abnormal ankle bone maturation human_phenotype HP:0006257 Abnormality of carpal bone ossification Abnormal ankle bone maturation ORCID:0000-0001-5208-3432 peter 2008-03-28T02:55:00Z HP:0004266 UMLS:C4021604 Abnormality of phalangeal joints of the hand Abnormality of the small joints of the hand human_phenotype HP:0006261 Abnormal phalangeal joint morphology of the hand Abnormality of the small joints of the hand A small/hypoplastic or absent/aplastic 5th finger. peter 2008-03-28T02:59:00Z UMLS:C4025074 Absent/small little finger Absent/small pinkie finger Absent/small pinky finger Absent/underdeveloped little finger Absent/underdeveloped pinkie finger Absent/underdeveloped pinky finger human_phenotype HP:0006262 Aplasia/Hypoplasia of the 5th finger A small/hypoplastic or absent/aplastic 5th finger. HPO:sdoelken Absent/small little finger ORCID:0000-0001-5208-3432 Absent/small pinkie finger ORCID:0000-0001-5208-3432 Absent/small pinky finger ORCID:0000-0001-5208-3432 Absent/underdeveloped little finger ORCID:0000-0001-5208-3432 Absent/underdeveloped pinkie finger ORCID:0000-0001-5208-3432 Absent/underdeveloped pinky finger ORCID:0000-0001-5208-3432 Small/hypoplastic or absent/aplastic fingers. peter 2008-03-28T03:09:00Z UMLS:C4025071 Absent/small fingers Absent/underdeveloped fingers human_phenotype HP:0006265 Aplasia/Hypoplasia of fingers Small/hypoplastic or absent/aplastic fingers. HPO:curators Absent/small fingers ORCID:0000-0001-5208-3432 Absent/underdeveloped fingers ORCID:0000-0001-5208-3432 Reduced size of the placenta. SNOMEDCT_US:289264006 UMLS:C0566694 Small placenta human_phenotype HP:0006266 Small placenta Reduced size of the placenta. HPO:probinson Small placenta Increased size of the placenta. SNOMEDCT_US:289263000 UMLS:C0566693 Large placenta Placental enlargement human_phenotype HP:0006267 Large placenta Increased size of the placenta. HPO:probinson Large placenta Underdevelopment of the spleen. UMLS:C1970617 Underdeveloped spleen human_phenotype HP:0006270 Hypoplastic spleen Underdevelopment of the spleen. HPO:curators Underdeveloped spleen ORCID:0000-0001-6908-9849 Short dental root. Underdeveloped tooth roots UMLS:C2678330 Decreased length of dental roots Decreased length of tooth roots Short dental roots Short tooth roots Underdeveloped dental roots human_phenotype HP:0006336 Short dental roots Short dental root. HPO:probinson Underdeveloped tooth roots ORCID:0000-0001-5889-4463 Decreased length of dental roots ORCID:0000-0001-5889-4463 Decreased length of tooth roots ORCID:0000-0001-5889-4463 Short dental roots Short tooth roots ORCID:0000-0001-5889-4463 Underdeveloped dental roots Shortening of the legs related to developmental hypoplasia of the bones of the leg. HP:0003054 SNOMEDCT_US:249786007 UMLS:C0426901 Short legs Short lower limbs human_phenotype HP:0006385 Short lower limbs Shortening of the legs related to developmental hypoplasia of the bones of the leg. HPO:probinson Short legs Short lower limbs An abnormal increase in the bone density of the long bones. UMLS:C1849307 Increased density of long bones human_phenotype HP:0006392 Increased density of long bones An abnormal increase in the bone density of the long bones. HPO:curators Increased density of long bones UMLS:C1840307 Short outer part of limbs human_phenotype HP:0006402 Distal shortening of limbs Short outer part of limbs ORCID:0000-0001-5208-3432 An anomaly of the metaphysis of the proximal femur (close to the hip). UMLS:C4025047 Abnormal wide portion of innermost thighbone human_phenotype HP:0006431 Proximal femoral metaphyseal abnormality An anomaly of the metaphysis of the proximal femur (close to the hip). HPO:probinson Abnormal wide portion of innermost thighbone ORCID:0000-0001-5208-3432 An abnormal enlargement of the distal epiphysis of the femur. UMLS:C1843105 Enlargement of the outermost thighbone end part Large distal femoral epiphyses human_phenotype HP:0006438 Enlargement of the distal femoral epiphysis An abnormal enlargement of the distal epiphysis of the femur. HPO:probinson Enlargement of the outermost thighbone end part ORCID:0000-0001-5208-3432 UMLS:C1844516 Increased density of shaft of long bone human_phenotype HP:0006440 Increased density of long bone diaphyses Increased density of shaft of long bone ORCID:0000-0001-5208-3432 UMLS:C1857193 human_phenotype HP:0006450 Multicentric ossification of proximal femoral epiphyses A chronic loss of ankle joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevent normal movement of the joints of the ankle. HP:0004985 HP:0006403 UMLS:C1837407 Ankle contracture Ankle contractures Contractures of the ankles human_phenotype HP:0006466 Ankle flexion contracture A chronic loss of ankle joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevent normal movement of the joints of the ankle. HPO:probinson An abnormality of the islet of Langerhans, i.e., of the regions of the pancreas that contain its endocrine cells. These are the alpha cells, which produce glucagon, the beta cells, which produce insulin and amylin, the delta cells, which produce somatostatin, the PP cells, which produce pancreatic polypeptide, and the epsilon cells, which produce ghrelin. peter 2008-03-28T04:41:00Z HP:0100567 UMLS:C4025043 human_phenotype HP:0006476 Abnormality of the pancreatic islet cells An abnormality of the islet of Langerhans, i.e., of the regions of the pancreas that contain its endocrine cells. These are the alpha cells, which produce glucagon, the beta cells, which produce insulin and amylin, the delta cells, which produce somatostatin, the PP cells, which produce pancreatic polypeptide, and the epsilon cells, which produce ghrelin. HPO:probinson An abnormality of the morphology of the tooth. peter 2008-03-28T05:41:00Z HP:0000697 MSH:D014071 SNOMEDCT_US:422775003 UMLS:C0040427 UMLS:C0262444 Abnormality of dental shape Abnormality of shape of tooth Abnormally shaped teeth Deformity of teeth Dental deformity Dental malformations Malformation of teeth Malformed teeth Misshapen teeth Misshapened teeth human_phenotype HP:0006482 Abnormality of dental morphology An abnormality of the morphology of the tooth. HPO:ibailleulforestier Abnormality of dental shape ORCID:0000-0001-5889-4463 Abnormality of shape of tooth ORCID:0000-0001-5889-4463 Abnormally shaped teeth Deformity of teeth ORCID:0000-0001-5889-4463 Dental deformity ORCID:0000-0001-5889-4463 Dental malformations ORCID:0000-0001-5889-4463 Malformation of teeth ORCID:0000-0001-5889-4463 Malformed teeth Misshapen teeth Misshapened teeth The presence of an altered number of of teeth. peter 2008-03-28T05:44:00Z SNOMEDCT_US:335443002 UMLS:C1290508 Abnormal complement of teeth Abnormal number of teeth Abnormal tooth count human_phenotype HP:0006483 Humans usually have 20 primary teeth (also called deciduous teeth) and 32 permanent teeth. This term comprises anomalies with too many or too few teeth. Abnormal number of teeth The presence of an altered number of of teeth. HPO:ibailleulforestier Abnormal complement of teeth ORCID:0000-0001-5889-4463 Abnormal number of teeth Abnormal tooth count ORCID:0000-0001-5889-4463 An abnormality of the dental root. peter 2008-03-28T05:52:00Z UMLS:C4025041 Abnormality of the dental root Abnormality of tooth root human_phenotype HP:0006486 Abnormality of the dental root An abnormality of the dental root. HPO:ibailleulforestier Abnormality of the dental root Abnormality of tooth root ORCID:0000-0001-5889-4463 An anomaly of the femoral metaphysis. peter 2008-03-28T06:02:00Z Abnormality of the wide portion of the femoral bone UMLS:C4025040 UMLS:C4280444 human_phenotype HP:0006489 Abnormality of the femoral metaphysis An anomaly of the femoral metaphysis. HPO:probinson Abnormality of the wide portion of the femoral bone ORCID:0000-0001-5208-3432 peter 2008-03-28T06:02:00Z UMLS:C4025039 Abnormality of the wide portion of the lower-limb bone human_phenotype HP:0006490 Abnormality of lower-limb metaphyses Abnormality of the wide portion of the lower-limb bone ORCID:0000-0001-5208-3432 Absence (due to failure to form) or underdevelopment of the bones of the lower limbs. peter 2008-03-28T06:04:00Z UMLS:C4025037 Absent/small lower limb bones Absent/underdeveloped lower limb bones human_phenotype HP:0006493 Aplasia/hypoplasia involving bones of the lower limbs Absence (due to failure to form) or underdevelopment of the bones of the lower limbs. HPO:probinson Absent/small lower limb bones ORCID:0000-0001-5208-3432 Absent/underdeveloped lower limb bones ORCID:0000-0001-5208-3432 peter 2008-03-28T06:08:00Z UMLS:C4025036 Absent/small foot bones Absent/underdeveloped foot bones human_phenotype HP:0006494 Aplasia/Hypoplasia involving bones of the feet Absent/small foot bones ORCID:0000-0001-5208-3432 Absent/underdeveloped foot bones ORCID:0000-0001-5208-3432 Absence (due to failure to form) or underdevelopment of the bones of the upper limbs. peter 2008-03-28T06:16:00Z UMLS:C4025035 Absent/small bones of the upper limbs Absent/underdeveloped bones of the upper limbs human_phenotype HP:0006496 Aplasia/hypoplasia involving bones of the upper limbs Absence (due to failure to form) or underdevelopment of the bones of the upper limbs. HPO:probinson Absent/small bones of the upper limbs ORCID:0000-0001-5208-3432 Absent/underdeveloped bones of the upper limbs ORCID:0000-0001-5208-3432 An anomaly of a growth plate of a femur. peter 2008-03-28T06:28:00Z HP:0006412 HP:0008811 UMLS:C4025034 Abnormality of thighbone end part human_phenotype HP:0006499 Abnormality of femoral epiphysis An anomaly of a growth plate of a femur. HPO:probinson Abnormality of thighbone end part ORCID:0000-0001-5208-3432 An anomaly of one or more epiphyses of one or both legs. peter 2008-03-28T06:31:00Z UMLS:C4021595 Abnormal shape of end part of lower limb end bone Abnormality involving the epiphyses of the lower limbs human_phenotype HP:0006500 Abnormality of lower limb epiphysis morphology Abnormal shape of end part of lower limb end bone ORCID:0000-0001-5208-3432 Absence or underdevelopment of the carpal bones. peter 2008-03-28T06:35:00Z UMLS:C4025033 Absent/small wrist bones Absent/underdeveloped wrist bones human_phenotype HP:0006502 Aplasia/Hypoplasia involving the carpal bones Absence or underdevelopment of the carpal bones. HPO:curators Absent/small wrist bones ORCID:0000-0001-5208-3432 Absent/underdeveloped wrist bones ORCID:0000-0001-5208-3432 Absence (due to failure to form) or underdevelopment of one or more forearm bones. peter 2008-03-28T06:45:00Z UMLS:C4025032 Absent/small forearm bones Absent/underdeveloped forearm bones human_phenotype HP:0006503 Aplasia/hypoplasia involving forearm bones Absence (due to failure to form) or underdevelopment of one or more forearm bones. HPO:probinson Absent/small forearm bones ORCID:0000-0001-5208-3432 Absent/underdeveloped forearm bones ORCID:0000-0001-5208-3432 An anomaly of one or more epiphyses of a limb. peter 2008-03-28T06:48:00Z UMLS:C4021593 Abnormal shape of end part of limb bones Abnormality involving the epiphyses of the limbs human_phenotype HP:0006505 An epiphysis is the expanded articular end of a long bone that developes from a secondary ossification center, and which during the period of growth is either entirely cartilaginous or is separated from the shaft by a cartilaginous disk. Abnormality of limb epiphysis morphology Abnormal shape of end part of limb bones ORCID:0000-0001-5208-3432 Absence (due to failure to form) or underdevelopment of the humerus. peter 2008-03-29T09:15:00Z UMLS:C4025031 Absent/small long bone in upper arm Absent/underdeveloped long bone in upper arm human_phenotype HP:0006507 Aplasia/hypoplasia of the humerus Absence (due to failure to form) or underdevelopment of the humerus. HPO:probinson Absent/small long bone in upper arm ORCID:0000-0001-5208-3432 Absent/underdeveloped long bone in upper arm ORCID:0000-0001-5208-3432 An abnormality of the pulmonary lymphatic chain. UMLS:C4025026 human_phenotype HP:0006529 Abnormal pulmonary lymphatics An abnormality of the pulmonary lymphatic chain. HPO:probinson UMLS:C4025025 human_phenotype HP:0006533 Bronchodysplasia UMLS:C4025024 Underdevelopment of the bronical cartilage human_phenotype HP:0006539 Bronchial cartilage hypoplasia Underdevelopment of the bronical cartilage ORCID:0000-0001-5208-3432 The presence of abnormal calcium deposition in the liver. UMLS:C1696466 Liver calcifications human_phenotype HP:0006559 Hepatic calcification The presence of abnormal calcium deposition in the liver. HPO:probinson The presence of reduced numbers of intrahepatic bile duct than normal. UMLS:C1861621 UMLS:C4021591 Hepatic ductopenia human_phenotype Intrahepatic duct deficiency HP:0006571 Reduced number of intrahepatic bile ducts The presence of reduced numbers of intrahepatic bile duct than normal. HPO:probinson HP:0006629 UMLS:C1861226 Small abnormally formed scapula Small abnormally formed shoulder blade human_phenotype HP:0006584 Small abnormally formed scapulae Small abnormally formed shoulder blade ORCID:0000-0001-5208-3432 Lack of development of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. UMLS:C4021589 Aplasia of the glenoid fossa human_phenotype HP:0006591 Absent glenoid fossa Lack of development of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. HPO:probinson Underdevelopment of the glenoid fossa, which is the cavity in the lateral part of the scapula which articulates with the head of the humerus. HP:0006632 UMLS:C1834384 Glenoid hypoplasia Hypoplastic glenoid fossa human_phenotype HP:0006633 Glenoid fossa hypoplasia Underdevelopment of the glenoid fossa, which is the cavity in the lateral part of the scapula which articulates with the head of the humerus. HPO:probinson UMLS:C1406921 human_phenotype HP:0006644 Thoracic dysplasia A localized outpouching of ventricular cavity that is generally associated with dyskinesia and paradoxical expansion during systole. SNOMEDCT_US:90539001 UMLS:C0392464 Ventricular aneurysm human_phenotype HP:0006698 Aneurysm is considered a severe form of dilatation. Ventricular aneurysms may have rim of calcium in the affected regions of the ventricular wall (which can become fibrotic). Thromboembolism is a potential complication. Ventricular aneurysms can be diagnosed by ventriculography. Dilatation of the ventricular cavity A localized outpouching of ventricular cavity that is generally associated with dyskinesia and paradoxical expansion during systole. HPO:probinson peter 2008-03-29T03:17:00Z UMLS:C4024996 Absent/small lungs Absent/underdeveloped lungs human_phenotype HP:0006703 Aplasia/Hypoplasia of the lungs Absent/small lungs ORCID:0000-0001-5208-3432 Absent/underdeveloped lungs ORCID:0000-0001-5208-3432 peter 2008-03-29T03:37:00Z MSH:C536330 SNOMEDCT_US:72925005 UMLS:C0158683 human_phenotype HP:0006706 Cystic liver disease An abnormality of the hepatic vasculature. peter 2008-03-29T03:41:00Z UMLS:C4024994 Abnormality of liver blood vessels Abnormality of the liver vasculature human_phenotype HP:0006707 Abnormality of the hepatic vasculature An abnormality of the hepatic vasculature. HPO:probinson Abnormality of liver blood vessels ORCID:0000-0001-5208-3432 peter 2008-03-29T03:53:00Z UMLS:C4024992 Absent/small outermost thorax bone Absent/underdeveloped thorax bone human_phenotype HP:0006711 Aplasia/Hypoplasia involving bones of the thorax Absent/small outermost thorax bone ORCID:0000-0001-5208-3432 Absent/underdeveloped thorax bone ORCID:0000-0001-5208-3432 peter 2008-03-29T03:54:00Z HP:0006636 UMLS:C1847363 Absent/small ribs Absent/underdeveloped ribs Hypoplastic or missing ribs human_phenotype HP:0006712 Aplasia/Hypoplasia of the ribs Absent/small ribs ORCID:0000-0001-5208-3432 Absent/underdeveloped ribs ORCID:0000-0001-5208-3432 peter 2008-03-29T03:58:00Z UMLS:C4024991 Absent/small shoulder blade Absent/underdeveloped shoulder blade human_phenotype HP:0006713 Aplasia/Hypoplasia of the scapulae Absent/small shoulder blade ORCID:0000-0001-5208-3432 Absent/underdeveloped shoulder blade ORCID:0000-0001-5208-3432 Underdevelopment of the cerebrum. HP:0001322 UMLS:C1855330 Small cerebrum Underdeveloped cerebrum human_phenotype HP:0006872 Cerebral hypoplasia Underdevelopment of the cerebrum. HPO:probinson Small cerebrum ORCID:0000-0001-5208-3432 Underdeveloped cerebrum ORCID:0000-0001-5208-3432 The presence of developmental dysplasia of the cortex of frontal lobe and the cortex of parietal lobe. UMLS:C4024959 human_phenotype HP:0006930 Frontoparietal cortical dysplasia The presence of developmental dysplasia of the cortex of frontal lobe and the cortex of parietal lobe. HPO:probinson The presence of calcium deposition in the choroid plexus. UMLS:C1863184 Calcified choroid plexus human_phenotype HP:0006960 Choroid plexus calcification The presence of calcium deposition in the choroid plexus. HPO:probinson A morphological abnormality of the metencephalon. UMLS:C4024951 human_phenotype HP:0007027 The metencephalon comprises the pons and the cerebellum; contains a portion of the fourth ventricle; and the trigeminal nerve, abducens nerve, facial nerve, and a portion of the vestibulocochlear nerve. The metencephalon is part of the hindbrain. Poorly formed metencephalon A morphological abnormality of the metencephalon. HPO:probinson The presence of dysplasia (abnormal growth or development) of the cerebellum. Cerebellar dysplasia is a neuroimaging finding that describes abnormalities of both the cerebellar cortex and white matter and is associated with variable neurodevelopmental outcome. UMLS:C3278322 human_phenotype HP:0007033 Any part of the cerebellum can be dysplastic, from small focal regions within one hemisphere to abnormal foliation throughout the cerebellum. Hypoplastic cerebella are frequently also dysmorphic, as observed in tubulinopathies and cobblestone malformations. Cerebellar dysplasia The presence of dysplasia (abnormal growth or development) of the cerebellum. Cerebellar dysplasia is a neuroimaging finding that describes abnormalities of both the cerebellar cortex and white matter and is associated with variable neurodevelopmental outcome. HPO:probinson PMID:25105227 PMID:27160001 Agenesis of the midbrain. UMLS:C4024913 human_phenotype HP:0007265 Midbrain and mesencephalon are synonymous. Absent mesencephalon Agenesis of the midbrain. KI:phemming Underdevelopment of the frontal lobe of the cerebrum. HP:0002424 UMLS:C1849172 Frontal lobe hypoplasia Hypoplastic frontal lobes Underdeveloped frontal lobe human_phenotype HP:0007333 Hypoplasia of the frontal lobes Underdevelopment of the frontal lobe of the cerebrum. HPO:sdoelken Underdeveloped frontal lobe ORCID:0000-0001-5208-3432 Any structural anomaly of the limbic system, a set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. UMLS:C1863392 Limbic malformation human_phenotype HP:0007343 Abnormal morphology of the limbic system UMLS:C1851431 human_phenotype HP:0007352 Cerebellar calcifications peter 2008-03-31T05:30:00Z HP:0006857 HP:0007368 UMLS:C3279222 Absent/small cerebellum Absent/underdeveloped cerebellum Atrophy/Degeneration affecting the cerebellum Atrophy/Hypoplasia of the cerebellum Cerebellar hypoplasia/atrophy human_phenotype HP:0007360 Aplasia/Hypoplasia of the cerebellum Absent/small cerebellum ORCID:0000-0001-5208-3432 Absent/underdeveloped cerebellum ORCID:0000-0001-5208-3432 An abnormality of the pons. peter 2008-03-31T05:32:00Z UMLS:C4024905 human_phenotype HP:0007361 The pons is the portion of the brainstem superior to the medulla oblongata. Abnormality of the pons An abnormality of the pons. HPO:probinson peter 2008-03-31T05:33:00Z UMLS:C4024904 Absent/small brainstem Absent/underdeveloped brainstem human_phenotype HP:0007362 Aplasia/Hypoplasia of the brainstem Absent/small brainstem ORCID:0000-0001-5208-3432 Absent/underdeveloped brainstem ORCID:0000-0001-5208-3432 peter 2008-03-31T05:43:00Z UMLS:C4024902 Absent/small cerebrum Absent/underdeveloped cerebrum human_phenotype HP:0007364 Aplasia/Hypoplasia of the cerebrum Absent/small cerebrum ORCID:0000-0001-6908-9849 Absent/underdeveloped cerebrum ORCID:0000-0001-6908-9849 An abnormality of the choroid plexus, which is the area in the cerebral ventricles in which cerebrospinal fluid is produced by modified ependymal cells. peter 2008-04-01T10:52:00Z UMLS:C4024893 human_phenotype HP:0007376 The choroid plexus is a structure in the ventricles of the brain where cerebrospinal fluid (CSF) is produced. Abnormality of the choroid plexus An abnormality of the choroid plexus, which is the area in the cerebral ventricles in which cerebrospinal fluid is produced by modified ependymal cells. HPO:probinson A tumor (abnormal growth of tissue) of the gastrointestinal tract. peter 2008-04-01T11:55:00Z MSH:D005770 NCIT:C3262 SNOMEDCT_US:126768004 UMLS:C0017185 GI tract tumor Gastrointestinal tract neoplasia Gastrointestinal tract neoplasm Gastrointestinal tract tumor Neoplasm of the GI tract human_phenotype HP:0007378 Neoplasm of the gastrointestinal tract A tumor (abnormal growth of tissue) of the gastrointestinal tract. HPO:probinson GI tract tumor ORCID:0000-0001-5208-3432 Gastrointestinal tract tumor Neoplasm of the GI tract A tumor (abnormal growth of tissue) of the genitourinary system. peter 2008-04-01T12:00:00Z MSH:D014565 NCIT:C3262 UMLS:C0042065 UMLS:C4020809 Genitourinary tract neoplasm Genitourinary tract tumors Neoplasm of the GU tract human_phenotype Genitourinary tract neoplasia HP:0007379 Neoplasm of the genitourinary tract A tumor (abnormal growth of tissue) of the genitourinary system. HPO:probinson Genitourinary tract tumors Neoplasm of the GU tract Underdevelopment of the sweat glands. UMLS:C1832455 Underdeveloped sweat glands human_phenotype HP:0007387 Hypoplastic sweat glands Underdevelopment of the sweat glands. HPO:curators Underdeveloped sweat glands ORCID:0000-0001-5208-3432 UMLS:C1860236 human_phenotype HP:0007400 Irregular hyperpigmentation Lack of subcutaneous adipose tissue. HP:0007519 UMLS:C0241267 UMLS:C4024855 Absent fat below the skin General absence of subcutaneous fat Lack of fatty tissue below the skin human_phenotype HP:0007485 Absence of subcutaneous fat Lack of subcutaneous adipose tissue. HPO:probinson Absent fat below the skin ORCID:0000-0001-5208-3432 Lack of fatty tissue below the skin The presence of fewer than normal sweat glands. HP:0007555 HP:0007594 UMLS:C4021574 Decreased sweat glands Decreased sweat pores human_phenotype HP:0007500 Decreased number of sweat glands The presence of fewer than normal sweat glands. HPO:probinson Decreased sweat glands Decreased sweat pores UMLS:C1832454 human_phenotype HP:0007515 Hypoplastic pilosebaceous units UMLS:C4024854 human_phenotype HP:0007521 Irregular hyperpigmentation of back UMLS:C4024819 human_phenotype HP:0007661 Abnormality of chorioretinal pigmentation Congenital underdevelopment of the iris. HP:0000638 HP:0007724 HP:0007998 SNOMEDCT_US:95714006 UMLS:C0344539 Hypoplastic iris Iris hypoplasia Underdeveloped iris human_phenotype HP:0007676 Hypoplasia of the iris Congenital underdevelopment of the iris. HPO:probinson Underdeveloped iris ORCID:0000-0001-5208-3432 UMLS:C4024816 human_phenotype HP:0007680 Depigmented fundus HPO:skoehler Abnormal development (dysgenesis) of the anterior segment of the eye globe. These structures are mainly of mesenchymal origin. HP:0007696 HP:0007699 HP:0008040 SNOMEDCT_US:65075004 UMLS:C0266525 Anterior chamber cleavage defect Anterior chamber cleavage disorder Anterior chamber malformation Anterior chamber mesodermal anomalies Anterior segment developmental abnormality Anterior segment dysgenesis Anterior segment mesencyhmal dysgenesis Anterior segment ocular dysgenesis human_phenotype HP:0007700 In anterior segment mesenchymal ocular dysgenesis (ASMOD), multiple tissues are affected, including the iris, cornea, and lens as well as the Schlemm's canal and trabecular meshwork drainage structures located at the anterior segment angle where the iris and cornea meet. These abnormalities may result from a primary defect in the migration and/or differentiation of the mesenchymal cells that contribute to development of the cornea, iris, and drainage structures. Ocular anterior segment dysgenesis Abnormal development (dysgenesis) of the anterior segment of the eye globe. These structures are mainly of mesenchymal origin. DDD:ncarter An abnormal reduction in the amount of pigmentation of the iris. SNOMEDCT_US:247032003 SNOMEDCT_US:70397008 UMLS:C0154920 Light eye color Reduced iris pigmentation human_phenotype HP:0007730 Iris hypopigmentation An abnormal reduction in the amount of pigmentation of the iris. HPO:probinson Light eye color https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 Abnormal development of the choroid and retina. UMLS:C4024809 human_phenotype HP:0007731 Chorioretinal dysplasia Abnormal development of the choroid and retina. HPO:probinson Underdevelopment of the lacrimal gland. UMLS:C1863200 Hypoplastic lacrimal gland Underdeveloped tear gland human_phenotype HP:0007732 Lacrimal gland hypoplasia Underdevelopment of the lacrimal gland. HPO:probinson Underdeveloped tear gland ORCID:0000-0001-5208-3432 Abnormally big lacrimal glands. UMLS:C1867030 Enlarged tear gland human_phenotype HP:0007734 Enlarged lacrimal glands Abnormally big lacrimal glands. HPO:probinson Enlarged tear gland ORCID:0000-0001-5208-3432 UMLS:C1854685 Retinal hypoplasia Underdeveloped retina human_phenotype HP:0007770 Hypoplasia of the retina Underdeveloped retina ORCID:0000-0001-5208-3432 Underdevelopment of the ciliary body. UMLS:C1836890 human_phenotype HP:0007774 Hypoplasia of the ciliary body Underdevelopment of the ciliary body. HPO:probinson Pigmentation of the outer white part of the eyeball UMLS:C1859882 human_phenotype HP:0007832 Pigmentation of the sclera Pigmentation of the outer white part of the eyeball ORCID:0000-0001-5208-3432 Deposition of calcium salts in the retina. UMLS:C1867289 human_phenotype HP:0007862 Retinal calcification Deposition of calcium salts in the retina. HPO:probinson Underdevelopment of the lacrimal puncta. UMLS:C4021564 Hypoplasia of the lacrimal puncta Hypoplastic lacrimal puncta human_phenotype HP:0007892 Hypoplasia of the lacrimal punctum Underdevelopment of the lacrimal puncta. HPO:probinson Hypoplasia of the lacrimal puncta Hypoplastic lacrimal puncta Reduced pigmentation of the fundus, typically generalised. Fundoscopy may reveal a low level pigment in both RPE and choroid with clear visibility of choroidal vessels (pale/albinoid) or low pigment level in the RPE with deep pigment in choroid so that visible choroidal vessels are separated by deeply pigmented zones (tesselated/tigroid). HP:0001111 HP:0001487 HP:0007746 HP:0007752 SNOMEDCT_US:95694000 UMLS:C0151891 Decreased fundus pigmentation Fundus hypopigmentation human_phenotype HP:0007894 Hypopigmentation of the fundus Reduced pigmentation of the fundus, typically generalised. Fundoscopy may reveal a low level pigment in both RPE and choroid with clear visibility of choroidal vessels (pale/albinoid) or low pigment level in the RPE with deep pigment in choroid so that visible choroidal vessels are separated by deeply pigmented zones (tesselated/tigroid). ORCID:0000-0003-0986-4123 UMLS:C1968574 Underdeveloped tear duct human_phenotype HP:0007900 Hypoplastic lacrimal duct Underdeveloped tear duct ORCID:0000-0001-5208-3432 Bleeding within the vitreous compartment of the eye. MSH:D014823 SNOMEDCT_US:31341008 UMLS:C0042909 Vitreous haemorrhage human_phenotype HP:0007902 The most common causes include proliferative diabetic retinopathy, vitreous detachment with or without retinal breaks, and trauma. Less common causes include vascular occlusive disease, retinal arterial macroaneurysm, hemoglobinopathies, age-related macular degeneration, intraocular tumors, and others. Vitreous hemorrhage Bleeding within the vitreous compartment of the eye. DDD:akelly PMID:16882398 Vitreous haemorrhage UMLS:C3275963 Abnormality of iris blood vessels human_phenotype HP:0007905 Abnormal iris vasculature Abnormality of iris blood vessels ORCID:0000-0001-5208-3432 The presence of developmental dysplasia of the retina. HP:0007901 HP:0008022 MSH:D015792 SNOMEDCT_US:95494009 UMLS:C0035313 Retinal dysgenesis human_phenotype HP:0007973 This feature is a congenital developmental anomaly of the retina characterized by abnormal growth and differentiation. The retina contains numerous tubular structures and rosettes. Retinal dysplasia (synonym: retinal dysgenesis) is often accompanied by retinal detachment and micropthalmos, but the latter features should be coded separately. Retinal dysplasia The presence of developmental dysplasia of the retina. HPO:probinson Underdevelopment of the stroma of iris. HP:0007991 HP:0008027 UMLS:C1860344 Hypoplastic iris stoma Iris stromal hypoplasia Underdeveloped iris stroma human_phenotype HP:0007990 Hypoplastic iris stroma Underdevelopment of the stroma of iris. HPO:probinson Underdeveloped iris stroma ORCID:0000-0001-6908-9849 Congenital malformation of the lacrimal duct associated with incomplete development of the bony nasolacrimal canal or craniofacial anomalies. UMLS:C4024757 Malformed tear ducts human_phenotype HP:0007993 Malformed lacrimal duct Congenital malformation of the lacrimal duct associated with incomplete development of the bony nasolacrimal canal or craniofacial anomalies. HPO:probinson Malformed tear ducts ORCID:0000-0001-5208-3432 Abnormal pigmentation of the iris. UMLS:C1834387 human_phenotype HP:0008034 Abnormal iris pigmentation Abnormal pigmentation of the iris. HPO:probinson Absence or underdevelopment of the lacrimal gland. UMLS:C1835602 Absent/underdeveloped lacrimal glands Absent/underdeveloped tear glands human_phenotype HP:0008038 Aplastic/hypoplastic lacrimal glands Absence or underdevelopment of the lacrimal gland. HPO:probinson Absent/underdeveloped lacrimal glands ORCID:0000-0001-5208-3432 Absent/underdeveloped tear glands ORCID:0000-0001-5208-3432 A structural abnormality of retinal vasculature. peter 2008-04-02T12:09:00Z UMLS:C4024753 Abnormality of retina blood vessels Abnormality of the retinal vasculature human_phenotype HP:0008046 Abnormal retinal vascular morphology A structural abnormality of retinal vasculature. HPO:probinson Abnormality of retina blood vessels ORCID:0000-0001-5208-3432 peter 2008-04-02T12:10:00Z UMLS:C4024752 Abnormality of eye blood vessels human_phenotype HP:0008047 Abnormality of the vasculature of the eye Abnormality of eye blood vessels ORCID:0000-0001-5208-3432 Absence or underdevelopment of the iris. peter 2008-04-02T01:50:00Z UMLS:C4024748 Absent/small iris Absent/underdeveloped iris human_phenotype HP:0008053 Aplasia/Hypoplasia of the iris Absence or underdevelopment of the iris. HPO:probinson Absent/small iris ORCID:0000-0001-5208-3432 Absent/underdeveloped iris ORCID:0000-0001-5208-3432 Absence or underdevelopment of the uvea, the pigmented middle layer of the eye consisting of the iris and ciliary body together with the choroid. peter 2008-04-02T03:24:00Z UMLS:C4024746 Absent/underdeveloped uvea human_phenotype HP:0008055 Aplasia/Hypoplasia affecting the uvea Absence or underdevelopment of the uvea, the pigmented middle layer of the eye consisting of the iris and ciliary body together with the choroid. HPO:probinson Absent/underdeveloped uvea ORCID:0000-0001-5208-3432 peter 2008-04-02T03:25:00Z UMLS:C4024745 Absent/small eye Absent/underdeveloped eye human_phenotype HP:0008056 Aplasia/Hypoplasia affecting the eye Absent/small eye ORCID:0000-0001-5208-3432 Absent/underdeveloped eye ORCID:0000-0001-5208-3432 peter 2008-04-02T03:27:00Z UMLS:C4024744 Absent/small fundus human_phenotype HP:0008057 Aplasia/Hypoplasia affecting the fundus Absent/small fundus ORCID:0000-0001-5208-3432 https://en.wikipedia.org/wiki/febrile_seizure peter 2008-04-02T03:30:00Z UMLS:C4024740 Absent/small retina Absent/underdeveloped retina human_phenotype HP:0008061 Aplasia/Hypoplasia of the retina Absent/small retina ORCID:0000-0001-5208-3432 Absent/underdeveloped retina ORCID:0000-0001-5208-3432 Absence or underdevelopment of the anterior segment of the eye. peter 2008-04-02T03:33:00Z UMLS:C4024739 human_phenotype HP:0008062 Aplasia/Hypoplasia affecting the anterior segment of the eye Absence or underdevelopment of the anterior segment of the eye. HPO:probinson Absence or underdevelopment of the lens. peter 2008-04-02T03:33:00Z UMLS:C4024738 Absent/small lens Absent/underdeveloped lens human_phenotype HP:0008063 Aplasia/Hypoplasia of the lens Absence or underdevelopment of the lens. HPO:probinson Absent/small lens ORCID:0000-0001-5208-3432 Absent/underdeveloped lens ORCID:0000-0001-5208-3432 peter 2008-04-02T03:44:00Z UMLS:C4024737 Absent/small skin Absent/underdeveloped skin human_phenotype HP:0008065 Aplasia/Hypoplasia of the skin Absent/small skin ORCID:0000-0001-5208-3432 Absent/underdeveloped skin ORCID:0000-0001-5208-3432 The presence of a fifth metatarsal bone that has not undergone ossification at an age when ossification is usually visible. UMLS:C1844712 human_phenotype HP:0008087 Nonossified fifth metatarsal The presence of a fifth metatarsal bone that has not undergone ossification at an age when ossification is usually visible. HPO:probinson An anomaly of the fifth metatarsal bone. UMLS:C4024733 Abnormality of the 5th long bone of foot human_phenotype HP:0008089 Abnormality of the fifth metatarsal bone An anomaly of the fifth metatarsal bone. HPO:probinson Abnormality of the 5th long bone of foot ORCID:0000-0001-5208-3432 Delayed maturation and calcification of any of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. HP:0008145 UMLS:C1846853 UMLS:C4280418 Tarsal delayed ossification human_phenotype Delayed ankle bone maturation HP:0008103 Delayed tarsal ossification Delayed maturation and calcification of any of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. HPO:probinson Delayed ankle bone maturation ORCID:0000-0001-5208-3432 UMLS:C1856746 Deformed ankle bones human_phenotype HP:0008119 Deformed tarsal bones Deformed ankle bones ORCID:0000-0001-5208-3432 UMLS:C4024719 Small adrenal cortex human_phenotype HP:0008182 Adrenocortical hypoplasia Small adrenal cortex ORCID:0000-0001-5208-3432 MSH:D050033 UMLS:C1563716 Thyroid dysplasia human_phenotype HP:0008188 Thyroid dysgenesis The congenital absence of the thyroid gland. MSH:D050033 UMLS:C0749420 UMLS:C4020805 human_phenotype Athyroidal hypothyroidism HP:0008191 Thyroid agenesis The congenital absence of the thyroid gland. HPO:probinson PMID:2918525 Abnormal development of the adrenal gland. UMLS:C1856017 Adrenal gland dysplasia Dysplastic adrenal glands human_phenotype HP:0008216 Adrenal gland dysgenesis Abnormal development of the adrenal gland. DDD:spark Enlargement of the adrenal gland. SNOMEDCT_US:419920004 UMLS:C1621895 Enlarged adrenal glands human_phenotype HP:0008221 Adrenal hyperplasia Enlargement of the adrenal gland. DDD:spark Enlarged adrenal glands Developmental hypoplasia of the adrenal medulla. UMLS:C4024717 Small adrenal medulla human_phenotype HP:0008239 Adrenal medullary hypoplasia Developmental hypoplasia of the adrenal medulla. HPO:probinson Small adrenal medulla ORCID:0000-0001-5208-3432 UMLS:C3151556 human_phenotype HP:0008306 Abnormal iron deposition in mitochondria An abnormality of the mitochondria in muscle tissue. UMLS:C4021546 Abnormal mitochondria in muscle human_phenotype HP:0008316 This finding is typically demonstrated by muscle biopsy. Abnormal mitochondria in muscle tissue An abnormality of the mitochondria in muscle tissue. HPO:probinson Any structural anomaly of the mitochondria. UMLS:C4014650 Abnormal mitochondrion morphology human_phenotype HP:0008322 This feature may be assessed by means of electron microscopy. Abnormal mitochondrial morphology Any structural anomaly of the mitochondria. HPO:probinson An increased urine level of any amino acid carrying two amino groups (Asparagine, glutamine and lysine, cystine, ornithine). UMLS:C4024698 HP:0008339 Diaminoaciduria An increased concentration of a branched chain amino acid in the blood. UMLS:C4024697 human_phenotype HP:0008344 Elevated plasma branched chain amino acids An increased concentration of a branched chain amino acid in the blood. HPO:gcarletti Absence or underdevelopment of the big toe. peter 2008-04-04T11:33:00Z HP:0004694 HP:0008118 HP:0008126 UMLS:C1836213 Absent/small big toe Absent/underdeveloped big toe Aplastic/hypoplastic halluces human_phenotype HP:0008362 Aplasia/Hypoplasia of the hallux Absence or underdevelopment of the big toe. HPO:curators Absent/small big toe ORCID:0000-0001-6908-9849 Absent/underdeveloped big toe ORCID:0000-0001-6908-9849 Absence or underdevelopment of the tarsal bones. peter 2008-04-04T11:35:00Z HP:0008109 UMLS:C1848671 Absent/small ankle bone Absent/underdeveloped ankle bone Aplastic/hypoplastic tarsals human_phenotype HP:0008363 Aplasia/Hypoplasia of the tarsal bones Absence or underdevelopment of the tarsal bones. HPO:curators Absent/small ankle bone ORCID:0000-0001-6908-9849 Absent/underdeveloped ankle bone ORCID:0000-0001-6908-9849 peter 2008-04-04T11:44:00Z SNOMEDCT_US:239742004 UMLS:C0343149 Contractures of the foot joints human_phenotype HP:0008366 Contractures involving the joints of the feet Contractures of the foot joints ORCID:0000-0001-6908-9849 An abnormality of the formation and mineralization of any of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. peter 2008-04-04T11:53:00Z UMLS:C4021544 UMLS:C4025075 Abnormal ossification of tarsal bones Hardening of ankle bones human_phenotype Abnormal maturation of ankle bones HP:0008369 Abnormal tarsal ossification An abnormality of the formation and mineralization of any of the tarsal bones, seven bones of the foot comprising the calcaneus, talus, cuboid, navicular, and the cuneiform bones. HPO:probinson Hardening of ankle bones ORCID:0000-0001-6908-9849 Abnormal maturation of ankle bones ORCID:0000-0001-5208-3432 Any abnormal process of ossification of the metatarsal bones, which normally are each ossified from two centers: one for the body, and one for the head (metatarsal II,III,IV, and V) and one for the body and one for the base (metatarsal I). The ossification process begins in the center of the body about the ninth week, and extends toward either extremity. The center for the base of the first metatarsal appears about the third year, and the centers for the heads of the other bones between the fifth and eighth years. They join the bodies between the eighteenth and twentieth years. peter 2008-04-04T11:59:00Z UMLS:C4021543 Abnormal ossification involving metatarsal bones human_phenotype Abnormal maturation of long bone of foot HP:0008371 Abnormal metatarsal ossification Any abnormal process of ossification of the metatarsal bones, which normally are each ossified from two centers: one for the body, and one for the head (metatarsal II,III,IV, and V) and one for the body and one for the base (metatarsal I). The ossification process begins in the center of the body about the ninth week, and extends toward either extremity. The center for the base of the first metatarsal appears about the third year, and the centers for the heads of the other bones between the fifth and eighth years. They join the bodies between the eighteenth and twentieth years. HPO:probinson Abnormal maturation of long bone of foot ORCID:0000-0001-5208-3432 Small, underdeveloped vertebral bodies. HP:0008431 SNOMEDCT_US:205456006 UMLS:C0345394 Underdeveloped vertebrae human_phenotype HP:0008417 Vertebral hypoplasia Small, underdeveloped vertebral bodies. HPO:probinson Underdeveloped vertebrae The presence of punctiform calcification of the bone of the vertebral bodies. UMLS:C4024678 human_phenotype HP:0008420 Punctate vertebral calcifications The presence of punctiform calcification of the bone of the vertebral bodies. HPO:probinson UMLS:C1863313 human_phenotype HP:0008421 Tall lumbar vertebral bodies The presence of developmental dysplasia of the vertebral column. UMLS:C4021853 human_phenotype HP:0008423 Spinal dysplasia The presence of developmental dysplasia of the vertebral column. HPO:probinson HP:0008415 UMLS:C1835570 Cervical vertebrae hypoplasia Underdeveloped cervical vertebrae human_phenotype HP:0008434 Hypoplastic cervical vertebrae Underdeveloped cervical vertebrae ORCID:0000-0001-6908-9849 UMLS:C2751478 human_phenotype HP:0008437 Bifid thoracic vertebrae Excessive growth of the bones of the vertebral bodies. UMLS:C1834057 human_phenotype HP:0008442 Vertebral hyperostosis Excessive growth of the bones of the vertebral bodies. HPO:curators SNOMEDCT_US:298380006 UMLS:C0575157 human_phenotype HP:0008443 Spinal deformities UMLS:C2751480 human_phenotype HP:0008447 Hypoplastic coccygeal vertebrae A developmental defect characterized by agenesis of one or more vertebral bodies. SNOMEDCT_US:15843004 UMLS:C0158776 Absent vertebrae human_phenotype HP:0008465 Absent vertebra A developmental defect characterized by agenesis of one or more vertebral bodies. PMID:26167231 Absent vertebrae Dysplasia of the cervical vertebral column. MSH:C566140 UMLS:C1861693 human_phenotype HP:0008469 Cervical vertebral dysplasia Dysplasia of the cervical vertebral column. HPO:probinson Decreased ossification of the cervical vertebral bodies, i.e., of the Cervical vertebrae set. UMLS:C4024670 human_phenotype HP:0008477 Poorly ossified cervical vertebrae Decreased ossification of the cervical vertebral bodies, i.e., of the Cervical vertebrae set. HPO:probinson HP:0002773 UMLS:C1863353 Small vertebrae Small vertebral bodies Underdeveloped back bones human_phenotype HP:0008479 Hypoplastic vertebral bodies Underdeveloped back bones https://orcid.org/0000-0002-6548-5200 peter 2008-04-04T02:30:00Z UMLS:C4024662 Absent/small vertebrae Absent/underdeveloped vertebrae human_phenotype HP:0008515 Aplasia/Hypoplasia of the vertebrae Absent/small vertebrae ORCID:0000-0001-5208-3432 Absent/underdeveloped vertebrae ORCID:0000-0001-5208-3432 peter 2008-04-04T02:33:00Z UMLS:C4024659 Absent/small backbone Absent/small spine Absent/small vertebral column Absent/underdeveloped backbone Absent/underdeveloped spine Absent/underdeveloped vertebral column human_phenotype HP:0008518 Aplasia/Hypoplasia involving the vertebral column Absent/small backbone ORCID:0000-0001-6908-9849 Absent/small spine ORCID:0000-0001-6908-9849 Absent/small vertebral column ORCID:0000-0001-5208-3432 Absent/underdeveloped backbone ORCID:0000-0001-6908-9849 Absent/underdeveloped spine ORCID:0000-0001-6908-9849 Absent/underdeveloped vertebral column ORCID:0000-0001-5208-3432 Underdevelopment of the external ear. HP:0000393 HP:0000409 HP:0008550 HP:0008618 HP:0008621 MSH:D065817 SNOMEDCT_US:35045004 UMLS:C0152423 Bilateral microtia Hypoplasia of the external ear Hypoplastic ears Hypoplastic pinna Small ears Small pinnae Underdeveloped ears human_phenotype HP:0008551 The definitions of microtia follow a widely used, surgically based, classification of ear anomalies outlined by Weerda 1988. As microtia indicates at least both decreased length and width, and in more severe forms it includes abnormal shape of structures, all forms are acknowledged to be bundled terms, but are retained here because they are well established. Microtia Underdevelopment of the external ear. HPO:probinson PMID:19152421 PMID:3270622 Small ears Underdeveloped ears The presence of a malformed cochlea. UMLS:C1862050 human_phenotype HP:0008554 A cochlear malformation may include a membranous abnormality, a bony abnormality, or a combination of the two. Cochlear malformation The presence of a malformed cochlea. HPO:probinson A malformation of the auricle of the ear. HP:0008594 UMLS:C1846460 External ear malformation human_phenotype HP:0008572 External ear malformation A malformation of the auricle of the ear. HPO:probinson External ear malformation Developmental hypoplasia of the cochlea. UMLS:C2676974 Hypoplastic cochlea Underdeveloped cochlea human_phenotype HP:0008586 Hypoplasia of the cochlea Developmental hypoplasia of the cochlea. HPO:probinson Underdeveloped cochlea ORCID:0000-0001-6908-9849 UMLS:C1857263 human_phenotype HP:0008608 Hypertrophic auricular cartilage An abnormality of the morphology or structure of the middle ear. UMLS:C1857456 Middle ear malformation Morphological abnormality of the middle ear human_phenotype HP:0008609 Morphological abnormality of the middle ear An abnormality of the morphology or structure of the middle ear. DDD:mbitner-glidicz Middle ear malformation Morphological abnormality of the middle ear An abnormality of the stapes, a stirrup-shaped ossicle in the middle ear. UMLS:C4021532 Stapedial abnormalities human_phenotype HP:0008628 Abnormality of the stapes An abnormality of the stapes, a stirrup-shaped ossicle in the middle ear. HPO:probinson Absence of sex glands (gonads are the organs that produce gametes; testis in males and ovary in females). UMLS:C4024652 Absent gonadal tissue Gonadal agenesis HP:0008633 Gonadal agenesis refers to the lack of development of gonads during fetal development; it may not be possible clinically to determine if gonal tissue was present at any point of development. For this reason, we regard agonadism and gonadal agenesis as synonymous. Agonadism Abnormal enlargement of the urinary bladder. UMLS:C4021531 Hypertrophic urinary bladder human_phenotype HP:0008635 Hypertrophy of the urinary bladder Abnormal enlargement of the urinary bladder. HPO:probinson UMLS:C0239761 Underdeveloped gonad human_phenotype HP:0008639 Gonadal hypoplasia Underdeveloped gonad ORCID:0000-0001-5208-3432 Aplasia or developmental hypoplasia of the fallopian tube. UMLS:C4020791 UMLS:C4024646 Absent/small fallopian tube Absent/underdeveloped fallopian tube human_phenotype Absent or rudimentary fallopian tubes HP:0008655 Aplasia/Hypoplasia of the fallopian tube Aplasia or developmental hypoplasia of the fallopian tube. HPO:probinson Absent/small fallopian tube ORCID:0000-0001-5208-3432 Absent/underdeveloped fallopian tube ORCID:0000-0001-5208-3432 Hypertrophy of the clitoris. HP:0000057 HP:0008728 SNOMEDCT_US:80212005 UMLS:C0156394 Clitoral enlargement Clitoromegaly Enlarged clitoris Hypertrophic clitoris Prominent clitoris human_phenotype HP:0008665 Increased size of the clitoris. Clitoral hypertrophy Hypertrophy of the clitoris. HPO:probinson Enlarged clitoris orcid.org/0000-0002-6548-5200 Absence or underdevelopment of the kidney. HP:0004744 HP:0008701 UMLS:C1857453 Absent/small kidney Absent/underdeveloped kidney Renal agenesis/hypoplasia Renal aplasia/hypoplasia human_phenotype HP:0008678 Renal hypoplasia/aplasia Absence or underdevelopment of the kidney. HPO:probinson Absent/small kidney ORCID:0000-0001-5208-3432 Absent/underdeveloped kidney ORCID:0000-0001-5208-3432 Absence or developmental hypoplasia of the uterus. UMLS:C4024640 Absent/small uterus Absent/underdeveloped uterus human_phenotype HP:0008684 Aplasia/hypoplasia of the uterus Absence or developmental hypoplasia of the uterus. HPO:probinson Absent/small uterus ORCID:0000-0001-5208-3432 Absent/underdeveloped uterus ORCID:0000-0001-5208-3432 UMLS:C1844923 Hypoplastic prostate Underdeveloped prostate human_phenotype HP:0008687 Hypoplasia of the prostate Underdeveloped prostate ORCID:0000-0001-6908-9849 Developmental hypoplasia of the fallopian tube. UMLS:C1968706 Underdeveloped fallopian tube human_phenotype Rudimentary fallopian tubes HP:0008697 Hypoplasia of the fallopian tube Developmental hypoplasia of the fallopian tube. HPO:probinson Underdeveloped fallopian tube ORCID:0000-0001-6908-9849 UMLS:C4024637 human_phenotype HP:0008702 Absent internal genitalia Deposition of calcium salts in gonadal tissue. UMLS:C4024636 human_phenotype HP:0008703 Gonadal calcification Deposition of calcium salts in gonadal tissue. HPO:probinson SNOMEDCT_US:253847002 UMLS:C0302885 human_phenotype HP:0008715 Testicular dysgenesis The presence of a diverticulum (sac or pouch) in the wall of the urethra. SNOMEDCT_US:90531003 UMLS:C0152443 human_phenotype HP:0008722 Urethral diverticulum The presence of a diverticulum (sac or pouch) in the wall of the urethra. HPO:curators Developmental hypoplasia of the ovary. SNOMEDCT_US:93279005 UMLS:C0685840 UMLS:C1835452 Underdeveloped ovary human_phenotype Hypoplastic ovary HP:0008724 Hypoplasia of the ovary Developmental hypoplasia of the ovary. HPO:probinson Underdeveloped ovary ORCID:0000-0001-5208-3432 Developmental hypoplasia of the vagina. HP:0011938 SNOMEDCT_US:253836009 UMLS:C0345309 UMLS:C1442988 Rudimentary vagina Underdeveloped vagina human_phenotype Hypoplastic vagina HP:0008726 Hypoplasia of the vagina Developmental hypoplasia of the vagina. HPO:probinson Underdeveloped vagina ORCID:0000-0001-5208-3432 Reduced volume of the testicle (the male gonad). HP:0000043 SNOMEDCT_US:276411001 UMLS:C0241355 Decreased testicular size Hypoplastic testes Small testes Small testis Testicular hypoplasia human_phenotype HP:0008734 Decreased testicular size Reduced volume of the testicle (the male gonad). HPO:probinson Decreased testicular size Small testes Small testis HP:0008632 SNOMEDCT_US:34911001 UMLS:C0266435 Underdeveloped penis human_phenotype HP:0008736 Hypoplasia of penis Underdeveloped penis Ossification affecting the set of cartilages of larynx. UMLS:C1855622 human_phenotype HP:0008747 This term describes abnormal ossification affecting one or more of the cartilages of the larnyx (cricoid cartilage, thyroid cartilage, epiglottic cartilage, arytenoid cartilage, corniculate cartilage, cuneiform cartilage, triticeal cartilage, and sesamoid cartilage). Cartilaginous ossification of larynx Ossification affecting the set of cartilages of larynx. HPO:probinson Underdevelopment of the larynx. HP:0005935 SNOMEDCT_US:253736003 UMLS:C0431527 Hypoplastic larynx human_phenotype HP:0008749 Laryngeal hypoplasia Underdevelopment of the larynx. HPO:probinson Presence of a gap in the posterior laryngotracheal wall with a continuity between the larynx and the esopahagus. MSH:C537875 SNOMEDCT_US:232461002 UMLS:C1840311 Laryngotracheal cleft Laryngotracheoesophageal cleft i human_phenotype HP:0008751 Embryologically, the trachea and esophagus share a common lumen until they are separated by the development of the tracheoesophageal septum. Failure of this fusion and incomplete development of the tracheoesophageal septum may lead to congenital abnormalities such as isolatedlaryngeal cleft, tracheoesophageal fistula, and esophageal atresia, depending on the severity of the abnormality. Patients with laryngeal cleft may present with feeding difficulty, chronic cough, stridor, pneumonia or respiratory distress, depending on the size of the cleft. Laryngeal cleft Presence of a gap in the posterior laryngotracheal wall with a continuity between the larynx and the esopahagus. HPO:probinson PMID:17178945 A malformation of the laryngeal cartilage. HP:0008375 UMLS:C4021530 Vocal impairment, severe, due to laryngeal cartilage abnormalities human_phenotype HP:0008752 Laryngeal cartilage malformation A malformation of the laryngeal cartilage. HPO:probinson Calcification (abnormal deposits of calcium) in the laryngeal tissues. HP:0008748 UMLS:C1859158 Laryngeal calcifications human_phenotype HP:0008754 Laryngeal calcification Calcification (abnormal deposits of calcium) in the laryngeal tissues. HPO:probinson Laryngeal calcifications The presence of aplasia or developmental hypoplasia of the ear. peter 2008-04-04T05:44:00Z UMLS:C4024627 Absent/small ear Absent/underdeveloped ear human_phenotype HP:0008771 Aplasia/Hypoplasia of the ear The presence of aplasia or developmental hypoplasia of the ear. HPO:probinson Absent/small ear ORCID:0000-0001-5208-3432 Absent/underdeveloped ear ORCID:0000-0001-5208-3432 The presence of aplasia or developmental hypoplasia of all or part of the external ear. peter 2008-04-04T05:45:00Z UMLS:C4024626 Absent/small external ear Absent/underdeveloped external ear human_phenotype HP:0008772 Aplasia/Hypoplasia of the external ear The presence of aplasia or developmental hypoplasia of all or part of the external ear. HPO:probinson Absent/small external ear ORCID:0000-0001-5208-3432 Absent/underdeveloped external ear ORCID:0000-0001-5208-3432 Aplasia or developmental hypoplasia of all or part of the middle ear. peter 2008-04-04T05:47:00Z HP:0008533 HP:0008548 UMLS:C4021529 Absent/small middle ear Absent/underdeveloped middle ear Hypoplastic/aplastic middle ear structures Middle ear hypoplasia/aplasia human_phenotype HP:0008773 Aplasia/Hypoplasia of the middle ear Aplasia or developmental hypoplasia of all or part of the middle ear. HPO:probinson Absent/small middle ear ORCID:0000-0001-5208-3432 Absent/underdeveloped middle ear ORCID:0000-0001-5208-3432 Aplasia or developmental hypoplasia of the inner ear. peter 2008-04-04T05:48:00Z UMLS:C4024625 Absent/small inner ear Absent/underdeveloped inner ear human_phenotype HP:0008774 Aplasia/Hypoplasia of the inner ear Aplasia or developmental hypoplasia of the inner ear. HPO:probinson Absent/small inner ear ORCID:0000-0001-5208-3432 Absent/underdeveloped inner ear ORCID:0000-0001-5208-3432 An abnormality of the prostate. peter 2008-04-04T06:01:00Z UMLS:C0747987 Abnormality of the prostate human_phenotype HP:0008775 Abnormal prostate morphology An abnormality of the prostate. HPO:probinson Abnormality of the prostate Any structural abnormality of the renal artery. peter 2008-04-04T06:13:00Z UMLS:C4024624 Abnormal kidney artery Abnormality of the renal artery human_phenotype HP:0008776 Abnormal renal artery morphology Any structural abnormality of the renal artery. HPO:probinson Abnormal kidney artery ORCID:0000-0001-5208-3432 A decreased ability to move the femur at the hip joint associated with a decreased range of motion of the hip. UMLS:C1851542 Limited hip movement human_phenotype HP:0008800 Limited hip movement A decreased ability to move the femur at the hip joint associated with a decreased range of motion of the hip. HPO:probinson Limited hip movement Underdevelopment of the femoral head. HP:0008831 UMLS:C1856920 Hypoplastic femoral head Small femoral heads Small head of thigh bone human_phenotype HP:0008802 Hypoplasia of the femoral head Underdevelopment of the femoral head. HPO:probinson Small head of thigh bone ORCID:0000-0001-5208-3432 The presence of developmental dysplasia of the acetabular part of hip bone. HP:0008799 MSH:D006617 UMLS:C1328407 Dysplastic acetabulae human_phenotype HP:0008807 Acetabular dysplasia The presence of developmental dysplasia of the acetabular part of hip bone. HPO:probinson Lack of ossification of the proximal epiphysis of the femur. UMLS:C1968686 Absent ossification of femoral capital epiphyses human_phenotype HP:0008820 The ossification center of the capital femoral epiphysis appears at the end of the first year after birth. Absent ossification of capital femoral epiphysis Lack of ossification of the proximal epiphysis of the femur. HPO:probinson Developmental delay of ossification of the proximal epiphysis of the femur. UMLS:C1855222 Delayed ossification of the proximal femoral epiphysis Delayed ossification proximal femoral epiphyses human_phenotype HP:0008828 The proximal femoral epiphyseal ossification center normally appears at about age 6 months. Delayed proximal femoral epiphyseal ossification Developmental delay of ossification of the proximal epiphysis of the femur. HPO:probinson Delayed ossification of the femoral head. UMLS:C1846446 UMLS:C4280410 human_phenotype Delayed maturation of the head of the thigh bone HP:0008829 Delayed femoral head ossification Delayed ossification of the femoral head. HPO:probinson Delayed maturation of the head of the thigh bone ORCID:0000-0001-5208-3432 There is normally one ossification center in the head of the femur. This term applies if there are multiple such centers. UMLS:C1846447 human_phenotype HP:0008835 Additionally, the ossification center of the capital femoral epiphysis appears at the end of the first year after birth. This is not what this term refers to. Multicentric femoral head ossification There is normally one ossification center in the head of the femur. This term applies if there are multiple such centers. HPO:probinson Underdevelopment of the bony pelvis. HP:0003373 HP:0008816 UMLS:C3536734 Hypoplastic pelvic bones Small pelvis human_phenotype HP:0008839 Hypoplastic pelvis Underdevelopment of the bony pelvis. HPO:probinson A type of disproportionate short stature characterized by a short limbs but an average-sized trunk. HP:0001523 HP:0003505 HP:0003509 HP:0008858 HP:0008869 HP:0008875 HP:0008880 HP:0008881 HP:0008889 HP:0008912 HP:0008914 HP:0008928 UMLS:C1849937 Brachymelic dwarfism Disproportionate short limb dwarfism Dwarfism, short-limbed Micromelic dwarfism Short limb dwarfism, disproportionate Short stature, disproportionate short limb Short stature, disproportionate short-limb Short-limb dwarfism Short-limbed dwarfism human_phenotype Short limb dwarfism HP:0008873 A type of dwarfism (marked short stature with adult height below 147 cm) in which the limbs are disproportionatley affected. Note that brachymelia is a general term refering to shortening of the limbs. Micromelia refers to the shortening of entire limbs (in contrast to rhizomelia, mesomelia, and acromelia, which refer to shortening of the proximal, middle, or distal portions of the limbs). Disproportionate short-limb short stature A type of disproportionate short stature characterized by a short limbs but an average-sized trunk. HPO:probinson Short limb dwarfism, disproportionate Short-limbed dwarfism Short limb dwarfism HPO:skoehler A loss of adipose tissue. HP:0008938 UMLS:C4024615 Loss of fat tissue human_phenotype HP:0008887 Adipose tissue loss A loss of adipose tissue. HPO:probinson Loss of fat tissue ORCID:0000-0001-5208-3432 Underdevelopment of muscles of the shoulder. UMLS:C1969001 Underdeveloped shoulder muscle human_phenotype HP:0008952 Shoulder muscle hypoplasia Underdevelopment of muscles of the shoulder. HPO:probinson Underdeveloped shoulder muscle ORCID:0000-0001-5208-3432 Underdevelopment of the muscuklature of the calf. UMLS:C3805450 Hypoplastic calf muscles Underdeveloped calf muscles human_phenotype HP:0008962 Calf muscle hypoplasia Underdevelopment of the muscuklature of the calf. HPO:probinson Underdeveloped calf muscles ORCID:0000-0001-5208-3432 Muscle hypertrophy primarily affecting the legs. UMLS:C1850663 human_phenotype HP:0008968 Muscle hypertrophy of the lower extremities Muscle hypertrophy primarily affecting the legs. HPO:curators Muscle hypertrophy affecting the calf muscles. HP:0003703 HP:0009024 UMLS:C1843057 Calf hypertrophy Increased size of calf muscles Muscular hypertrophy of the calf muscles human_phenotype HP:0008981 Distal lower limb hypertrophy Calf muscle hypertrophy Muscle hypertrophy affecting the calf muscles. HPO:curators Increased size of calf muscles ORCID:0000-0001-5208-3432 Underdevelopment of muscles of the neck. UMLS:C1969000 UMLS:C4280408 UMLS:C4280409 Decreased size of neck muscle Small neck muscle Underdevelopment of neck muscle human_phenotype Deficiency of neck muscle Hypotrophic neck muscle HP:0008984 Neck muscle hypoplasia Underdevelopment of muscles of the neck. HPO:curators Decreased size of neck muscle ORCID:0000-0001-5889-4463 Small neck muscle ORCID:0000-0001-5889-4463 Underdevelopment of neck muscle ORCID:0000-0001-5889-4463 Deficiency of neck muscle ORCID:0000-0001-5889-4463 Hypotrophic neck muscle ORCID:0000-0001-5889-4463 An abnormal increase in the amount of intramuscular fat tissue. UMLS:C1835389 Increased IM fat Increased intramuscular fat human_phenotype HP:0008985 Increased intramuscular fat An abnormal increase in the amount of intramuscular fat tissue. HPO:curators Increased IM fat Increased intramuscular fat Congenital lack, i.e., aplasia of the diaphragm. SNOMEDCT_US:702613006 SNOMEDCT_US:72424001 UMLS:C0221360 Absent diaphragm human_phenotype Agenesis of diaphragm HP:0008986 An extremely large diaphragmatic defect, or apparent absence of the hemidiaphragm, is called agenesis of the diaphragm; this defect probably represents the severe end of the Bochdalek hernia spectrum rather than a distinct entity. Agenesis of the diaphragm Congenital lack, i.e., aplasia of the diaphragm. HPO:probinson Absent diaphragm ORCID:0000-0001-5208-3432 An abnormal increase in the amount of intraabdominal fat tissue. UMLS:C1835390 human_phenotype HP:0008993 Increased intraabdominal fat An abnormal increase in the amount of intraabdominal fat tissue. HPO:curators Loss (reduction of previously present) of subcutaneous adipose tissue in the region of the trunk. HP:0008989 UMLS:C1835384 Loss of fat tissue in trunk Loss of subcutaneous truncal adipose tissue Loss of truncal adipose tissue human_phenotype HP:0009002 Loss of truncal subcutaneous adipose tissue Loss (reduction of previously present) of subcutaneous adipose tissue in the region of the trunk. HPO:probinson Loss of fat tissue in trunk ORCID:0000-0001-5208-3432 The presence of an abnormally increased amount of subcutaneous adipose tissue in the trunk of the body. UMLS:C1837781 Increased fat below the skin in trunk human_phenotype HP:0009003 Increased subcutaneous truncal adipose tissue The presence of an abnormally increased amount of subcutaneous adipose tissue in the trunk of the body. HPO:curators Increased fat below the skin in trunk ORCID:0000-0001-5208-3432 Underdevelopment of the musculature. HP:0009034 SNOMEDCT_US:205530002 UMLS:C0240414 Muscle hypoplasia Poorly developed skeletal musculature Underdeveloped muscle Underdeveloped muscles human_phenotype HP:0009004 Hypoplasia of the musculature Underdevelopment of the musculature. HPO:sdoelken Poorly developed skeletal musculature Underdeveloped muscle ORCID:0000-0001-5208-3432 Underdevelopment of muscles of the arm. UMLS:C1846478 Underdevelopment of upper limb muscles human_phenotype HP:0009016 Upper limb muscle hypoplasia Underdevelopment of muscles of the arm. HPO:curators Underdevelopment of upper limb muscles ORCID:0000-0001-5208-3432 The presence of an abnormally increased amount of connective tissue. UMLS:C1866021 human_phenotype HP:0009025 Increased connective tissue The presence of an abnormally increased amount of connective tissue. HPO:curators UMLS:C4024602 Loss of fat tissue below the skin from upper limbs human_phenotype HP:0009056 Loss of subcutaneous adipose tissue from upper limbs Loss of fat tissue below the skin from upper limbs ORCID:0000-0001-5208-3432 An abnormal accumulation of lipids in skeletal muscle. HP:0100949 UMLS:C1837262 Fat accumulation in muscle fibers Fat deposits in muscle fibers Increased muscle lipid content Lipid accumulation in skeletal muscle Muscle lipidosis Skeletal muscle lipid accumulation human_phenotype HP:0009058 Increased neutral lipid content may be observed on muscle biopsies specimen with the specific staining of Sudan black or oil red O techniques by optic microscopy. Increased muscle lipid content An abnormal accumulation of lipids in skeletal muscle. HPO:probinson PMID:20691590 Fat accumulation in muscle fibers Fat deposits in muscle fibers Increased muscle lipid content Lipid accumulation in skeletal muscle Skeletal muscle lipid accumulation peter 2008-04-04T08:40:00Z UMLS:C4024597 Absent/small pelvis Absent/underdeveloped pelvis human_phenotype HP:0009103 Aplasia/Hypoplasia involving the pelvis Absent/small pelvis ORCID:0000-0001-5208-3432 Absent/underdeveloped pelvis ORCID:0000-0001-5208-3432 An abnormality of the formation and mineralization of any bone of the bony pelvis. peter 2008-04-04T08:42:00Z UMLS:C4021525 UMLS:C4280402 Abnormal ossification involving the bones of the pelvis human_phenotype Abnormal maturation of the pelvis bone HP:0009106 Abnormal pelvis bone ossification An abnormality of the formation and mineralization of any bone of the bony pelvis. HPO:probinson Abnormal maturation of the pelvis bone ORCID:0000-0001-5208-3432 peter 2008-04-04T08:42:00Z UMLS:C4024595 human_phenotype Abnormal maturation of thigh bone head and neck HP:0009107 Abnormal ossification involving the femoral head and neck HPO:skoehler Abnormal maturation of thigh bone head and neck ORCID:0000-0001-5208-3432 peter 2008-04-04T08:44:00Z UMLS:C4024594 Absent/small head and neck of thighbone Absent/underdeveloped head and neck of thighbone human_phenotype HP:0009108 Aplasia/Hypoplasia involving the femoral head and neck Absent/small head and neck of thighbone ORCID:0000-0001-5208-3432 Absent/underdeveloped head and neck of thighbone ORCID:0000-0001-5208-3432 Absence (due to failure to form) or underdevelopment of one or more components of the skeleton. peter 2008-04-05T10:53:00Z UMLS:C4024592 Absent/small skeleton Absent/underdeveloped skeleton human_phenotype HP:0009115 Aplasia/hypoplasia involving the skeleton Absence (due to failure to form) or underdevelopment of one or more components of the skeleton. HPO:probinson Absent/small skeleton ORCID:0000-0001-5208-3432 Absent/underdeveloped skeleton ORCID:0000-0001-5208-3432 peter 2008-04-05T10:53:00Z UMLS:C4024591 human_phenotype HP:0009116 Aplasia/Hypoplasia involving bones of the skull An abnormality of the axial skeleton, which comprises the skull, the vertebral column, the ribs and the sternum. peter 2008-04-05T11:16:00Z UMLS:C4020785 UMLS:C4024586 human_phenotype Abnormality of the axial skeleton HP:0009121 Abnormal axial skeleton morphology An abnormality of the axial skeleton, which comprises the skull, the vertebral column, the ribs and the sternum. HPO:probinson Absence (due to failure to form) or underdevelopment of bones of the axial skeleton. peter 2008-04-05T11:29:00Z UMLS:C4024585 human_phenotype HP:0009122 Aplasia/hypoplasia affecting bones of the axial skeleton Absence (due to failure to form) or underdevelopment of bones of the axial skeleton. HPO:probinson An abnormality of adipose tissue, which is loose connective tissue composed of adipocytes. peter 2008-04-05T11:40:00Z UMLS:C4021524 Abnormality of adipose tissue Abnormality of fat tissue Abnormality of fatty tissue human_phenotype HP:0009124 Abnormal adipose tissue morphology An abnormality of adipose tissue, which is loose connective tissue composed of adipocytes. HPO:curators Abnormality of adipose tissue Abnormality of fat tissue ORCID:0000-0001-5208-3432 Abnormality of fatty tissue An increase in adipose tissue mass by hyperplastic growth (increase in the number of adipocytes) or by hypertrophic growth (increase in the size of adipocytes occurring primarily by lipid accumulation within the cell). peter 2008-04-05T11:43:00Z UMLS:C4024583 Increased adipose tissue Increased fat tissue human_phenotype HP:0009126 Increased adipose tissue An increase in adipose tissue mass by hyperplastic growth (increase in the number of adipocytes) or by hypertrophic growth (increase in the size of adipocytes occurring primarily by lipid accumulation within the cell). HPO:curators Increased adipose tissue Increased fat tissue ORCID:0000-0001-5208-3432 peter 2008-04-07T02:00:00Z UMLS:C4024582 Abnormal limb muscles Muscle issues in the arms and/or legs human_phenotype HP:0009127 Abnormality of the musculature of the limbs Abnormal limb muscles ORCID:0000-0001-5208-3432 Muscle issues in the arms and/or legs peter 2008-04-07T02:01:00Z UMLS:C4024581 Absent/small muscles of extremities Absent/underdeveloped muscles of extremities human_phenotype HP:0009128 Aplasia/Hypoplasia involving the musculature of the extremities Absent/small muscles of extremities ORCID:0000-0001-5208-3432 Absent/underdeveloped muscles of extremities ORCID:0000-0001-5208-3432 A disease or lesion affecting the muscles of the thorax. peter 2008-04-07T05:06:00Z UMLS:C4024580 human_phenotype HP:0009131 Abnormality of the musculature of the thorax A disease or lesion affecting the muscles of the thorax. HPO:curators This term applies to all changes in bone mineral density of the tarsal bones, which (depending on severity) can be seen on x-rays as a change in density and or structure of the bone. peter 2008-04-17T02:39:00Z UMLS:C4021522 Abnormality of bone mineral density involving tarsal bones human_phenotype HP:0009132 Abnormal tarsal bone mineral density This term applies to all changes in bone mineral density of the tarsal bones, which (depending on severity) can be seen on x-rays as a change in density and or structure of the bone. HPO:probinson peter 2008-04-17T02:45:00Z UMLS:C4024578 Duplication involving bones of the feet human_phenotype HP:0009136 Duplication involving bones of the feet Duplication involving bones of the feet peter 2008-05-02T01:23:00Z UMLS:C4024574 Duplication of bones involving the upper extremities human_phenotype HP:0009142 Duplication of bones involving the upper extremities Duplication of bones involving the upper extremities peter 2008-05-02T01:29:00Z UMLS:C4024573 human_phenotype HP:0009144 Supernumerary bones of the axial skeleton Any structural anomaly of a cerebral artery. The cerebral arteries comprise three main pairs of arteries and their branches, which supply the cerebrum of the brain. These are the anterior cerebral artery, the middle cerebral artery, and the posterior cerebral artery. peter 2008-05-02T01:39:00Z UMLS:C4021520 Abnormality of cerebral artery Abnormality of the cerebral arteries human_phenotype HP:0009145 Abnormal cerebral artery morphology Any structural anomaly of a cerebral artery. The cerebral arteries comprise three main pairs of arteries and their branches, which supply the cerebrum of the brain. These are the anterior cerebral artery, the middle cerebral artery, and the posterior cerebral artery. HPO:probinson Abnormality of cerebral artery Abnormality of the cerebral arteries Abnormally large size of the epiphysis located at the proximal end of the distal phalanx of the 5th finger with respect to age-dependent norms. peter 2008-12-22T01:39:32Z UMLS:C4024572 Enlarged end part of the outermost bone of little finger Enlarged end part of the outermost bone of pinkie finger Enlarged end part of the outermost bone of pinky finger human_phenotype HP:0009147 Enlarged epiphysis of the distal phalanx of the 5th finger Abnormally large size of the epiphysis located at the proximal end of the distal phalanx of the 5th finger with respect to age-dependent norms. HPO:curators Enlarged end part of the outermost bone of little finger ORCID:0000-0001-5208-3432 Enlarged end part of the outermost bone of pinkie finger ORCID:0000-0001-5208-3432 Enlarged end part of the outermost bone of pinky finger ORCID:0000-0001-5208-3432 Abnormally small size of the epiphysis located at the proximal end of the distal phalanx of the 5th finger with respect to age-dependent norms. peter 2008-12-22T01:40:08Z UMLS:C4024571 Small end part of the outermost bone of little finger Small end part of the outermost bone of pinkie finger Small end part of the outermost bone of pinky finger human_phenotype HP:0009148 Small epiphysis of the distal phalanx of the 5th finger Abnormally small size of the epiphysis located at the proximal end of the distal phalanx of the 5th finger with respect to age-dependent norms. HPO:curators Small end part of the outermost bone of little finger ORCID:0000-0001-5208-3432 Small end part of the outermost bone of pinkie finger ORCID:0000-0001-5208-3432 Small end part of the outermost bone of pinky finger ORCID:0000-0001-5208-3432 A triangular appearance of the epiphysis of the distal phalanx of the little finger of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. peter 2008-12-22T01:40:48Z HP:0009137 UMLS:C4021519 Delta-shaped epiphysis of the distal phalanx of the 5th finger Triangular end part of the outermost bone of little finger Triangular end part of the outermost bone of pinkie finger Triangular end part of the outermost bone of pinky finger human_phenotype HP:0009149 Triangular epiphysis of the distal phalanx of the 5th finger A triangular appearance of the epiphysis of the distal phalanx of the little finger of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. HPO:curators Triangular end part of the outermost bone of little finger ORCID:0000-0001-5208-3432 Triangular end part of the outermost bone of pinkie finger ORCID:0000-0001-5208-3432 Triangular end part of the outermost bone of pinky finger ORCID:0000-0001-5208-3432 Abnormality of the proximal phalanx of the little (5th) finger. peter 2008-12-22T02:00:20Z UMLS:C4024570 Abnormality of the innermost bone little finger Abnormality of the innermost bone pinkie finger Abnormality of the innermost bone pinky finger human_phenotype HP:0009150 Abnormality of the proximal phalanx of the 5th finger Abnormality of the proximal phalanx of the little (5th) finger. HPO:curators Abnormality of the innermost bone little finger ORCID:0000-0001-5208-3432 Abnormality of the innermost bone pinkie finger ORCID:0000-0001-5208-3432 Abnormality of the innermost bone pinky finger ORCID:0000-0001-5208-3432 Abnormality of one or all of the epiphyses of the proximal, middle, and distal phalanges of the 5th finger. peter 2008-12-22T02:07:27Z UMLS:C4024569 Abnormality of end part of little finger bone Abnormality of end part of pinkie finger bone Abnormality of end part of pinky finger bone human_phenotype HP:0009152 Abnormality of the epiphyses of the 5th finger Abnormality of one or all of the epiphyses of the proximal, middle, and distal phalanges of the 5th finger. HPO:sdoelken Abnormality of end part of little finger bone ORCID:0000-0001-5208-3432 Abnormality of end part of pinkie finger bone ORCID:0000-0001-5208-3432 Abnormality of end part of pinky finger bone ORCID:0000-0001-5208-3432 Abnormality of the epiphysis of the proximal phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. peter 2008-12-22T05:47:42Z UMLS:C4024568 Abnormality of end part of the innermost bone of little finger Abnormality of end part of the innermost bone of pinkie finger Abnormality of end part of the innermost bone of pinky finger human_phenotype HP:0009153 Abnormality of the epiphysis of the proximal phalanx of the 5th finger Abnormality of the epiphysis of the proximal phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. HPO:curator Abnormality of end part of the innermost bone of little finger ORCID:0000-0001-5208-3432 Abnormality of end part of the innermost bone of pinkie finger ORCID:0000-0001-5208-3432 Abnormality of end part of the innermost bone of pinky finger ORCID:0000-0001-5208-3432 A triangular appearance of the epiphysis of the proximal phalanx of the little finger of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. peter 2008-12-22T05:50:39Z HP:0009156 UMLS:C4021518 Delta-shaped epiphysis of the proximal phalanx of the 5th finger Triangular end part of the innermost bone of little finger Triangular end part of the innermost bone of pinkie finger Triangular end part of the innermost bone of pinky finger human_phenotype HP:0009154 Triangular epiphysis of the proximal phalanx of the 5th finger A triangular appearance of the epiphysis of the proximal phalanx of the little finger of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. HPO:curators Delta-shaped epiphysis of the proximal phalanx of the 5th finger Triangular end part of the innermost bone of little finger ORCID:0000-0001-5208-3432 Triangular end part of the innermost bone of pinkie finger ORCID:0000-0001-5208-3432 Triangular end part of the innermost bone of pinky finger ORCID:0000-0001-5208-3432 Abnormally large size of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger with respect to age-dependent norms. peter 2008-12-22T05:50:39Z UMLS:C4024566 Enlarged end part of the innermost bone of little finger Enlarged end part of the innermost bone of pinkie finger Enlarged end part of the innermost bone of pinky finger human_phenotype HP:0009158 Enlarged epiphysis of the proximal phalanx of the 5th finger Abnormally large size of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger with respect to age-dependent norms. HPO:curators Enlarged end part of the innermost bone of little finger ORCID:0000-0001-5208-3432 Enlarged end part of the innermost bone of pinkie finger ORCID:0000-0001-5208-3432 Enlarged end part of the innermost bone of pinky finger ORCID:0000-0001-5208-3432 Abnormally small size of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger with respect to age-dependent norms. peter 2008-12-22T05:50:39Z UMLS:C4024565 Small end part of the innermost bone of little finger Small end part of the innermost bone of pinkie finger Small end part of the innermost bone of pinky finger human_phenotype HP:0009159 Small epiphysis of the proximal phalanx of the 5th finger Abnormally small size of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger with respect to age-dependent norms. HPO:curators Small end part of the innermost bone of little finger ORCID:0000-0001-5208-3432 Small end part of the innermost bone of pinkie finger ORCID:0000-0001-5208-3432 Small end part of the innermost bone of pinky finger ORCID:0000-0001-5208-3432 Absence of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger. peter 2008-12-22T05:50:39Z UMLS:C4024564 Absent end part of the innermost bone of little finger Absent end part of the innermost bone of pinkie finger Absent end part of the innermost bone of pinky finger human_phenotype HP:0009160 Absent epiphysis of the proximal phalanx of the 5th finger Absence of the epiphysis located at the proximal end of the proximal phalanx of the 5th finger. HPO:curators Absent end part of the innermost bone of little finger ORCID:0000-0001-5208-3432 Absent end part of the innermost bone of pinkie finger ORCID:0000-0001-5208-3432 Absent end part of the innermost bone of pinky finger ORCID:0000-0001-5208-3432 Absence or underdevelopment (hypoplasia) of the middle phalanx of the little (5th) finger. peter 2008-12-22T05:55:56Z HP:0006242 UMLS:C1834034 Absent/hypoplastic middle phalanx of 5th finger Absent/small middle bone of pinky finger Absent/underdeveloped middle bone of little finger Absent/underdeveloped middle bone of pinkie finger Absent/underdeveloped middle bone of pinky finger human_phenotype HP:0009161 Aplasia/Hypoplasia of the middle phalanx of the 5th finger Absence or underdevelopment (hypoplasia) of the middle phalanx of the little (5th) finger. HPO:curators Absent/small middle bone of pinky finger ORCID:0000-0001-5208-3432 Absent/underdeveloped middle bone of little finger ORCID:0000-0001-5208-3432 Absent/underdeveloped middle bone of pinkie finger ORCID:0000-0001-5208-3432 Absent/underdeveloped middle bone of pinky finger ORCID:0000-0001-5208-3432 peter 2008-12-22T06:53:39Z HP:0006154 UMLS:C1968592 Abnormal calcification of the wrist bones Carpal calcifications human_phenotype HP:0009164 Abnormal calcification of the carpal bones Abnormal calcification of the wrist bones ORCID:0000-0001-5208-3432 A triangular appearance of the epiphyses of the metacarpals. Thess epiphyses are located at the distal end of the metacarpals. doelkens 2008-12-30T02:03:34Z UMLS:C4024558 Triangular end part of the long bone of hand human_phenotype HP:0009171 Triangular epiphyses of the metacarpals A triangular appearance of the epiphyses of the metacarpals. Thess epiphyses are located at the distal end of the metacarpals. HPO:curators Triangular end part of the long bone of hand ORCID:0000-0001-5889-4463 Displacement of the 5th finger from its normal position. peter 2008-12-29T03:29:20Z HP:0006036 UMLS:C4021515 Displaced little finger Displaced pinkie finger Displaced pinky finger Laterally displaced fifth finger human_phenotype HP:0009179 Deviation of the 5th finger Displacement of the 5th finger from its normal position. HPO:sdoelken Displaced little finger ORCID:0000-0001-5208-3432 Displaced pinkie finger ORCID:0000-0001-5208-3432 Displaced pinky finger ORCID:0000-0001-5208-3432 Displacement of the 5th finger towards the ulnar side. peter 2008-12-29T03:30:05Z UMLS:C4024553 human_phenotype HP:0009180 Ulnar deviation of the 5th finger Displacement of the 5th finger towards the ulnar side. HPO:sdoelken Triangular shaped middle phalanx of the 5th (little) finger. A triangular or so called delta shaped phalanx is a typical result after a bracket epiphysis of the affected phalanx. peter 2008-12-29T04:05:33Z UMLS:C4024552 Triangular shaped middle little finger bone Triangular shaped middle pinkie finger bone Triangular shaped middle pinky finger bone human_phenotype HP:0009182 Triangular shaped middle phalanx of the 5th finger Triangular shaped middle phalanx of the 5th (little) finger. A triangular or so called delta shaped phalanx is a typical result after a bracket epiphysis of the affected phalanx. HPO:curators Triangular shaped middle little finger bone ORCID:0000-0001-5208-3432 Triangular shaped middle pinkie finger bone ORCID:0000-0001-5208-3432 Triangular shaped middle pinky finger bone ORCID:0000-0001-5208-3432 Chronic loss of joint motion in the 5th finger due to structural changes in non-bony tissue. The term camptodactyly of the 5th finger is used if the distal and/or proximal interphalangeal joints are affected. peter 2008-12-29T04:11:30Z HP:0001184 UMLS:C1865702 human_phenotype 5th finger camptodactyly Fifth finger camptodactyly HP:0009183 Joint contracture of the 5th finger Chronic loss of joint motion in the 5th finger due to structural changes in non-bony tissue. The term camptodactyly of the 5th finger is used if the distal and/or proximal interphalangeal joints are affected. HPO:sdoelken Chronic loss of joint motion of the distal interphalangeal joint of the 5th finger due to structural changes in non-bony tissue. peter 2008-12-29T04:16:15Z UMLS:C4024551 human_phenotype HP:0009184 Contracture of the distal interphalangeal joint of the 5th finger Chronic loss of joint motion of the distal interphalangeal joint of the 5th finger due to structural changes in non-bony tissue. HPO:probinson Proximal interphalangeal (PIP) flexion deformity of the little finger. That is, the PIP joint of a little finger is bent (flexed) and cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement. peter 2008-12-29T04:16:58Z HP:0005047 HP:0006062 UMLS:C3554612 human_phenotype HP:0009185 Contracture of the proximal interphalangeal joint of the 5th finger Proximal interphalangeal (PIP) flexion deformity of the little finger. That is, the PIP joint of a little finger is bent (flexed) and cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement. HPO:probinson Chronic loss of joint motion of the metacarpophalangeal joint of the 5th finger due to structural changes in non-bony tissue. peter 2008-12-29T04:18:00Z UMLS:C4024550 human_phenotype HP:0009186 Contracture of the metacarpophalangeal joint of the 5th finger Chronic loss of joint motion of the metacarpophalangeal joint of the 5th finger due to structural changes in non-bony tissue. HPO:curator A secondary ossification center in the distal phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. doelkens 2008-12-30T12:28:19Z UMLS:C4024548 human_phenotype HP:0009188 Pseudoepiphysis of the distal phalanx of the 5th finger A secondary ossification center in the distal phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. HPO:curators Absence or underdevelopment (hypoplasia) of the proximal phalanx of the little (5th) finger. doelkens 2009-01-05T05:57:28Z UMLS:C4024544 Absent/small innermost little finger bone Absent/small innermost pinkie finger bone Absent/small innermost pinky finger bone Absent/underdeveloped innermost pinky finger bone human_phenotype HP:0009192 Aplasia/Hypoplasia of the proximal phalanx of the 5th finger Absence or underdevelopment (hypoplasia) of the proximal phalanx of the little (5th) finger. HPO:curators Absent/small innermost little finger bone ORCID:0000-0001-5208-3432 Absent/small innermost pinkie finger bone ORCID:0000-0001-5208-3432 Absent/small innermost pinky finger bone ORCID:0000-0001-5208-3432 Absent/underdeveloped innermost pinky finger bone ORCID:0000-0001-5208-3432 A pseudoepiphysis is a secondary ossification center distinct from the normal epiphysis. The normal metacarpal epiphyses are located at the distal ends of the metacarpal bones. Accessory epiphyses (which are also known as pseudoepiphyses) can also occasionally be observed at the proximal ends of the metacarpals, usually involving the 2nd metacarpal bone. doelkens 2008-12-30T02:03:34Z HP:0006091 HP:0006164 UMLS:C1860253 Accessory proximal metacarpal ossification centers Metacarpal pseudoepiphyses human_phenotype HP:0009193 Pseudoepiphyses of the metacarpals A pseudoepiphysis is a secondary ossification center distinct from the normal epiphysis. The normal metacarpal epiphyses are located at the distal ends of the metacarpal bones. Accessory epiphyses (which are also known as pseudoepiphyses) can also occasionally be observed at the proximal ends of the metacarpals, usually involving the 2nd metacarpal bone. HPO:doelkens Abnormally small size of the epiphyses located at the distal end of the metacarpals in respect to age-dependent norms. doelkens 2008-12-30T02:03:34Z UMLS:C4024543 Small end part of the long bone of hand human_phenotype HP:0009194 Small epiphyses of the metacarpals Abnormally small size of the epiphyses located at the distal end of the metacarpals in respect to age-dependent norms. HPO:curators Small end part of the long bone of hand ORCID:0000-0001-5208-3432 Absence of the epiphyses of the metacarpal bones, which are normally located at the distal ends of the metacarpals. doelkens 2008-12-30T02:03:34Z HP:0006013 UMLS:C4021513 Absent end part of the long bone of hand Absent metacarpal ossification center human_phenotype HP:0009196 Absent metacarpal epiphyses Absence of the epiphyses of the metacarpal bones, which are normally located at the distal ends of the metacarpals. HPO:curators Absent end part of the long bone of hand ORCID:0000-0001-5208-3432 Abnormality of the epiphysis of the distal phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. doelkens 2009-01-05T04:41:32Z HP:0004228 UMLS:C4021512 Abnormality of end part of the outermost bone of the little finger Abnormality of end part of the outermost bone of the pinkie finger Abnormality of end part of the outermost bone of the pinky finger Abnormality of the epiphysis of the terminal phalanx of the little finger human_phenotype HP:0009198 Abnormality of the epiphysis of the distal phalanx of the 5th finger Abnormality of the epiphysis of the distal phalanx of the fifth finger. This epiphysis is located on the proximal end of the phalanx. HPO:curators Abnormality of end part of the outermost bone of the little finger Abnormality of end part of the outermost bone of the pinkie finger Abnormality of end part of the outermost bone of the pinky finger A secondary ossification center in the proximal phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. doelkens 2009-01-05T05:10:13Z UMLS:C4024540 human_phenotype HP:0009200 Pseudoepiphysis of the proximal phalanx of the 5th finger A secondary ossification center in the proximal phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. HPO:curators Absence of the epiphysis located at the proximal end of the middle phalanx of the 5th finger. doelkens 2009-01-05T05:22:18Z UMLS:C4024537 Absent end part of the middle bone of the little finger Absent end part of the middle bone of the pinkie finger Absent end part of the middle bone of the pinky finger human_phenotype HP:0009203 Absent epiphysis of the middle phalanx of the 5th finger Absence of the epiphysis located at the proximal end of the middle phalanx of the 5th finger. HPO:curators Absent end part of the middle bone of the little finger ORCID:0000-0001-5208-3432 Absent end part of the middle bone of the pinkie finger ORCID:0000-0001-5208-3432 Absent end part of the middle bone of the pinky finger ORCID:0000-0001-5208-3432 Abnormally large size of the epiphysis located at the proximal end of the middle phalanx of the 5th finger with respect to age-dependent norms. doelkens 2009-01-05T05:22:18Z UMLS:C4024534 Enlarged end part of the middle bone of the little finger Enlarged end part of the middle bone of the pinkie finger Enlarged end part of the middle bone of the pinky finger human_phenotype HP:0009206 Enlarged epiphysis of the middle phalanx of the 5th finger Abnormally large size of the epiphysis located at the proximal end of the middle phalanx of the 5th finger with respect to age-dependent norms. HPO:curators Enlarged end part of the middle bone of the little finger ORCID:0000-0001-5208-3432 Enlarged end part of the middle bone of the pinkie finger ORCID:0000-0001-5208-3432 Enlarged end part of the middle bone of the pinky finger ORCID:0000-0001-5208-3432 A secondary ossification center in the middle phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. doelkens 2009-01-05T05:22:18Z UMLS:C4024530 human_phenotype HP:0009210 Pseudoepiphysis of the middle phalanx of the 5th finger A secondary ossification center in the middle phalanx of the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. HPO:curators Abnormally small size of the epiphysis located at the proximal end of the middle phalanx of the 5th finger with respect to age-dependent norms. doelkens 2009-01-05T05:22:18Z UMLS:C4024529 Small end part of the middle bone of the little finger Small end part of the middle bone of the pinkie finger Small end part of the middle bone of the pinky finger human_phenotype HP:0009211 Small epiphysis of the middle phalanx of the 5th finger Abnormally small size of the epiphysis located at the proximal end of the middle phalanx of the 5th finger with respect to age-dependent norms. HPO:curators Small end part of the middle bone of the little finger ORCID:0000-0001-5208-3432 Small end part of the middle bone of the pinkie finger ORCID:0000-0001-5208-3432 Small end part of the middle bone of the pinky finger ORCID:0000-0001-5208-3432 A triangular appearance of the epiphysis of the middle phalanx of the little finger of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. doelkens 2009-01-05T05:22:18Z UMLS:C4021511 Delta-shaped epiphysis of the middle phalanx of the 5th finger Triangular end part of the middle bone of the little finger Triangular end part of the middle bone of the pinkie finger Triangular end part of the middle bone of the pinky finger human_phenotype HP:0009213 Triangular epiphysis of the middle phalanx of the 5th finger A triangular appearance of the epiphysis of the middle phalanx of the little finger of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. HPO:curators Triangular end part of the middle bone of the little finger ORCID:0000-0001-5208-3432 Triangular end part of the middle bone of the pinkie finger ORCID:0000-0001-5208-3432 Triangular end part of the middle bone of the pinky finger ORCID:0000-0001-5208-3432 Hypoplastic/small proximal phalanx of the fifth finger. doelkens 2009-01-05T06:01:34Z UMLS:C4021509 Hypoplastic/small proximal phalanx of the 5th finger Short innermost little finger bone Short innermost pinkie finger bone Short innermost pinky finger bone Short proximal phalanx of the fifth finger human_phenotype HP:0009226 Short proximal phalanx of the 5th finger Hypoplastic/small proximal phalanx of the fifth finger. HPO:skoehler Short innermost little finger bone ORCID:0000-0001-5208-3432 Short innermost pinkie finger bone ORCID:0000-0001-5208-3432 Short innermost pinky finger bone ORCID:0000-0001-5208-3432 Short proximal phalanx of the fifth finger Triangular shaped proximal phalanx of the 5th (little) finger. A triangular or so called delta shaped phalanx is a typical result after a bracket epiphysis of the affected phalanx. doelkens 2009-01-05T06:11:33Z UMLS:C4024511 Triangular shaped innermost little finger bone Triangular shaped innermost pinkie finger bone Triangular shaped innermost pinky finger bone human_phenotype HP:0009233 Triangular shaped proximal phalanx of the 5th finger Triangular shaped proximal phalanx of the 5th (little) finger. A triangular or so called delta shaped phalanx is a typical result after a bracket epiphysis of the affected phalanx. HPO:curators Triangular shaped innermost little finger bone ORCID:0000-0001-5208-3432 Triangular shaped innermost pinkie finger bone ORCID:0000-0001-5208-3432 Triangular shaped innermost pinky finger bone ORCID:0000-0001-5208-3432 Hypoplasia (congenital reduction in size) of the fifth finger, also known as the little finger. doelkens 2009-01-05T06:54:07Z HP:0001205 HP:0004208 HP:0004210 HP:0004211 HP:0004215 HP:0004217 HP:0005804 HP:0005888 UMLS:C1842878 Fifth finger brachydactyly Hypoplastic phalanges of the little finger Hypoplastic/small 5th finger Hypoplastic/small little finger Short 5th finger Short fifth finger Short fifth fingers Short little finger Short phalanges of the little finger Short pinkie finger Short pinky finger human_phenotype HP:0009237 Short 5th finger Hypoplasia (congenital reduction in size) of the fifth finger, also known as the little finger. HPO:sdoelken Short 5th finger Short fifth finger Short fifth fingers Short little finger Short pinkie finger ORCID:0000-0001-5208-3432 Short pinky finger ORCID:0000-0001-5208-3432 doelkens 2009-01-05T07:25:50Z UMLS:C4024507 Absent/small outermost bone of little finger Absent/small outermost bone of pinkie finger Absent/small outermost bone of pinky finger Absent/underdeveloped outermost bone of pinky finger human_phenotype HP:0009239 Aplasia/Hypoplasia of the distal phalanx of the 5th finger Absent/small outermost bone of little finger ORCID:0000-0001-5208-3432 Absent/small outermost bone of pinkie finger ORCID:0000-0001-5208-3432 Absent/small outermost bone of pinky finger ORCID:0000-0001-5208-3432 Absent/underdeveloped outermost bone of pinky finger ORCID:0000-0001-5208-3432 Triangular shaped distal phalanx of the 5th (little) finger. A triangular or so called delta shaped phalanx is a typical result after a bracket epiphysis of the affected phalanx. doelkens 2009-01-05T07:25:50Z UMLS:C4024502 Triangular shaped outermost little finger bone Triangular shaped outermost pinkie finger bone Triangular shaped outermost pinky finger bone human_phenotype HP:0009245 Triangular shaped distal phalanx of the 5th finger Triangular shaped distal phalanx of the 5th (little) finger. A triangular or so called delta shaped phalanx is a typical result after a bracket epiphysis of the affected phalanx. HPO:curators Triangular shaped outermost little finger bone ORCID:0000-0001-5208-3432 Triangular shaped outermost pinkie finger bone ORCID:0000-0001-5208-3432 Triangular shaped outermost pinky finger bone ORCID:0000-0001-5208-3432 doelkens 2009-01-13T10:50:19Z UMLS:C4024413 human_phenotype HP:0009370 Type A brachydactyly Aplasia/Hypoplasia of the phalanges of the 5th finger. doelkens 2009-01-13T11:58:25Z UMLS:C4024410 Absent/small little finger bones Absent/small pinkie finger bones Absent/small pinky finger bones Absent/underdeveloped pinky finger bones human_phenotype HP:0009376 Aplasia/Hypoplasia of the phalanges of the 5th finger Aplasia/Hypoplasia of the phalanges of the 5th finger. HPO:curators Absent/small little finger bones ORCID:0000-0001-5208-3432 Absent/small pinkie finger bones ORCID:0000-0001-5208-3432 Absent/small pinky finger bones ORCID:0000-0001-5208-3432 Absent/underdeveloped pinky finger bones ORCID:0000-0001-5208-3432 Triangular shaped phalanges of the 5th (little) finger. A triangular or so called delta shaped phalanx is a typical result after a bracket epiphysis of the affected phalanx. doelkens 2009-01-13T12:00:35Z UMLS:C4024409 Triangular shaped little finger bones Triangular shaped pinkie finger bones Triangular shaped pinky finger bones human_phenotype HP:0009378 Triangular shaped phalanges of the 5th finger Triangular shaped phalanges of the 5th (little) finger. A triangular or so called delta shaped phalanx is a typical result after a bracket epiphysis of the affected phalanx. HPO:curators Triangular shaped little finger bones ORCID:0000-0001-5208-3432 Triangular shaped pinkie finger bones ORCID:0000-0001-5208-3432 Triangular shaped pinky finger bones ORCID:0000-0001-5208-3432 Aplasia of one or more fingers. doelkens 2009-01-13T01:05:32Z HP:0004093 SNOMEDCT_US:71358006 UMLS:C0728895 Absent fingers human_phenotype HP:0009380 Aplasia of the fingers Aplasia of one or more fingers. HPO:curators Absent fingers Abnormally short finger associated with developmental hypoplasia. doelkens 2009-01-13T01:07:38Z HP:0004098 HP:0006015 SNOMEDCT_US:249765007 UMLS:C0239594 UMLS:C1844548 Hypoplastic digits Hypoplastic fingers Hypoplastic/small fingers Short finger Stubby finger Stubby fingers human_phenotype HP:0009381 Short finger Abnormally short finger associated with developmental hypoplasia. HPO:probinson Short finger Stubby finger ORCID:0000-0001-5208-3432 Stubby fingers Absence of one or more epiphyses of the 5th finger. doelkens 2009-01-13T01:19:03Z UMLS:C4024407 Absent end part of little finger bone Absent end part of pinkie finger bone Absent end part of pinky finger bone human_phenotype HP:0009382 Absent epiphyses of the 5th finger Absence of one or more epiphyses of the 5th finger. HPO:curators Absent end part of little finger bone ORCID:0000-0001-5208-3432 Absent end part of pinkie finger bone ORCID:0000-0001-5208-3432 Absent end part of pinky finger bone ORCID:0000-0001-5208-3432 Abnormally large size of the epiphyses of the 5th finger with respect to age-dependent norms. doelkens 2009-01-13T01:19:03Z UMLS:C4024404 Enlarged end part of the little finger bones Enlarged end part of the pinkie finger bones Enlarged end part of the pinky finger bones human_phenotype HP:0009385 Enlarged epiphyses of the 5th finger Abnormally large size of the epiphyses of the 5th finger with respect to age-dependent norms. HPO:curators Enlarged end part of the little finger bones ORCID:0000-0001-5208-3432 Enlarged end part of the pinkie finger bones ORCID:0000-0001-5208-3432 Enlarged end part of the pinky finger bones ORCID:0000-0001-5208-3432 A secondary ossification center in the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. doelkens 2009-01-13T01:19:03Z UMLS:C4024400 human_phenotype HP:0009389 Pseudoepiphyses of the 5th finger A secondary ossification center in the fifth finger that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. HPO:curators Abnormally small size of the epiphyses of the 5th finger with respect to age-dependent norms. doelkens 2009-01-13T01:19:03Z UMLS:C4024399 Small end part of little finger bone Small end part of pinkie finger bone Small end part of pinky finger bone human_phenotype HP:0009390 Small epiphyses of the 5th finger Abnormally small size of the epiphyses of the 5th finger with respect to age-dependent norms. HPO:curators Small end part of little finger bone ORCID:0000-0001-5208-3432 Small end part of pinkie finger bone ORCID:0000-0001-5208-3432 Small end part of pinky finger bone ORCID:0000-0001-5208-3432 A triangular appearance of the epiphyses of the 5th finger of the hand. doelkens 2009-01-13T01:19:03Z UMLS:C4021483 Delta-shaped epiphyses of the 5th finger Triangular end part of the little finger Triangular end part of the pinkie finger Triangular end part of the pinky finger human_phenotype HP:0009392 Triangular epiphyses of the 5th finger A triangular appearance of the epiphyses of the 5th finger of the hand. HPO:curators Triangular end part of the little finger ORCID:0000-0001-5208-3432 Triangular end part of the pinkie finger ORCID:0000-0001-5208-3432 Triangular end part of the pinky finger ORCID:0000-0001-5208-3432 Bending or curvature of a finger toward the ulnar side (i.e., away from the thumb). The deviation is at the metacarpal-phalangeal joint, and this finding is distinct from clinodactyly. doelkens 2009-01-15T09:39:43Z HP:0001200 HP:0004096 SNOMEDCT_US:276662009 SNOMEDCT_US:367510009 UMLS:C0231679 Finger bends toward pinky Ulnar Drift human_phenotype HP:0009465 Ulnar deviation of finger Bending or curvature of a finger toward the ulnar side (i.e., away from the thumb). The deviation is at the metacarpal-phalangeal joint, and this finding is distinct from clinodactyly. HPO:probinson PMID:19125433 Finger bends toward pinky https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 Contractures of one ore more joints of the hands meaning chronic loss of joint motion due to structural changes in non-bony tissue. doelkens 2009-01-15T09:59:59Z HP:0001160 HP:0001237 HP:0004094 HP:0005814 HP:0006096 HP:0006173 HP:0006215 HP:0006238 HP:0006255 HP:0009409 HP:0009472 HP:0010563 MEDDRA:10010821 SNOMEDCT_US:86414002 UMLS:C0158113 Contractures involving the hands Contractures of the hands human_phenotype HP:0009473 Joint contracture of the hand Contractures of one ore more joints of the hands meaning chronic loss of joint motion due to structural changes in non-bony tissue. HPO:sdoelken MEDDRA:10010821 Contracture of hand joint Displacement of the hand or of fingers of the hand from their normal position. doelkens 2009-01-15T10:45:01Z UMLS:C4024338 Displaced hand or fingers of the hand human_phenotype HP:0009484 Deviation of the hand or of fingers of the hand Displacement of the hand or of fingers of the hand from their normal position. HPO:curators Displaced hand or fingers of the hand ORCID:0000-0001-5208-3432 Divergence of the longitudinal axis of the hand at the wrist in a posterior (ulnar) direction (i.e., towards the little finger). doelkens 2009-01-15T10:51:52Z SNOMEDCT_US:249757009 UMLS:C0241521 Ulnar deviation of hands Ulnar deviation of the hands human_phenotype HP:0009487 Ulnar deviation of the hand Divergence of the longitudinal axis of the hand at the wrist in a posterior (ulnar) direction (i.e., towards the little finger). HPO:probinson PMID:19125433 Ulnar deviation of hands HPO:skoehler Ulnar deviation of the hands HPO:skoehler Underdevelopment of the pharynx. peter 2009-01-21T05:24:16Z Small pharynx UMLS:C4024295 UMLS:C4280396 UMLS:C4280397 UMLS:C4280398 UMLS:C4280399 UMLS:C4280400 Decreased size of pharynx Underdevelopment of pharynx Decreased diameter of pharynx Decreased length of pharynx Decreased volume of pharynx Decreased width of pharynx human_phenotype Hypotrophic pharynx HP:0009555 Hypoplasia of the pharynx Underdevelopment of the pharynx. HPO:curators Small pharynx ORCID:0000-0001-5889-4463 Decreased size of pharynx ORCID:0000-0001-5889-4463 Underdevelopment of pharynx ORCID:0000-0001-5889-4463 Decreased diameter of pharynx ORCID:0000-0001-5889-4463 Decreased length of pharynx ORCID:0000-0001-5889-4463 Decreased volume of pharynx ORCID:0000-0001-5889-4463 Decreased width of pharynx ORCID:0000-0001-5889-4463 Hypotrophic pharynx ORCID:0000-0001-5889-4463 Abnormality of one or all of the epiphyses of the proximal, and distal phalanges of the thumb and/or the 1st metacarpal. doelkens 2009-01-29T11:46:15Z HP:0004074 UMLS:C4021429 Abnormality of end part of thumb long bone Abnormality of the epiphyses of the thumb Abnormality of thumb epiphyses human_phenotype HP:0009599 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). Abnormality of thumb epiphysis Abnormality of one or all of the epiphyses of the proximal, and distal phalanges of the thumb and/or the 1st metacarpal. HPO:probinson Abnormality of end part of thumb long bone ORCID:0000-0001-5208-3432 Chronic loss of joint motion in the thumb due to structural changes in non-bony tissue. The term camptodactyly is used if the distal and/or proximal interphalangeal joints are affected. doelkens 2009-01-29T01:06:31Z HP:0004061 HP:0006043 SNOMEDCT_US:239736003 UMLS:C0409346 Contracture of thumb Flexion deformities of thumbs Joint contractures of the thumb human_phenotype HP:0009600 Flexion contracture of thumb Chronic loss of joint motion in the thumb due to structural changes in non-bony tissue. The term camptodactyly is used if the distal and/or proximal interphalangeal joints are affected. HPO:probinson Hypoplastic/small or absent thumb. doelkens 2009-01-29T01:08:24Z HP:0002950 HP:0006225 MSH:C536903 UMLS:C3179508 Absent or hypoplastic thumbs Absent/hypoplastic thumb Absent/hypoplastic thumbs Absent/small thumb Absent/underdeveloped thumb Aplasia/hypoplasia of thumbs Aplastic/hypoplastic thumbs Hypoplastic to aplastic thumbs Hypoplastic/absent thumb Thumb aplasia/hypoplasia human_phenotype HP:0009601 Aplasia/Hypoplasia of the thumb Hypoplastic/small or absent thumb. HPO:probinson Absent/small thumb ORCID:0000-0001-5208-3432 Absent/underdeveloped thumb ORCID:0000-0001-5208-3432 A structural anomaly of one or more phalanges of the thumb. doelkens 2009-01-29T01:10:39Z HP:0004063 HP:0004064 UMLS:C4021428 Abnormality of the thumb bones Abnormality of thumb phalanges human_phenotype HP:0009602 Abnormality of thumb phalanx A structural anomaly of one or more phalanges of the thumb. HPO:probinson Abnormality of the thumb bones ORCID:0000-0001-5208-3432 Displacement of the thumb from its normal position. doelkens 2009-01-29T01:49:57Z HP:0004062 UMLS:C3552414 Abnormal thumb placement Deviated thumb Displacement of the thumb human_phenotype HP:0009603 Deviation of the thumb Displacement of the thumb from its normal position. HPO:curators Abnormal thumb placement ORCID:0000-0001-5208-3432 Complete duplication of the distal phalanx of the thumb. On x-ray two separate bones appear side to side. doelkens 2009-01-29T03:28:16Z HP:0004084 HP:0005784 UMLS:C4021427 Complete duplication of outermost bone of the thumb human_phenotype HP:0009606 Complete duplication of distal phalanx of the thumb Complete duplication of the distal phalanx of the thumb. On x-ray two separate bones appear side to side. HPO:curators Complete duplication of outermost bone of the thumb ORCID:0000-0001-5208-3432 Complete duplication of the proximal phalanx of the thumb. On x-ray two separate bones appear side to side. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-01-29T03:32:28Z HP:0004078 UMLS:C4024273 Complete duplication of the innermost bone of the thumb human_phenotype HP:0009608 Complete duplication of proximal phalanx of the thumb Complete duplication of the proximal phalanx of the thumb. On x-ray two separate bones appear side to side. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:probinson Complete duplication of the innermost bone of the thumb ORCID:0000-0001-5208-3432 Partail or complete duplication of the first metacarpal bone. doelkens 2009-01-29T03:33:31Z UMLS:C4021426 Partial/complete duplication of the 1st long bone of hand Partial/complete duplication of the 1st metacarpal human_phenotype HP:0009609 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin. This term applies if the first metacarpal is completely or partially duplicated. Depending on the severity, the appearance on x-ray can vary from a notched metacarpal (the duplicated bone is almost completely fused with the metacarpal), a partially fused appearance of the two bones (in most cases the fused bone resembles a Y-shape), or two separate metacarpal bones appearing side to side. Duplication of the 1st metacarpal Partail or complete duplication of the first metacarpal bone. HPO:probinson Partial/complete duplication of the 1st long bone of hand ORCID:0000-0001-5208-3432 Partial duplication of the distal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx) to a partially fused appearance of the two bones. doelkens 2009-01-29T03:48:49Z HP:0004086 HP:0005703 HP:0005827 HP:0005848 HP:0006090 UMLS:C1860162 Bifid distal phalanx of thumb Bifid terminal phalanges of thumbs Bifid thumb distal phalanx Incipient distal thumb phalanx duplication Notched outermost bone of the thumb Notched outermost bone of thumb Notched terminal thumb phalanx human_phenotype HP:0009611 Note that with bifid distal phalanx, the terminal phalanx of the thumb is clefted but is still one bone. With duplication of the terminal phalanx of the thumb, the distal phalanx is split into two bones that are located side by side. With triphalangeal thumb, the thumb has three phalanxes located one after the other. Bifid distal phalanx of the thumb Partial duplication of the distal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx) to a partially fused appearance of the two bones. HPO:sdoelken Notched outermost bone of the thumb ORCID:0000-0001-5208-3432 Complete or partial duplication of the distal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones, or two separate bones appearing side to side. doelkens 2009-01-29T03:51:43Z UMLS:C4021425 Double thumb distal phalanges Duplicated terminal phalanx of thumb Duplication of distal thumb phalanx Duplication of terminal thumb phalanx Duplication of the outermost bone of the thumb Partial/complete duplication of the distal phalanx of the thumb human_phenotype HP:0009612 Duplication of the distal phalanx of the thumb Complete or partial duplication of the distal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones, or two separate bones appearing side to side. HPO:sdoelken Duplication of the outermost bone of the thumb ORCID:0000-0001-5208-3432 Complete or partial duplication of the proximal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones, or two separate bones appearing side to side. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-01-29T03:59:56Z UMLS:C4021424 Notched innermost bone of thumb Partial/complete duplication of the proximal phalanx of the thumb human_phenotype HP:0009613 Duplication of the proximal phalanx of the thumb Complete or partial duplication of the proximal phalanx of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones, or two separate bones appearing side to side. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:sdoelken Notched innermost bone of thumb ORCID:0000-0001-5208-3432 This term applies if the proximal phalanx of the thumb is partially duplicated. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx) to a partially fused appearance of the two bones. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-01-29T04:01:27Z UMLS:C4024272 Notched thumb bone human_phenotype HP:0009614 Bifid proximal phalanx of the thumb This term applies if the proximal phalanx of the thumb is partially duplicated. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx) to a partially fused appearance of the two bones. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:probinson Notched thumb bone ORCID:0000-0001-5208-3432 Complete duplication of the first metacarpal bone. doelkens 2009-01-29T04:06:17Z UMLS:C4024271 Complete duplication of the first long bone of hand human_phenotype HP:0009615 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin, equivalent to the proximal phalanges of the other digits. This term applies if the first metacarpal is completely duplicated. On x-ray two separate metacarpal bones appear side to side. This term applies if the first metacarpal is completely duplicated. Complete duplication of the first metacarpal Complete duplication of the first metacarpal bone. HPO:probinson Complete duplication of the first long bone of hand ORCID:0000-0001-5208-3432 Partial duplication of the first metacarpal bone. doelkens 2009-01-29T04:06:17Z UMLS:C4021423 Notched first long bone of hand partial duplication of the first metacarpal human_phenotype HP:0009616 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin (equivalent to the proximal phalanges of the other digits). This term applies if the first metacarpal is partially duplicated. Depending on the severity the appearance on x-ray can vary from a notched metacarpal (the duplicated bone is almost completely fused with the metacarpal) to a partially fused appearance of the two bones. In most cases the fused bone resembles a Y-shape. Bifid first metacarpal Partial duplication of the first metacarpal bone. HPO:probinson Notched first long bone of hand ORCID:0000-0001-5208-3432 Any anomaly of the distal phalanx of thumb. doelkens 2009-01-29T04:13:47Z HP:0004081 UMLS:C4021422 Abnormality of terminal thumb phalanx Abnormality of the outermost bone of the thumb human_phenotype HP:0009617 Abnormality of the distal phalanx of the thumb Any anomaly of the distal phalanx of thumb. HPO:probinson Abnormality of the outermost bone of the thumb ORCID:0000-0001-5208-3432 An anomaly of the shape or form of the proximal phalanx of the thumb. doelkens 2009-01-29T04:13:47Z HP:0004076 UMLS:C4021421 Abnormal innermost thumb bone Abnormality of proximal thumb phalanx human_phenotype HP:0009618 In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Abnormality of the proximal phalanx of the thumb An anomaly of the shape or form of the proximal phalanx of the thumb. HPO:curators Abnormal innermost thumb bone ORCID:0000-0001-5208-3432 In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:probinson Chronic loss of joint motion of the carpometacarpal joint of the thumb due to structural changes in non-bony tissue. This joint is formed by the first metacarpal and the trapezial bone and is also called Articulatio carpometacarpalis pollicis, carpometacarpal articulation of thumb, carpometacarpal joint of thumb or first carpometacarpal articulation. Seldom referred to as thumb saddle joint. doelkens 2009-01-29T04:52:18Z UMLS:C4024269 human_phenotype HP:0009624 Contractures of the carpometacarpal joint of the thumb Chronic loss of joint motion of the carpometacarpal joint of the thumb due to structural changes in non-bony tissue. This joint is formed by the first metacarpal and the trapezial bone and is also called Articulatio carpometacarpalis pollicis, carpometacarpal articulation of thumb, carpometacarpal joint of thumb or first carpometacarpal articulation. Seldom referred to as thumb saddle joint. HPO:probinson Chronic loss of joint motion of the metacarpophalangeal joint of the thumb due to structural changes in non-bony tissue. This joint is also called Articulatio metacarpophalangealis pollicis. doelkens 2009-01-29T04:52:18Z UMLS:C2108151 human_phenotype HP:0009625 Contractures of the metacarpophalangeal joint of the thumb Chronic loss of joint motion of the metacarpophalangeal joint of the thumb due to structural changes in non-bony tissue. This joint is also called Articulatio metacarpophalangealis pollicis. HPO:probinson Chronic loss of joint motion of the interphalangeal joint of the thumb due to structural changes in non-bony tissue. This joint is also called Articulatio interphalangealis pollicis. doelkens 2009-01-29T04:52:18Z HP:0005697 UMLS:C2108146 Interphalangeal extension contractures of thumbs human_phenotype HP:0009626 Contractures of the interphalangeal joint of the thumb Chronic loss of joint motion of the interphalangeal joint of the thumb due to structural changes in non-bony tissue. This joint is also called Articulatio interphalangealis pollicis. HPO:probinson This term applies if the proximal phalanx of the thumb is either small/hypoplastic or absent. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-01-29T05:09:41Z UMLS:C4024268 Absent/small innermost thumb bone Absent/underdeveloped innermost thumb bone human_phenotype HP:0009629 Aplasia/Hypoplasia of the proximal phalanx of the thumb This term applies if the proximal phalanx of the thumb is either small/hypoplastic or absent. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:curators Absent/small innermost thumb bone ORCID:0000-0001-5208-3432 Absent/underdeveloped innermost thumb bone ORCID:0000-0001-5208-3432 Hypoplastic (short) proximal phalanx of the thumb. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-01-29T05:11:02Z HP:0004079 HP:0006073 UMLS:C1855091 Hypoplastic/small proximal phalanx of the thumb Short proximal phalanges of thumb Short proximal thumb bone Short proximal thumb phalanx human_phenotype HP:0009638 Short proximal phalanx of thumb Hypoplastic (short) proximal phalanx of the thumb. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:probinson Short proximal thumb bone ORCID:0000-0001-5889-4463 doelkens 2009-01-29T05:19:33Z UMLS:C4024261 Absent/small outermost thumb bone Absent/underdeveloped outermost thumb bone human_phenotype HP:0009641 Aplasia/Hypoplasia of the distal phalanx of the thumb Absent/small outermost thumb bone ORCID:0000-0001-5208-3432 Absent/underdeveloped outermost thumb bone ORCID:0000-0001-5208-3432 Hypoplastic (short) distal phalanx of the thumb. doelkens 2009-01-29T05:22:06Z HP:0004085 HP:0004087 UMLS:C1862313 Hypoplastic terminal thumb phalanx Hypoplastic/small distal phalanx of the thumb Short outermost bone of the thumb Short terminal thumb phalanx Short thumb terminal phalanx Small terminal thumb phalanx human_phenotype HP:0009650 Short distal phalanx of the thumb Hypoplastic (short) distal phalanx of the thumb. HPO:sdoelken Short outermost bone of the thumb ORCID:0000-0001-5208-3432 doelkens 2009-01-29T05:29:26Z HP:0005834 UMLS:C4024256 Absent/small thumb bones Absent/underdeveloped thumb bones human_phenotype HP:0009658 Aplasia/Hypoplasia of the phalanges of the thumb Absent/small thumb bones ORCID:0000-0001-5208-3432 Absent/underdeveloped thumb bones ORCID:0000-0001-5208-3432 Hypoplastic (short) thumb phalanx. doelkens 2009-01-29T05:35:50Z HP:0004069 HP:0004071 UMLS:C4021411 Hypoplastic thumb phalanges Hypoplastic/small phalanges of the thumb Short thumb bone Short thumb phalanges human_phenotype HP:0009660 Short phalanx of the thumb Hypoplastic (short) thumb phalanx. HPO:probinson Short thumb bone ORCID:0000-0001-5208-3432 Abnormality of the epiphysis of the distal phalanx of the thumb. This epiphysis is located on the proximal end of the phalanx. doelkens 2009-01-29T05:49:31Z HP:0004089 UMLS:C4021410 Abnormality of terminal thumb epiphysis Abnormality of the end part of the outermost bone of the thumb human_phenotype HP:0009662 Abnormality of the epiphysis of the distal phalanx of the thumb Abnormality of the epiphysis of the distal phalanx of the thumb. This epiphysis is located on the proximal end of the phalanx. HPO:curators Abnormality of the end part of the outermost bone of the thumb ORCID:0000-0001-5208-3432 This term applies if the epiphysis of the proximal phalanx of the thumb, which is located at the proximal end of the phalanx, does not appear in concordance with gender and age dependant norms as seen on x-rays. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-01-29T05:49:31Z UMLS:C4024254 Abnormality of end part of thumb innermost long bone human_phenotype HP:0009663 Abnormality of the epiphysis of the proximal phalanx of the thumb This term applies if the epiphysis of the proximal phalanx of the thumb, which is located at the proximal end of the phalanx, does not appear in concordance with gender and age dependant norms as seen on x-rays. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:curators Abnormality of end part of thumb innermost long bone ORCID:0000-0001-5208-3432 Absence of the epiphysis located at the proximal end of the proximal phalanx of the thumb. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-01-30T09:17:13Z UMLS:C4024253 Absent end part of thumb innermost long bone human_phenotype HP:0009664 Absent epiphysis of the proximal phalanx of the thumb Absence of the epiphysis located at the proximal end of the proximal phalanx of the thumb. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:curators Absent end part of thumb innermost long bone ORCID:0000-0001-5208-3432 Abnormally large size of the epiphysis located at the proximal end of the proximal phalanx of the thumb with respect to age-dependent norms. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-01-30T09:17:13Z UMLS:C4024250 Enlarged end part of thumb innermost long bone human_phenotype HP:0009667 Enlarged epiphysis of the proximal phalanx of the thumb Abnormally large size of the epiphysis located at the proximal end of the proximal phalanx of the thumb with respect to age-dependent norms. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:curators Enlarged end part of thumb innermost long bone ORCID:0000-0001-5208-3432 A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of the proximal phalanx of the thumb. doelkens 2009-01-30T09:17:13Z UMLS:C4024246 human_phenotype HP:0009671 Pseudoepiphysis of the proximal phalanx of the thumb A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of the proximal phalanx of the thumb. HPO:probinson Abnormally small size of the epiphysis located at the proximal end of the proximal phalanx of the thumb with respect to age-dependent norms. doelkens 2009-01-30T09:17:13Z UMLS:C4024245 Small end part of thumb innermost long bone human_phenotype HP:0009672 Small epiphysis of the proximal phalanx of the thumb Abnormally small size of the epiphysis located at the proximal end of the proximal phalanx of the thumb with respect to age-dependent norms. HPO:probinson Small end part of thumb innermost long bone ORCID:0000-0001-5208-3432 A triangular appearance of the epiphysis of the proximal phalanx of the thumb of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-01-30T09:17:13Z UMLS:C4024243 Triangular end part of thumb innermost long bone human_phenotype HP:0009674 Triangular epiphysis of the proximal phalanx of the thumb A triangular appearance of the epiphysis of the proximal phalanx of the thumb of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:curators Triangular end part of thumb innermost long bone ORCID:0000-0001-5208-3432 Absence of the epiphysis located at the proximal end of the distal phalanx of the thumb. doelkens 2009-01-30T09:18:09Z UMLS:C4024242 Absent end part of thumb outermost long bone human_phenotype HP:0009675 Absent epiphysis of the distal phalanx of the thumb Absence of the epiphysis located at the proximal end of the distal phalanx of the thumb. HPO:curators Absent end part of thumb outermost long bone ORCID:0000-0001-5208-3432 Abnormally large size of the epiphysis located at the proximal end of the distal phalanx of the thumb with respect to age-dependent norms. doelkens 2009-01-30T09:18:09Z HP:0004092 UMLS:C4021408 Enlarged end part of thumb outermost long bone Large terminal thumb phalanx epiphysis human_phenotype HP:0009678 Enlarged epiphysis of the distal phalanx of the thumb Abnormally large size of the epiphysis located at the proximal end of the distal phalanx of the thumb with respect to age-dependent norms. HPO:curators Enlarged end part of thumb outermost long bone ORCID:0000-0001-5208-3432 A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of the distal phalanx of the thumb. doelkens 2009-01-30T09:18:09Z UMLS:C4024237 Pseudoepiphysis of the outermost bone of the thumb human_phenotype HP:0009682 Pseudoepiphysis of the distal phalanx of the thumb A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of the distal phalanx of the thumb. HPO:probinson Pseudoepiphysis of the outermost bone of the thumb ORCID:0000-0001-5208-3432 Abnormally small size of the epiphysis located at the proximal end of the distal phalanx of the thumb with respect to age-dependent norms. doelkens 2009-01-30T09:18:09Z UMLS:C4024236 Small end part of thumb outermost bone human_phenotype HP:0009683 Small epiphysis of the distal phalanx of the thumb Abnormally small size of the epiphysis located at the proximal end of the distal phalanx of the thumb with respect to age-dependent norms. HPO:probinson Small end part of thumb outermost bone ORCID:0000-0001-5208-3432 A triangular appearance of the epiphysis of the distal phalanx of the thumb of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. doelkens 2009-01-30T09:18:09Z UMLS:C4024234 Triangular end part of thumb outermost bone Triangular epiphysis of the outermost bone of the thumb human_phenotype HP:0009685 Triangular epiphysis of the distal phalanx of the thumb A triangular appearance of the epiphysis of the distal phalanx of the thumb of the hand. This epiphysis is located at the proximal end of the phalanx and is normally nearly flat. HPO:curators Triangular end part of thumb outermost bone ORCID:0000-0001-5208-3432 Triangular epiphysis of the outermost bone of the thumb ORCID:0000-0001-5208-3432 Absence of one or more epiphyses of the thumb. doelkens 2009-01-30T09:20:16Z UMLS:C4024233 human_phenotype HP:0009686 Absent epiphyses of the thumb Absence of one or more epiphyses of the thumb. HPO:curators Abnormally large size of the epiphyses of the thumb with respect to age-dependent norms. doelkens 2009-01-30T09:20:16Z UMLS:C4021406 Enlarged end part of thumb long bone Enlarged epiphyses of the thumb human_phenotype HP:0009689 Enlarged thumb epiphysis Abnormally large size of the epiphyses of the thumb with respect to age-dependent norms. HPO:probinson Enlarged end part of thumb long bone ORCID:0000-0001-5208-3432 A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of one or more phalanges of the thumb. doelkens 2009-01-30T09:20:16Z UMLS:C3552484 Pseudoepiphyses of the thumb human_phenotype HP:0009693 Pseudoepiphysis of the thumb A pseudoepiphysis (which is a secondary ossification center distinct from the normal epiphysis) of one or more phalanges of the thumb. HPO:probinson Abnormally small size of one or more of the epiphyses of the thumb with respect to age-dependent norms. doelkens 2009-01-30T09:20:16Z UMLS:C4021402 Small end part of thumb long bone Small epiphyses of the thumb human_phenotype HP:0009694 Small thumb epiphysis Abnormally small size of one or more of the epiphyses of the thumb with respect to age-dependent norms. HPO:probinson Small end part of thumb long bone ORCID:0000-0001-5889-4463 doelkens 2009-01-30T09:20:16Z UMLS:C4024231 Triangular end part of the thumb bone human_phenotype HP:0009696 Triangular epiphyses of the thumb Triangular end part of the thumb bone ORCID:0000-0001-5208-3432 Chronic loss of joint motion in one or more distal interphalangeal joints of the fingers. doelkens 2009-01-30T04:01:28Z UMLS:C4024230 human_phenotype HP:0009697 Contracture of the distal interphalangeal joint of the fingers Chronic loss of joint motion in one or more distal interphalangeal joints of the fingers. HPO:probinson An abnormality of the epididymis. peter 2009-01-30T11:44:43Z UMLS:C4024222 human_phenotype HP:0009714 The epididymis is the structure that connects efferent ductules to vas deferens. Abnormality of the epididymis An abnormality of the epididymis. HPO:probinson Nephrosclerosis refers to thickening or scarring ("sclerosis") resulting from damage to the renal arterioles, also referred to as arteriosclerosis of the kidney arteries. peter 2009-01-31T01:15:08Z MSH:D009400 SNOMEDCT_US:32916005 UMLS:C0027719 Scarring of kidney arteries Thickening of kidney artiries human_phenotype HP:0009741 Nephrosclerosis Nephrosclerosis refers to thickening or scarring ("sclerosis") resulting from damage to the renal arterioles, also referred to as arteriosclerosis of the kidney arteries. HPO:curators Scarring of kidney arteries ORCID:0000-0001-5208-3432 Thickening of kidney artiries ORCID:0000-0001-5208-3432 An abnormality of the spinal dura mater, which is the outermost of the three layers of the meninges surrounding the spinal cord. peter 2009-01-31T02:20:51Z UMLS:C4024214 Abnormality of the spinal dura mater human_phenotype HP:0009744 Abnormal spinal dura mater morphology An abnormality of the spinal dura mater, which is the outermost of the three layers of the meninges surrounding the spinal cord. HPO:curators Small or missing phalangeal bones of the fingers of the hand. doelkens 2009-02-02T11:38:04Z HP:0006056 HP:0006100 HP:0009801 UMLS:C1848670 Aplastic/hypoplastic phalanges Aplastic/hypoplastic phalanges of the hand Hypoplastic/absent phalanges human_phenotype HP:0009767 Aplasia/Hypoplasia of the phalanges of the hand Small or missing phalangeal bones of the fingers of the hand. HPO:probinson doelkens 2009-02-02T11:38:04Z HP:0006085 HP:0009874 UMLS:C2673397 Delta phalanx/delta-like phalanx Triangular shaped hand bones human_phenotype HP:0009774 Triangular shaped phalanges of the hand Triangular shaped hand bones ORCID:0000-0001-5208-3432 Hypoplasia (congenital reduction in size) of the thumb. doelkens 2009-02-02T05:46:42Z HP:0001183 HP:0001186 HP:0001589 HP:0005699 HP:0006151 HP:0009628 MSH:C536903 SNOMEDCT_US:253936008 UMLS:C0431890 Hypoplastic thumb Hypoplastic thumbs Hypoplastic/small thumb Short thumb Short thumbs Small thumbs Thumb brachydactyly Thumb hypoplasia human_phenotype HP:0009778 Short thumb Hypoplasia (congenital reduction in size) of the thumb. HPO:probinson Short thumb Short thumbs Small thumbs Absence or underdevelopment involving the musculature of the thigh. peter 2009-02-03T05:16:42Z UMLS:C4024207 Absent/small thigh muscles Absent/underdeveloped thigh muscles human_phenotype HP:0009786 Aplasia/Hypoplasia of the musculature of the thigh Absence or underdevelopment involving the musculature of the thigh. HPO:curators Absent/small thigh muscles ORCID:0000-0001-5208-3432 Absent/underdeveloped thigh muscles ORCID:0000-0001-5208-3432 The presence of two or more accessory spleens. peter 2009-02-11T05:44:01Z SNOMEDCT_US:10362008 UMLS:C0266631 Extra spleen human_phenotype HP:0009799 Supernumerary spleens The presence of two or more accessory spleens. HPO:curators Extra spleen ORCID:0000-0001-5208-3432 Short (hypoplastic) phalanx of finger, affecting one or more phalanges. doelkens 2009-02-12T05:57:11Z HP:0001168 HP:0005771 HP:0006087 HP:0006126 UMLS:C0877165 Hypoplastic phalanges Hypoplastic phalanges of hands Hypoplastic/small phalanges of the hand Phalangeal hypoplasia Rudimentary phalanges Short finger bones Short phalanges Shortened phalanges human_phenotype HP:0009803 Short phalanx of finger Short (hypoplastic) phalanx of finger, affecting one or more phalanges. HPO:sdoelken Short finger bones The presence of a reduced number of teeth as in Hypodontia or as in Anodontia. 2009-02-14T06:20:53Z Tooth agenesis UMLS:C4024202 UMLS:C4083050 Decreased tooth count Failure of development of some teeth Reduced number of teeth human_phenotype Decreased number of teeth Fewer teeth than normal Missing some teeth HP:0009804 Hypodontia describes a situation when there are fewer than the normal number of teeth, whereby 6 teeth or fewer teeth are missing (oligodontia refers to the condition of missing more than 6 teeth and the congenital absence of all teeth is called anodontia). Reduced number of teeth The presence of a reduced number of teeth as in Hypodontia or as in Anodontia. HPO:sdoelken Decreased tooth count ORCID:0000-0001-5889-4463 Failure of development of some teeth ORCID:0000-0001-5889-4463 Reduced number of teeth Decreased number of teeth ORCID:0000-0001-5889-4463 Fewer teeth than normal ORCID:0000-0001-5889-4463 Missing some teeth ORCID:0000-0001-5889-4463 A structural abnormality of a diaphysis of the arm. doelkens 2009-02-23T04:55:36Z HP:0003857 UMLS:C4021389 Abnormality involving the diaphyses of the upper limbs Abnormality of shaft of long bone of the upper limbs Diaphyseal abnormality of the upper limbs human_phenotype HP:0009808 Anomaly of the upper limb diaphyses A structural abnormality of a diaphysis of the arm. UToronto:htrang Abnormality of shaft of long bone of the upper limbs ORCID:0000-0001-5208-3432 An anomaly of one or more metaphyses of the arms. doelkens 2009-02-23T04:55:36Z HP:0003847 UMLS:C4021388 Abnormality of the wide portion of upper limb bone Metaphyseal abnormality of the upper limbs human_phenotype HP:0009809 Abnormality of upper limb metaphysis An anomaly of one or more metaphyses of the arms. HPO:probinson Abnormality of the wide portion of upper limb bone ORCID:0000-0001-5208-3432 doelkens 2009-02-23T04:57:56Z UMLS:C4021387 Abnormality of the joints of the upper limbs Abnormality of upper limb joint human_phenotype HP:0009810 Abnormality of upper limb joint Abnormality of the joints of the upper limbs Abnormality of upper limb joint An anomaly of the joint that connects the upper and the lower arm. doelkens 2009-02-23T04:59:43Z HP:0002966 UMLS:C4021386 Abnormality of the elbow Abnormality of the elbows human_phenotype HP:0009811 Abnormality of the elbow An anomaly of the joint that connects the upper and the lower arm. HPO:probinson Abnormality of the elbow Abnormality of the elbows Peromelia affecting only the upper limbs. That is, the distal parts of the arm are missing leading to stump formation. doelkens 2009-02-23T05:06:12Z UMLS:C4024199 human_phenotype HP:0009814 Upper limb peromelia Peromelia affecting only the upper limbs. That is, the distal parts of the arm are missing leading to stump formation. HPO:sdoelken Absence (due to failure to form) or underdevelopment of the extremities. doelkens 2009-02-23T05:06:40Z HP:0002969 HP:0006497 UMLS:C0239399 Absent/small extremities Absent/underdeveloped extremities Short or absent limbs Shortened limbs human_phenotype HP:0009815 Aplasia/hypoplasia of the extremities Absence (due to failure to form) or underdevelopment of the extremities. HPO:probinson Absent/small extremities ORCID:0000-0001-5208-3432 Absent/underdeveloped extremities ORCID:0000-0001-5208-3432 Leg shortening because of underdevelopment of one or more bones of the lower extremity. doelkens 2009-02-23T05:09:32Z HP:0003087 HP:0005884 HP:0006399 SNOMEDCT_US:253959002 UMLS:C0345371 Hypoplasia involving bones of the lower limbs Hypoplasia of the lower limbs Lower limb undergrowth Underdeveloped lower limb bones human_phenotype HP:0009816 Lower limb undergrowth Leg shortening because of underdevelopment of one or more bones of the lower extremity. HPO:probinson Lower limb undergrowth Underdeveloped lower limb bones ORCID:0000-0001-5208-3432 Peromelia affecting only the lower limbs. That is, the distal parts of the leg are missing leading to stump formation. doelkens 2009-02-23T05:11:07Z UMLS:C4024196 human_phenotype HP:0009820 Lower limb peromelia Peromelia affecting only the lower limbs. That is, the distal parts of the leg are missing leading to stump formation. HPO:sdoelken Forearm shortening because of underdevelopment of one or more bones of the forearm. doelkens 2009-02-23T05:11:42Z HP:0003024 HP:0003968 HP:0006405 UMLS:C1855299 Forearm undergrowth Hypoplasia involving forearm bones Short forearm bones Short forearms Shortened forearm human_phenotype HP:0009821 Forearm undergrowth Forearm shortening because of underdevelopment of one or more bones of the forearm. HPO:probinson Forearm undergrowth Short forearm bones Short forearms Shortened forearm Arm shortening because of underdevelopment of one or more bones of the upper extremity. doelkens 2009-02-23T05:13:20Z HP:0003056 HP:0006364 UMLS:C1837406 Hypoplasia involving bones of the upper limbs Short arms Shortening of the arms Upper limb undergrowth human_phenotype HP:0009824 Upper limb undergrowth Arm shortening because of underdevelopment of one or more bones of the upper extremity. HPO:probinson Short arms Shortening of the arms Upper limb undergrowth Limb shortening because of underdevelopment of one or more bones of the extremities. doelkens 2009-02-23T05:16:44Z HP:0003058 HP:0005049 HP:0005057 UMLS:C0239399 Hypoplasia involving bones of the extremities Limb undergrowth Short limb Short limbs limb shortening human_phenotype HP:0009826 Limb undergrowth Limb shortening because of underdevelopment of one or more bones of the extremities. HPO:probinson Limb undergrowth Short limb Short limbs HPO:skoehler limb shortening The distal parts of the limbs are missing leading to a stump formation. doelkens 2009-02-23T05:17:25Z UMLS:C4024192 human_phenotype HP:0009828 Peromelia The distal parts of the limbs are missing leading to a stump formation. HPO:probinson Any anomaly of distal phalanx of finger. doelkens 2009-03-11T12:01:39Z HP:0005919 UMLS:C4021385 Abnormal terminal phalanges of the hand Abnormality of the distal phalanges of the hand Abnormality of the distal phalanx of finger Abnormality of the outermost finger bone human_phenotype HP:0009832 Abnormal distal phalanx morphology of finger Any anomaly of distal phalanx of finger. HPO:probinson Abnormality of the outermost finger bone ORCID:0000-0001-5208-3432 An anomaly of middle phalanx of finger. doelkens 2009-03-11T12:01:39Z UMLS:C4024191 Abnormality of the middle finger bones of the hand Abnormality of the middle phalanges of the hand human_phenotype HP:0009833 Abnormal middle phalanx morphology of the hand An anomaly of middle phalanx of finger. HPO:probinson Abnormality of the middle finger bones of the hand ORCID:0000-0001-5208-3432 doelkens 2009-03-11T12:01:39Z UMLS:C4024190 Abnormality of the innermost finger bones of the hand Abnormality of the proximal phalanges of the hand human_phenotype HP:0009834 Abnormal proximal phalanx morphology of the hand Abnormality of the innermost finger bones of the hand ORCID:0000-0001-5208-3432 Absence or underdevelopment of the distal phalanges. doelkens 2009-03-11T12:10:11Z HP:0005635 HP:0006037 HP:0006066 HP:0006235 UMLS:C1861336 Absent/hypoplastic distal phalanges Absent/small outermost finger bone of the hand Absent/underdeveloped outermost finger bone of the hand Aplasia/Hypoplasia of the distal phalanges Aplastic/hypoplastic distal phalanges Hypoplastic to absent terminal phalanges Hypoplastic/aplastic distal phalanges Hypoplastic/aplastic distal phalanx human_phenotype Small or absent distal phalanges HP:0009835 Aplasia/Hypoplasia of the distal phalanges of the hand Absence or underdevelopment of the distal phalanges. HPO:curators Absent/small outermost finger bone of the hand ORCID:0000-0001-5208-3432 Absent/underdeveloped outermost finger bone of the hand ORCID:0000-0001-5208-3432 Small or absent distal phalanges HPO:skoehler doelkens 2009-03-11T12:15:55Z HP:0005810 HP:0006063 HP:0006148 UMLS:C1862152 Absent/hypoplastic middle phalanges Absent/small middle finger bone of the hand Absent/underdeveloped middle finger bone of the hand Aplasia/hypoplasia of middle phalanges Aplastic/hypoplastic middle phalanges Hypoplastic/aplastic middle phalanx Short to absent middle phalanges Short/absent middle phalanges human_phenotype HP:0009843 Aplasia/Hypoplasia of the middle phalanges of the hand Absent/small middle finger bone of the hand ORCID:0000-0001-5208-3432 Absent/underdeveloped middle finger bone of the hand ORCID:0000-0001-5208-3432 doelkens 2009-03-11T12:15:55Z HP:0009876 UMLS:C4024183 Triangular shaped middle finger bones of the hand human_phenotype HP:0009850 Triangular shaped middle phalanges of the hand Triangular shaped middle finger bones of the hand ORCID:0000-0001-5208-3432 doelkens 2009-03-11T12:16:33Z UMLS:C4024182 Absent/small innermost finger bones of the hand Absent/underdeveloped innermost finger bones of the hand human_phenotype HP:0009851 Aplasia/Hypoplasia of the proximal phalanges of the hand Absent/small innermost finger bones of the hand ORCID:0000-0001-5208-3432 Absent/underdeveloped innermost finger bones of the hand ORCID:0000-0001-5208-3432 doelkens 2009-03-11T12:16:33Z HP:0009877 UMLS:C4024177 human_phenotype Triangular shaped innermost finger bone HP:0009858 Triangular shaped proximal phalanges of the hand Triangular shaped innermost finger bone ORCID:0000-0001-5208-3432 doelkens 2009-03-11T01:53:07Z HP:0006061 HP:0009842 UMLS:C4024176 Triangular shaped outermost bone of the hand human_phenotype HP:0009875 Triangular shaped distal phalanges of the hand Triangular shaped outermost bone of the hand ORCID:0000-0001-5889-4463 Short distance from the end of the finger to the most distal interphalangeal crease or the distal interphalangeal joint flexion point. That is, hypoplasia of one or more of the distal phalanx of finger. doelkens 2009-04-24T04:29:30Z HP:0001198 HP:0001202 HP:0001221 HP:0001229 HP:0005669 HP:0006075 HP:0006076 HP:0006132 HP:0006199 HP:0006223 UMLS:C1839829 Brachytelophalangy Distal phalangeal hypoplasia Hypoplasia of the distal phalanges Hypoplasia of the distal phalanges of the hand Hypoplasic terminal phalanges Hypoplastic distal phalanges Hypoplastic terminal phalanges Short distal phalanges Short outermost finger bone Terminal phalangeal hypoplasia of hand human_phenotype HP:0009882 This term differs from Partial absence of the finger because in that term, the phalanx must be missing, whereas in this term it may be small, but present. Distal phalangeal lengths can be assessed subjectively by comparing that digit segment to the rest of the digit, to other normal digits in that patient, or to typical patients of that age or build. Regarding the subjective definition, for individuals who do not have flexion creases, one may determine this by flexing the DIP joint and estimating the length of the terminal segment of the digit. Alternatively, one may be able to palpate the joint. Short distal phalanx of finger Short distance from the end of the finger to the most distal interphalangeal crease or the distal interphalangeal joint flexion point. That is, hypoplasia of one or more of the distal phalanx of finger. HPO:probinson PMID:19125433 Short outermost finger bone ORCID:0000-0001-5208-3432 This term applies if one or more of the distal phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. doelkens 2009-04-24T04:33:55Z HP:0001228 HP:0010007 UMLS:C1849343 Bifid terminal phalanges Duplication of the outermost bone of hand Notched outermost bone of hand Partial/complete duplication of the distal phalanges of the hand human_phenotype HP:0009883 Duplication of the distal phalanx of hand This term applies if one or more of the distal phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. HPO:sdoelken Duplication of the outermost bone of hand ORCID:0000-0001-5208-3432 Notched outermost bone of hand ORCID:0000-0001-5208-3432 An abnormality of hair pigmentation (color). peter 2009-04-30T06:00:53Z UMLS:C4024172 Abnormality of hair color Abnormality of hair pigmentation human_phenotype HP:0009887 Abnormality of hair pigmentation An abnormality of hair pigmentation (color). HPO:curators Abnormality of hair color ORCID:0000-0001-5889-4463 Abnormality of hair pigmentation Abnormally increased hair growth with a localized distribution. peter 2009-04-30T06:29:20Z UMLS:C4024170 Localised hirsutism Localized abnormal hair growth human_phenotype HP:0009889 Localized hirsutism Abnormally increased hair growth with a localized distribution. HPO:curators Localised hirsutism Localized abnormal hair growth ORCID:0000-0001-5889-4463 Complete absence of any auricular structures. peter 2009-04-30T06:53:41Z MSH:D065817 SNOMEDCT_US:57436000 UMLS:C0702139 UMLS:C1408788 human_phenotype Absent ear Absent ears Congenital absence of external ear HP:0009892 Complete absence of the auricle (external ear). The skin of the cheek passes smoothly over the aural area without definite elevation or depression. Anotia Complete absence of any auricular structures. HPO:probinson PMID:19125421 Absent ear Absent ears HPO:skoehler Congenital absence of external ear HPO:skoehler Abnormality of the temporal bone of the skull, which is situated at the sides and base of the skull roughly underlying the region of the face known as the temple. peter 2009-05-01T03:33:17Z UMLS:C4024163 Abnormality of the temporal bone human_phenotype HP:0009911 Abnormal temporal bone morphology Abnormality of the temporal bone of the skull, which is situated at the sides and base of the skull roughly underlying the region of the face known as the temple. HPO:probinson Underdevelopment or absence of the nose or parts thereof. peter 2009-05-05T06:44:04Z SNOMEDCT_US:204519007 SNOMEDCT_US:93278002 UMLS:C0685684 UMLS:C4024159 UMLS:C4280392 Decreased nasal size Decreased size of nose Hypoplasia of the nose Hypotrophic nose human_phenotype HP:0009924 Aplasia/Hypoplasia involving the nose Underdevelopment or absence of the nose or parts thereof. HPO:curators Decreased nasal size ORCID:0000-0001-5889-4463 Decreased size of nose ORCID:0000-0001-5889-4463 Hypoplasia of the nose ORCID:0000-0001-5889-4463 Hypotrophic nose ORCID:0000-0001-5889-4463 The presence of only a single nostril. peter 2009-05-10T10:33:56Z SNOMEDCT_US:95266003 UMLS:C0685682 Mono nostril One nostril Single nare Single nostril human_phenotype HP:0009932 The single opening may occur in the midline or it can occur on one side, that is, it can be symmetric or asymmetric. Although the columella is invariably absent, this is implicit and does not need to be separately specified. Single naris The presence of only a single nostril. PMID:19152422 Mono nostril ORCID:0000-0001-5889-4463 One nostril ORCID:0000-0001-5889-4463 Single nare ORCID:0000-0001-5889-4463 Single nostril The presence of more than two nostrils. peter 2009-05-10T10:37:41Z UMLS:C4021372 Accessory nares Accessory nostril Extra nostril Supernumerary nares Supernumerary nostrils human_phenotype HP:0009934 Supernumerary naris The presence of more than two nostrils. PMID:19152422 Accessory nares ORCID:0000-0001-5889-4463 Accessory nostril ORCID:0000-0001-5889-4463 Extra nostril ORCID:0000-0001-5889-4463 Supernumerary nares ORCID:0000-0001-5889-4463 Excess facial hair. peter 2009-05-10T10:58:49Z Excessive face hair UMLS:C1850041 UMLS:C2128203 human_phenotype HP:0009937 Facial hirsutism Excess facial hair. HPO:curators Excessive face hair ORCID:0000-0001-5208-3432 Lack or loss of the soft tissues between the zygomata and mandible. peter 2009-05-10T11:17:18Z UMLS:C4024154 Depressed cheeks Hollow cheeks Sunken cheeks human_phenotype HP:0009938 Sunken cheeks Lack or loss of the soft tissues between the zygomata and mandible. PMID:19125436 Depressed cheeks Hollow cheeks Sunken cheeks Complete or partial duplication of the phalanges of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones (bifid), two separate bones appearing side to side, or completely duplicated phalanges (proximal and distal phalanx of the thumb and/or 1st metacarpal). In contrast to the phalanges of the digits 2-5 (proximal, middle and distal), the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. doelkens 2009-05-15T12:51:02Z HP:0009661 UMLS:C4021370 Complete/partial duplication of phalanges of the thumb Duplicated thumbs Duplication of phalanx of thumb human_phenotype Duplicated thumb HP:0009942 Duplication of thumb phalanx Complete or partial duplication of the phalanges of the thumb. Depending on the severity, the appearance on x-ray can vary from a notched phalanx (the duplicated bone is almost completely fused with the phalanx), a partially fused appearance of the two bones (bifid), two separate bones appearing side to side, or completely duplicated phalanges (proximal and distal phalanx of the thumb and/or 1st metacarpal). In contrast to the phalanges of the digits 2-5 (proximal, middle and distal), the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:sdoelken Duplicated thumbs HPO:skoehler A complete duplication affecting one or more of the phalanges of the thumb. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. doelkens 2009-05-15T12:51:35Z HP:0002801 HP:0004067 UMLS:C3554724 Complete duplication of the phalanges of the thumb Complete duplication of thumb bones Digitalization of thumb Digitalization of thumbs human_phenotype HP:0009943 Complete duplication of thumb phalanx A complete duplication affecting one or more of the phalanges of the thumb. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. HPO:probinson Complete duplication of thumb bones ORCID:0000-0001-5208-3432 A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the thumb. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. doelkens 2009-05-15T12:51:57Z HP:0001244 HP:0004070 UMLS:C4082168 Bifid thumb Notching of thumb phalanges Partial duplication of the phalanges of the thumb Partial duplication of the thumb bones human_phenotype HP:0009944 Partial duplication of thumb phalanx A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the thumb. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. HPO:probinson Partial duplication of the thumb bones ORCID:0000-0001-5208-3432 This term applies if one or more of the phalanges of the 5th finger are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. doelkens 2009-05-26T02:23:38Z UMLS:C4021354 Partial/complete duplication of little finger bone Partial/complete duplication of phalanges of the 5th finger Partial/complete duplication of pinkie finger bone Partial/complete duplication of pinky finger bone human_phenotype HP:0009985 Duplication of phalanx of 5th finger This term applies if one or more of the phalanges of the 5th finger are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. HPO:sdoelken Partial/complete duplication of little finger bone ORCID:0000-0001-5208-3432 Partial/complete duplication of pinkie finger bone ORCID:0000-0001-5208-3432 Partial/complete duplication of pinky finger bone ORCID:0000-0001-5208-3432 A complete duplication affecting one or more of the phalanges of the 5th finger. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. doelkens 2009-05-26T02:24:20Z UMLS:C4024128 Complete duplication of the little finger bone Complete duplication of the pinkie finger bone Complete duplication of the pinky finger bone human_phenotype HP:0009986 Complete duplication of the phalanges of the 5th finger A complete duplication affecting one or more of the phalanges of the 5th finger. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. HPO:curators Complete duplication of the little finger bone ORCID:0000-0001-5208-3432 Complete duplication of the pinkie finger bone ORCID:0000-0001-5208-3432 Complete duplication of the pinky finger bone ORCID:0000-0001-5208-3432 A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the 5th finger. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. doelkens 2009-05-26T02:24:20Z UMLS:C4024127 Partial duplication of the little finger bone Partial duplication of the pinkie finger bone Partial duplication of the pinky finger bone human_phenotype HP:0009987 Partial duplication of the phalanges of the 5th finger A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the 5th finger. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. HPO:curators Partial duplication of the little finger bone ORCID:0000-0001-5208-3432 Partial duplication of the pinkie finger bone ORCID:0000-0001-5208-3432 Partial duplication of the pinky finger bone ORCID:0000-0001-5208-3432 Partial or complete duplication of the distal phalanx of little finger. doelkens 2009-05-26T02:24:20Z UMLS:C4021353 Duplication of the outermost little finger bone Duplication of the outermost pinkie finger bone Duplication of the outermost pinky finger bone Partial/complete duplication of the distal phalanx of the 5th finger human_phenotype HP:0009988 Duplication of the distal phalanx of the 5th finger Partial or complete duplication of the distal phalanx of little finger. HPO:probinson Duplication of the outermost little finger bone ORCID:0000-0001-5208-3432 Duplication of the outermost pinkie finger bone ORCID:0000-0001-5208-3432 Duplication of the outermost pinky finger bone ORCID:0000-0001-5208-3432 Partial or complete duplication of the fifth middle phalanx of hand. doelkens 2009-05-26T02:24:20Z UMLS:C4021352 Duplication of the middle little finger bone Duplication of the middle pinkie finger bone Duplication of the middle pinky finger bone Partial/complete duplication of the middle phalanx of the 5th finger human_phenotype HP:0009989 Duplication of the middle phalanx of the 5th finger Partial or complete duplication of the fifth middle phalanx of hand. HPO:probinson Duplication of the middle little finger bone ORCID:0000-0001-5208-3432 Duplication of the middle pinkie finger bone ORCID:0000-0001-5208-3432 Duplication of the middle pinky finger bone ORCID:0000-0001-5208-3432 Partial or complete duplication of the fifth proximal phalanx of hand. doelkens 2009-05-26T02:24:20Z UMLS:C4021351 Duplication of the innermost little finger bone Duplication of the innermost pinkie finger bone Duplication of the innermost pinky finger bone Partial/complete duplication of the proximal phalanx of the 5th finger human_phenotype HP:0009990 Duplication of the proximal phalanx of the 5th finger Partial or complete duplication of the fifth proximal phalanx of hand. HPO:probinson Duplication of the innermost little finger bone ORCID:0000-0001-5208-3432 Duplication of the innermost pinkie finger bone ORCID:0000-0001-5208-3432 Duplication of the innermost pinky finger bone ORCID:0000-0001-5208-3432 Complete duplication of the distal phalanx of little finger. doelkens 2009-05-26T02:24:33Z UMLS:C4024126 Complete duplication of the outermost little finger bone Complete duplication of the outermost pinkie finger bone Complete duplication of the outermost pinky finger bone human_phenotype HP:0009991 Complete duplication of the distal phalanx of the 5th finger Complete duplication of the distal phalanx of little finger. HPO:probinson Complete duplication of the outermost little finger bone ORCID:0000-0001-5208-3432 Complete duplication of the outermost pinkie finger bone ORCID:0000-0001-5208-3432 Complete duplication of the outermost pinky finger bone ORCID:0000-0001-5208-3432 Complete duplication of the fifth middle phalanx of hand. doelkens 2009-05-26T02:24:33Z UMLS:C4024125 Complete duplication of the middle little finger bone Complete duplication of the middle pinkie finger bone Complete duplication of the middle pinky finger bone human_phenotype HP:0009992 Complete duplication of the middle phalanx of the 5th finger Complete duplication of the fifth middle phalanx of hand. HPO:probinson Complete duplication of the middle little finger bone ORCID:0000-0001-5208-3432 Complete duplication of the middle pinkie finger bone ORCID:0000-0001-5208-3432 Complete duplication of the middle pinky finger bone ORCID:0000-0001-5208-3432 Complete duplication of the fifth proximal phalanx of hand. doelkens 2009-05-26T02:24:33Z UMLS:C4024124 Complete duplication of the innermost little finger bone Complete duplication of the innermost pinkie finger bone Complete duplication of the innermost pinky finger bone human_phenotype HP:0009993 Complete duplication of the proximal phalanx of the 5th finger Complete duplication of the fifth proximal phalanx of hand. HPO:probinson Complete duplication of the innermost little finger bone ORCID:0000-0001-5208-3432 Complete duplication of the innermost pinkie finger bone ORCID:0000-0001-5208-3432 Complete duplication of the innermost pinky finger bone ORCID:0000-0001-5208-3432 Partial duplication of the distal phalanx of little finger, seen on x-rays as a broad and/or bifid phalanx. doelkens 2009-05-26T02:24:47Z UMLS:C4021350 Bifid terminal phalanx of the 5th finger Notched outermost pinky finger bone Partial duplication of outermost little finger bone Partial duplication of outermost pinkie finger bone Partial duplication of outermost pinky finger bone human_phenotype HP:0009994 Partial duplication of the distal phalanx of the 5th finger Partial duplication of the distal phalanx of little finger, seen on x-rays as a broad and/or bifid phalanx. HPO:sdoelken Notched outermost pinky finger bone ORCID:0000-0001-5208-3432 Partial duplication of outermost little finger bone ORCID:0000-0001-5208-3432 Partial duplication of outermost pinkie finger bone ORCID:0000-0001-5208-3432 Partial duplication of outermost pinky finger bone ORCID:0000-0001-5208-3432 Partial duplication of the fifth middle phalanx of hand, seen on x-rays as a broad and/or bifid phalanx. doelkens 2009-05-26T02:24:47Z UMLS:C4024123 Partial duplication of the middle little finger bone Partial duplication of the middle pinkie finger bone Partial duplication of the middle pinky finger bone human_phenotype HP:0009995 Partial duplication of the middle phalanx of the 5th finger Partial duplication of the fifth middle phalanx of hand, seen on x-rays as a broad and/or bifid phalanx. HPO:sdoelken Partial duplication of the middle little finger bone ORCID:0000-0001-5208-3432 Partial duplication of the middle pinkie finger bone ORCID:0000-0001-5208-3432 Partial duplication of the middle pinky finger bone ORCID:0000-0001-5208-3432 Partial or complete duplication of the fifth proximal phalanx of hand, seen on x-rays as a broad and/or bifid phalanx. doelkens 2009-05-26T02:24:47Z UMLS:C4024122 Partial duplication of the innermost little finger bone Partial duplication of the innermost pinkie finger bone Partial duplication of the innermost pinky finger bone human_phenotype HP:0009996 Partial duplication of the proximal phalanx of the 5th finger Partial or complete duplication of the fifth proximal phalanx of hand, seen on x-rays as a broad and/or bifid phalanx. HPO:sdoelken Partial duplication of the innermost little finger bone ORCID:0000-0001-5208-3432 Partial duplication of the innermost pinkie finger bone ORCID:0000-0001-5208-3432 Partial duplication of the innermost pinky finger bone ORCID:0000-0001-5208-3432 This term applies if one or more of the phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. doelkens 2009-05-26T02:28:25Z HP:0009143 UMLS:C4021349 Duplication of finger bones human_phenotype HP:0009997 Duplication of phalanx of hand This term applies if one or more of the phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. HPO:sdoelken Duplication of finger bones A complete duplication affecting one or more of the phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, is a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. doelkens 2009-05-26T02:30:16Z UMLS:C4024121 Complete duplication of hand bones human_phenotype HP:0009998 Complete duplication of phalanx of hand A complete duplication affecting one or more of the phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, is a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. HPO:curators Complete duplication of hand bones ORCID:0000-0001-5208-3432 A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. doelkens 2009-05-26T02:30:35Z UMLS:C4024120 Partial duplication of hand bones human_phenotype HP:0009999 Partial duplication of the phalanx of hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. HPO:curators Partial duplication of hand bones ORCID:0000-0001-5208-3432 A complete duplication affecting one or more of the proximal phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. doelkens 2009-05-26T03:55:02Z UMLS:C4024119 Complete duplication of the innermost bones of the hand human_phenotype HP:0010000 Complete duplication of the proximal phalanges of the hand A complete duplication affecting one or more of the proximal phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accesory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a Pseudoepiphyses (see according terms) sometimes also referred to as Hyperphalangism. HPO:curators Complete duplication of the innermost bones of the hand ORCID:0000-0001-5208-3432 A complete duplication affecting one or more of the distal phalanges of the hand. doelkens 2009-05-26T03:55:02Z UMLS:C4024118 Complete duplication of the outermost bones of the hand human_phenotype HP:0010001 As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accessory bone appearing in the proximo-distal axis on x-rays, is actually a different entity called a pseudoepiphysis (see corresponding terms), sometimes also referred to as hyperphalangism. Complete duplication of the distal phalanges of the hand A complete duplication affecting one or more of the distal phalanges of the hand. HPO:sdoelken Complete duplication of the outermost bones of the hand ORCID:0000-0001-5208-3432 A complete duplication affecting one or more of the middle phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accessory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a pseudoepiphysis (see corresponding terms) sometimes also referred to as hyperphalangism. doelkens 2009-05-26T03:55:02Z UMLS:C4024117 Complete duplication of the middle bones of the hand human_phenotype HP:0010002 Complete duplication of the middle phalanges of the hand A complete duplication affecting one or more of the middle phalanges of the hand. As opposed to a partial duplication were there is still a variable degree of fusion between the duplicated bones, a complete duplication leads to two separate bones appearing side to side (radio-ulnar axis) as seen on x-rays. A duplication leading to an accessory bone appearing in the proximo-distal axis on x-rays, this is actually a different entity called a pseudoepiphysis (see corresponding terms) sometimes also referred to as hyperphalangism. HPO:sdoelken Complete duplication of the middle bones of the hand ORCID:0000-0001-5208-3432 A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the proximal phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. doelkens 2009-05-26T03:55:29Z UMLS:C4024116 Partial duplication of the innermost bones of the hand human_phenotype HP:0010003 Partial duplication of the proximal phalanges of the hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the proximal phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. HPO:curators Partial duplication of the innermost bones of the hand ORCID:0000-0001-5208-3432 A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the distal phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. doelkens 2009-05-26T03:55:29Z HP:0006196 UMLS:C4021348 Bifid terminal phalanges of the hand Partial duplication of the outermost bone of the hand human_phenotype HP:0010004 Partial duplication of the distal phalanges of the hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the distal phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. HPO:curators Partial duplication of the outermost bone of the hand ORCID:0000-0001-5208-3432 A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the middle phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. doelkens 2009-05-26T03:55:29Z UMLS:C4024115 Partial duplication of the middle bones of hand human_phenotype HP:0010005 Partial duplication of the middle phalanges of the hand A partial duplication, depending on severity leading to a broad or bifid appearance, affecting one or more of the middle phalanges of the hand. As opposed to a complete duplication there is still a variable degree of fusion between the duplicated bones. HPO:curators Partial duplication of the middle bones of hand ORCID:0000-0001-5208-3432 This term applies if one or more of the proximal phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. doelkens 2009-05-26T05:29:46Z UMLS:C4021347 Duplication of the innermost bones of hand Partial/complete duplication of the proximal phalanges of the hand human_phenotype HP:0010006 Duplication of the proximal phalanx of hand This term applies if one or more of the proximal phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. HPO:sdoelken Duplication of the innermost bones of hand ORCID:0000-0001-5208-3432 This term applies if one or more of the middle phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. doelkens 2009-05-26T05:29:46Z UMLS:C4021346 Duplication of the middle bones of hand Partial/complete duplication of the middle phalanges of the hand human_phenotype HP:0010008 Duplication of the middle phalanx of hand This term applies if one or more of the middle phalanges of the hand are either partially duplicated, depending on severity leading to a broad or bifid appearance of the phalanges, or completely duplicated. HPO:sdoelken Duplication of the middle bones of hand ORCID:0000-0001-5208-3432 A structural anomaly of the first metacarpal. doelkens 2009-05-27T03:35:21Z UMLS:C4024114 Abnormality of the 1st long bone of hand human_phenotype HP:0010009 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits. Abnormality of the 1st metacarpal A structural anomaly of the first metacarpal. HPO:probinson Abnormality of the 1st long bone of hand ORCID:0000-0001-5208-3432 Any abnormality of the fifth metacarpal bone. doelkens 2009-05-27T03:35:21Z UMLS:C4024110 Abnormality of the 5th long bone of hand human_phenotype HP:0010013 Abnormality of the 5th metacarpal Any abnormality of the fifth metacarpal bone. HPO:curators Abnormality of the 5th long bone of hand ORCID:0000-0001-5208-3432 In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). The epiphysis of the first metacarpal is localized at the proximal end (as seen in the proximal phalanges of the other digits), whereas the epiphyses of the other metacarpal bones are located at the distal end. This term applies if the epiphysis of the 1st metacarpal is in any way abnormal, referring to age and gender depending norms, as seen on x-rays. doelkens 2009-05-27T03:43:11Z UMLS:C4024109 Abnormality of the end part of the 1st long bone of hand human_phenotype HP:0010014 Abnormality of the epiphysis of the 1st metacarpal In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). The epiphysis of the first metacarpal is localized at the proximal end (as seen in the proximal phalanges of the other digits), whereas the epiphyses of the other metacarpal bones are located at the distal end. This term applies if the epiphysis of the 1st metacarpal is in any way abnormal, referring to age and gender depending norms, as seen on x-rays. HPO:curators Abnormality of the end part of the 1st long bone of hand ORCID:0000-0001-5208-3432 doelkens 2009-05-27T04:02:50Z UMLS:C4024108 Absent end part of the 1st long bone of hand human_phenotype HP:0010015 Absent epiphysis of the 1st metacarpal Absent end part of the 1st long bone of hand ORCID:0000-0001-5208-3432 Abnormally large size of the epiphyses of the 1st metacarpal with respect to age-dependent norms. doelkens 2009-05-27T04:02:50Z UMLS:C4024105 Enlarged end part of the 1st long bone of hand human_phenotype HP:0010018 Enlarged epiphysis of the 1st metacarpal Abnormally large size of the epiphyses of the 1st metacarpal with respect to age-dependent norms. HPO:probinson Enlarged end part of the 1st long bone of hand ORCID:0000-0001-5208-3432 The epiphysis of the first metacarpal is localized at the proximal end of the metacarpal bone although an accessory epiphysis may be located at the distal end of the metacarpal. doelkens 2009-05-27T04:02:50Z UMLS:C4024101 human_phenotype HP:0010022 This feature can be seen for example in Holt-Oram Syndrome. Pseudoepiphysis of the 1st metacarpal The epiphysis of the first metacarpal is localized at the proximal end of the metacarpal bone although an accessory epiphysis may be located at the distal end of the metacarpal. HPO:probinson Abnormally small size of the epiphysis of the 1st metacarpal with respect to age-dependent norms. doelkens 2009-05-27T04:02:50Z UMLS:C4024100 Small end part of the 1st long bone of hand human_phenotype HP:0010023 Small epiphysis of the 1st metacarpal Abnormally small size of the epiphysis of the 1st metacarpal with respect to age-dependent norms. HPO:probinson Small end part of the 1st long bone of hand ORCID:0000-0001-5208-3432 doelkens 2009-05-27T04:02:50Z UMLS:C4024099 Triangular end part of the 1st long bone of hand human_phenotype HP:0010025 Triangular epiphysis of the 1st metacarpal Triangular end part of the 1st long bone of hand ORCID:0000-0001-5208-3432 Aplasia or Hypoplasia affecting the 1st metacarpal. In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). doelkens 2009-05-27T04:24:30Z UMLS:C4024098 Absent/small 1st long bone of hand Absent/underdeveloped 1st long bone of hand human_phenotype HP:0010026 Aplasia/Hypoplasia of the 1st metacarpal Aplasia or Hypoplasia affecting the 1st metacarpal. In contrast to the metacarpals 2-5, the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5 (whereas the proximal phalanx of the thumb is equivalent to the middle phalanges of the other digits). HPO:curators Absent/small 1st long bone of hand ORCID:0000-0001-5208-3432 Absent/underdeveloped 1st long bone of hand ORCID:0000-0001-5208-3432 A developmental defect characterized by reduced length of the first metacarpal (long bone) of the hand. doelkens 2009-05-27T04:24:50Z HP:0001190 HP:0001499 HP:0005898 HP:0006141 UMLS:C1849311 First metacarpal hypoplasia First metacarpals hypoplastic Hypoplastic 1st metacarpal Short first metacarpal Short first metacarpals Shortened 1st long bone of hand human_phenotype HP:0010034 In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Short 1st metacarpal A developmental defect characterized by reduced length of the first metacarpal (long bone) of the hand. HPO:probinson Shortened 1st long bone of hand ORCID:0000-0001-5208-3432 In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the thumb is embryologically equivalent to the middle phalanges of the other digits, whereas the first metacarpal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. HPO:probinson Aplasia or Hypoplasia affecting the 5th metacarpal. doelkens 2009-05-27T04:37:31Z UMLS:C4024085 Absent/small 5th long bone of hand Absent/underdeveloped 5th long bone of hand human_phenotype HP:0010045 Aplasia/Hypoplasia of the 5th metacarpal Aplasia or Hypoplasia affecting the 5th metacarpal. HPO:curators Absent/small 5th long bone of hand ORCID:0000-0001-5208-3432 Absent/underdeveloped 5th long bone of hand ORCID:0000-0001-5208-3432 Short fifth metacarpal bone. doelkens 2009-05-27T04:37:44Z HP:0005737 HP:0006004 HP:0006222 UMLS:C1861388 Fifth metacarpal hypoplasia Hypoplastic 5th metacarpal Short fifth metacarpal Short fifth metacarpals Shortened 5th long bone of hand human_phenotype HP:0010047 Short 5th metacarpal Short fifth metacarpal bone. HPO:probinson Shortened 5th long bone of hand ORCID:0000-0001-5208-3432 Developmental defect associated with absence of one or more metacarpal bones. doelkens 2009-05-27T04:40:58Z HP:0005911 UMLS:C1846473 Absent long bone of hand Absent metacarpal Absent metacarpals human_phenotype HP:0010048 Aplasia of metacarpal bones Developmental defect associated with absence of one or more metacarpal bones. HPO:probinson Absent long bone of hand ORCID:0000-0001-5208-3432 Diminished length of one or more metacarpal bones in relation to the others of the same hand or to the contralateral metacarpal. doelkens 2009-05-27T04:40:58Z HP:0001164 HP:0005695 HP:0005717 HP:0005909 HP:0006047 HP:0006183 HP:0006186 UMLS:C1837084 Brachymetacarpalia Hypoplastic metacarpal Metacarpal hypoplasia Short metacarpals Shortened long bone of hand Shortened long bones of hand Shortened metacarpals Shortening of metacarpals human_phenotype Short metacarpal bones HP:0010049 Short metacarpals can involve any of the metacarpal bones, and the affected ray should be specified. The assessment of isolated short metacarpal can be made by viewing the dorsum of the hand when clenched. Note that if metacarpals F2-5 are affected, the correct term is Short palm. Short metacarpal Diminished length of one or more metacarpal bones in relation to the others of the same hand or to the contralateral metacarpal. PMID:19125433 Shortened long bone of hand ORCID:0000-0001-5208-3432 Short metacarpal bones HPO:skoehler Displacement of the big toe from its normal position. doelkens 2009-05-29T11:36:44Z HP:0004700 UMLS:C4021344 Displacement of big toe Displacement of the hallux human_phenotype HP:0010051 Deviation of the hallux Displacement of the big toe from its normal position. HPO:curators Displacement of big toe ORCID:0000-0001-5208-3432 An abnormal shape or form of the proximal phalanx of the big toe. doelkens 2009-05-29T11:47:46Z UMLS:C4024084 Abnormal innermost big toe bone Abnormality of the proximal phalanx of the hallux human_phenotype HP:0010052 In contrast to the proximal phalanges of the digits 2-5, the proximal phalanx of the big toe is embryologically equivalent to the middle phalanges of the other digits, whereas the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the other digits. Abnormal morphology of the proximal phalanx of the hallux An abnormal shape or form of the proximal phalanx of the big toe. HPO:probinson Abnormal innermost big toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T11:49:11Z UMLS:C4024083 Abnormality of the outermost bone of the big toe human_phenotype HP:0010053 Abnormality of the distal phalanx of the hallux Abnormality of the outermost bone of the big toe ORCID:0000-0001-5208-3432 An anomaly of the first metatarsal bone. doelkens 2009-05-29T11:49:54Z UMLS:C4024082 Abnormality of the 1st long bone of foot human_phenotype HP:0010054 In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities of the first metatarsal. Abnormality of the first metatarsal bone An anomaly of the first metatarsal bone. HPO:probinson Abnormality of the 1st long bone of foot ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:00:08Z UMLS:C4024081 Abnormality of the end part of the big toe bone human_phenotype HP:0010056 Abnormality of the epiphyses of the hallux Abnormality of the end part of the big toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:00:08Z UMLS:C4024080 Abnormal big toe bones human_phenotype HP:0010057 Abnormality of the phalanges of the hallux Abnormal big toe bones ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:10:46Z UMLS:C4024079 Absent/small big toe bone Absent/underdeveloped big toe bone human_phenotype HP:0010058 Aplasia/Hypoplasia of the phalanges of the hallux Absent/small big toe bone ORCID:0000-0001-5208-3432 Absent/underdeveloped big toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:10:46Z UMLS:C4024077 Triangular shaped bones of big toe human_phenotype HP:0010065 Triangular shaped phalanges of the hallux Triangular shaped bones of big toe ORCID:0000-0001-5208-3432 Partial or complete duplication of one or more phalanx of big toe. doelkens 2009-05-29T12:10:46Z HP:0001784 HP:0005785 HP:0005851 UMLS:C1860164 UMLS:C4020691 Duplicated hallux Duplication of big toe bone Duplication of great toes Duplication of phalanx of big toe Hallucal duplication Partial/complete duplication of the phalanges of the hallux human_phenotype HP:0010066 Duplication of phalanx of hallux Partial or complete duplication of one or more phalanx of big toe. HPO:probinson Duplication of big toe bone ORCID:0000-0001-5208-3432 Duplication of great toes Absence or underdevelopment of the first metatarsal bone. doelkens 2009-05-29T12:13:57Z UMLS:C4024076 Absent/small 1st long bone of foot Absent/underdeveloped 1st long bone of foot human_phenotype HP:0010067 Aplasia/hypoplasia of the 1st metatarsal Absence or underdevelopment of the first metatarsal bone. HPO:probinson Absent/small 1st long bone of foot ORCID:0000-0001-5208-3432 Absent/underdeveloped 1st long bone of foot ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:13:57Z UMLS:C4024070 Triangular shaped 1st long bone of foot human_phenotype HP:0010074 Triangular shaped 1st metatarsal Triangular shaped 1st long bone of foot ORCID:0000-0001-5208-3432 A developmental defect consisting in the duplication of the first metatarsal bone. doelkens 2009-05-29T12:13:57Z UMLS:C1851855 Duplicated 1st long bone of foot Duplicated first metatarsals human_phenotype HP:0010075 Duplication of the 1st metatarsal A developmental defect consisting in the duplication of the first metatarsal bone. HPO:probinson Duplicated 1st long bone of foot ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:16:28Z UMLS:C4024069 Absent/small outermost big toe bone Absent/underdeveloped outermost big toe bone human_phenotype HP:0010076 Aplasia/Hypoplasia of the distal phalanx of the hallux Absent/small outermost big toe bone ORCID:0000-0001-5208-3432 Absent/underdeveloped outermost big toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:16:28Z UMLS:C4024062 Triangular shaped outermost bone of the big toe human_phenotype HP:0010083 Triangular shaped distal phalanx of the hallux Triangular shaped outermost bone of the big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:16:28Z UMLS:C4021339 Duplication of the outermost bone of big toe Partial/complete duplication of the distal phalanx of the hallux human_phenotype HP:0010084 Duplication of the distal phalanx of the hallux Duplication of the outermost bone of big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:17:16Z UMLS:C4024061 Absent/small innermost big toe bone Absent/underdeveloped innermost big toe bone human_phenotype HP:0010085 Aplasia/Hypoplasia of the proximal phalanx of the hallux Absent/small innermost big toe bone ORCID:0000-0001-5208-3432 Absent/underdeveloped innermost big toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:17:16Z UMLS:C4024055 Triangular shaped innermost bone of big toe human_phenotype HP:0010092 Triangular shaped proximal phalanx of the hallux Triangular shaped innermost bone of big toe ORCID:0000-0001-5208-3432 Partial or complete duplication of the proximal phalanx of big toe. doelkens 2009-05-29T12:17:16Z UMLS:C4024054 Duplication of the innermost bone of big toe human_phenotype HP:0010093 Duplication of the proximal phalanx of the hallux Partial or complete duplication of the proximal phalanx of big toe. HPO:sdoelken Duplication of the innermost bone of big toe ORCID:0000-0001-5208-3432 Complete duplication of the proximal phalanx of big toe. doelkens 2009-05-29T12:18:59Z UMLS:C4024053 Complete duplication of the innermost bone of big toe human_phenotype HP:0010094 Complete duplication of the proximal phalanx of the hallux Complete duplication of the proximal phalanx of big toe. HPO:sdoelken Complete duplication of the innermost bone of big toe ORCID:0000-0001-5208-3432 Partial duplication of the proximal phalanx of big toe. doelkens 2009-05-29T12:18:59Z UMLS:C4024052 Partial duplication of the innermost bone of big toe human_phenotype HP:0010095 Partial duplication of the proximal phalanx of the hallux Partial duplication of the proximal phalanx of big toe. HPO:sdoelken Partial duplication of the innermost bone of big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:19:30Z UMLS:C4024051 Complete duplication of the outermost bone of the big toe human_phenotype HP:0010096 Complete duplication of the distal phalanx of the hallux Complete duplication of the outermost bone of the big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:19:30Z HP:0008091 UMLS:C4021337 Bifid distal phalanx of hallux Notched outermost bone of big toe Partial duplication of the outermost bone of big toe human_phenotype HP:0010097 Partial duplication of the distal phalanx of the hallux Notched outermost bone of big toe ORCID:0000-0001-5208-3432 Partial duplication of the outermost bone of big toe ORCID:0000-0001-5208-3432 A developmental defect consisting in the complete duplication of the first metatarsal bone. doelkens 2009-05-29T12:20:12Z HP:0008121 UMLS:C4024050 Complete duplication of the 1st long bone of foot human_phenotype HP:0010098 Complete duplication of the 1st metatarsal A developmental defect consisting in the complete duplication of the first metatarsal bone. HPO:probinson Complete duplication of the 1st long bone of foot ORCID:0000-0001-5208-3432 A developmental defect consisting in the duplication of part of the first metatarsal bone. doelkens 2009-05-29T12:20:12Z UMLS:C4024049 Partial duplication of the 1st long bone of foot human_phenotype HP:0010099 Partial duplication of the 1st metatarsal A developmental defect consisting in the duplication of part of the first metatarsal bone. HPO:probinson Partial duplication of the 1st long bone of foot ORCID:0000-0001-5208-3432 Complete duplication of one or more phalanx of big toe. doelkens 2009-05-29T12:22:12Z UMLS:C4021336 Complete duplication of big toe bones Complete duplication of the phalanges of the hallux human_phenotype HP:0010100 Complete duplication of hallux phalanx Complete duplication of one or more phalanx of big toe. HPO:probinson Complete duplication of big toe bones ORCID:0000-0001-5208-3432 doelkens 2009-05-29T12:22:12Z HP:0004678 UMLS:C1855005 Partial duplication of big toe partial duplication of hallux human_phenotype HP:0010101 Partial duplication of the phalanges of the hallux Partial duplication of big toe ORCID:0000-0001-5208-3432 Underdevelopment (hypoplasia) of the distal phalanx of big toe. doelkens 2009-05-29T12:41:37Z UMLS:C4021335 Hypoplastic/small distal phalanx of the hallux Small distal phalanx of big toe Small distal phalanx of hallux Small outermost bone of big toe human_phenotype HP:0010103 Short distal phalanx of hallux Underdevelopment (hypoplasia) of the distal phalanx of big toe. HPO:probinson Small outermost bone of big toe ORCID:0000-0001-5208-3432 Short first metatarsal bone. doelkens 2009-05-29T12:42:09Z HP:0004680 UMLS:C1841688 First metatarsal hypoplasia First metatarsals hypoplastic Short 1st long bone of foot human_phenotype HP:0010105 Short first metatarsal Short first metatarsal bone. HPO:probinson Short 1st long bone of foot ORCID:0000-0001-5208-3432 Underdevelopment (hypoplasia) of the proximal phalanx of big toe. doelkens 2009-05-29T12:43:40Z HP:0008101 HP:0008129 UMLS:C1862159 Hypoplastic proximal phalanx of the hallux Short innermost big toe bone Short proximal phalanges of halluces Short proximal phalanx of halluces Small proximal phalanx of big toe Small proximal phalanx of hallux human_phenotype HP:0010107 Short proximal phalanx of hallux Underdevelopment (hypoplasia) of the proximal phalanx of big toe. HPO:probinson Short innermost big toe bone ORCID:0000-0001-5208-3432 Underdevelopment (hypoplasia) of the big toe. doelkens 2009-05-29T12:46:14Z HP:0001843 HP:0001861 HP:0005610 HP:0008105 UMLS:C1865992 Hypoplastic big toes Hypoplastic hallux Short big toe Short halluces Small hallux human_phenotype HP:0010109 Short hallux Underdevelopment (hypoplasia) of the big toe. HPO:probinson Short big toe ORCID:0000-0001-5208-3432 Underdevelopment (hypoplasia) of a phalanx of big toe. doelkens 2009-05-29T12:49:19Z UMLS:C4021334 Hypoplastic phalanges of the hallux Short bone of big toe human_phenotype HP:0010111 Short phalanx of hallux Underdevelopment (hypoplasia) of a phalanx of big toe. HPO:probinson Hypoplastic phalanges of the hallux Short bone of big toe ORCID:0000-0001-5208-3432 Failure to form (agenesis) of one or more epiphyses of the big toe. doelkens 2009-05-29T01:16:38Z UMLS:C4020906 Absent end part of big toe bone Absent epiphyses of the hallux human_phenotype HP:0010113 Absent hallux epiphysis Failure to form (agenesis) of one or more epiphyses of the big toe. HPO:probinson Absent end part of big toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:16:38Z UMLS:C4024043 Enlarged end part of the big toe bone human_phenotype HP:0010116 Enlarged epiphyses of the hallux Enlarged end part of the big toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:16:38Z UMLS:C4024039 human_phenotype HP:0010120 Pseudoepiphyses of the hallux doelkens 2009-05-29T01:16:38Z UMLS:C4024038 Small end part of the big toe bone human_phenotype HP:0010121 Small epiphyses of the hallux Small end part of the big toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:16:38Z UMLS:C4024036 Triangular end part of the big toe bone human_phenotype HP:0010123 Triangular epiphyses of the hallux Triangular end part of the big toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:17:54Z UMLS:C4024035 Abnormality of the end part of the outermost bone of the big toe bone human_phenotype HP:0010124 Abnormality of the epiphysis of the distal phalanx of the hallux Abnormality of the end part of the outermost bone of the big toe bone ORCID:0000-0001-5208-3432 In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities of the epiphysis of the first metatarsal bone. doelkens 2009-05-29T01:17:54Z UMLS:C4024034 Abnormality of the end part of the 1st long bone of foot human_phenotype HP:0010125 Abnormality of the epiphysis of the 1st metatarsal In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities of the epiphysis of the first metatarsal bone. HPO:curators Abnormality of the end part of the 1st long bone of foot ORCID:0000-0001-5208-3432 In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities affecting the proximal phalanx of the hallux. doelkens 2009-05-29T01:17:54Z UMLS:C4024033 Abnormality of the end part of the innermost bone of the big toe human_phenotype HP:0010126 Abnormality of the epiphysis of the proximal phalanx of the hallux In contrast to the metatarsals 2-5, the first metatarsal is embryologically of phalangeal origin and as such equivalent to the proximal phalanges of the digits 2-5, whereas the proximal phalanx of the big toe is equivalent to the middle phalanges of the other digits. This term applies to abnormalities affecting the proximal phalanx of the hallux. HPO:curators Abnormality of the end part of the innermost bone of the big toe ORCID:0000-0001-5208-3432 Failure to form (agenesis) of the epiphysis of the proximal phalanx of the hallux. doelkens 2009-05-29T01:22:23Z UMLS:C4024032 Absent end part of the innermost bone of the big toe human_phenotype HP:0010127 Absent epiphysis of the proximal phalanx of the hallux Failure to form (agenesis) of the epiphysis of the proximal phalanx of the hallux. HPO:probinson Absent end part of the innermost bone of the big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:22:23Z UMLS:C4024029 Enlarged end part of the innermost bone of the big toe human_phenotype HP:0010130 Enlarged epiphysis of the proximal phalanx of the hallux Enlarged end part of the innermost bone of the big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:22:23Z UMLS:C4024025 human_phenotype HP:0010134 Pseudoepiphysis of the proximal phalanx of the hallux doelkens 2009-05-29T01:22:23Z UMLS:C4024024 Small end part of the innermost bone of the big toe human_phenotype HP:0010135 Small epiphysis of the proximal phalanx of the hallux Small end part of the innermost bone of the big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:22:23Z UMLS:C4024022 Triangular end part of the innermost bone of the big toe human_phenotype HP:0010137 Triangular epiphysis of the proximal phalanx of the hallux Triangular end part of the innermost bone of the big toe ORCID:0000-0001-5208-3432 Failure to form (agenesis) of the epiphysis of the distal phalanx of the hallux. doelkens 2009-05-29T01:22:47Z UMLS:C4024021 Absent end part of the outermost bone of the big toe human_phenotype HP:0010138 Absent epiphysis of the distal phalanx of the hallux Failure to form (agenesis) of the epiphysis of the distal phalanx of the hallux. HPO:probinson Absent end part of the outermost bone of the big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:22:47Z UMLS:C4024018 Enlarged end part of the outermost bone of the big toe human_phenotype HP:0010141 Enlarged epiphysis of the distal phalanx of the hallux Enlarged end part of the outermost bone of the big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:22:47Z UMLS:C4024014 human_phenotype HP:0010145 Pseudoepiphysis of the distal phalanx of the hallux doelkens 2009-05-29T01:22:47Z UMLS:C4024013 Small end part of the outermost bone of the big toe human_phenotype HP:0010146 Small epiphysis of the distal phalanx of the hallux Small end part of the outermost bone of the big toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:22:47Z UMLS:C4024011 Triangular end part of the outermost bone of the big toe human_phenotype HP:0010148 Triangular epiphysis of the distal phalanx of the hallux Triangular end part of the outermost bone of the big toe ORCID:0000-0001-5208-3432 Failure to form (agenesis) of the epiphysis of the 1st metatarsal. doelkens 2009-05-29T01:24:17Z UMLS:C4024010 Absent end part of the 1st long bone of foot human_phenotype HP:0010149 Absent epiphysis of the 1st metatarsal Failure to form (agenesis) of the epiphysis of the 1st metatarsal. HPO:probinson Absent end part of the 1st long bone of foot ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:24:17Z UMLS:C4024007 Enlarged end part of the 1st long bone of foot human_phenotype HP:0010152 Enlarged epiphysis of the 1st metatarsal Enlarged end part of the 1st long bone of foot ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:24:17Z UMLS:C4024003 human_phenotype HP:0010156 Pseudoepiphysis of the 1st metatarsal doelkens 2009-05-29T01:24:17Z UMLS:C4024002 Small end part of the 1st long bone of foot human_phenotype HP:0010157 Small epiphysis of the 1st metatarsal Small end part of the 1st long bone of foot ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:24:17Z UMLS:C4024000 Triangular end part of the 1st long bone of foot human_phenotype HP:0010159 Triangular epiphysis of the 1st metatarsal Triangular end part of the 1st long bone of foot ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:30:42Z UMLS:C4023999 Abnormality of the end part of the toe bones human_phenotype HP:0010160 Abnormality of the epiphyses of the toes Abnormality of the end part of the toe bones ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:31:17Z UMLS:C4023998 Abnormality of the long bones of the toes human_phenotype HP:0010161 Abnormality of the phalanges of the toes Abnormality of the long bones of the toes ORCID:0000-0001-5208-3432 Absence of the epiphyses of the phalanges of the toes. doelkens 2009-05-29T01:34:06Z UMLS:C4023997 Absent end part of the toe bones human_phenotype HP:0010162 Absent epiphyses of the toes Absence of the epiphyses of the phalanges of the toes. HPO:sdoelken Absent end part of the toe bones ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:34:06Z UMLS:C4023994 Enlarged end part of the toe bones human_phenotype HP:0010165 Enlarged epiphyses of the toes Enlarged end part of the toe bones ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:34:06Z UMLS:C4023990 human_phenotype HP:0010169 Pseudoepiphyses of the toes doelkens 2009-05-29T01:34:06Z UMLS:C4023989 Small end part of the toe bones human_phenotype HP:0010170 Small epiphyses of the toes Small end part of the toe bones ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:34:06Z UMLS:C4023988 Triangular end part of the toe bones human_phenotype HP:0010172 Triangular epiphyses of the toes Triangular end part of the toe bones ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:39:26Z UMLS:C4023987 Absent/small toe bones Absent/underdeveloped toe bones human_phenotype HP:0010173 Aplasia/Hypoplasia of the phalanges of the toes Absent/small toe bones ORCID:0000-0001-5208-3432 Absent/underdeveloped toe bones ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:39:26Z UMLS:C4023983 Triangular shaped toe bones human_phenotype HP:0010180 Triangular shaped phalanges of the toes Triangular shaped toe bones ORCID:0000-0001-5208-3432 Partial/complete duplication of one or more phalanx of toe. doelkens 2009-05-29T01:39:26Z UMLS:C4021328 Duplicated toe bone Partial/complete duplication of the phalanges of the toes human_phenotype HP:0010181 Duplication of phalanx of toe Partial/complete duplication of one or more phalanx of toe. HPO:probinson Duplicated toe bone ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:51:38Z UMLS:C4023982 Abnormality of the outermost bone of the toes human_phenotype HP:0010182 Abnormality of the distal phalanges of the toes Abnormality of the outermost bone of the toes ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:51:38Z UMLS:C4023981 Abnormal middle bones of toe human_phenotype HP:0010183 Abnormality of the middle phalanges of the toes Abnormal middle bones of toe ORCID:0000-0001-5208-3432 A morphological anomaly of one or more proximal phalanges of one or more toes. doelkens 2009-05-29T01:51:38Z UMLS:C4021327 Abnormal innermost toe bone Abnormality of the proximal phalanges of the toes human_phenotype HP:0010184 Abnormality of toe proximal phalanx A morphological anomaly of one or more proximal phalanges of one or more toes. HPO:probinson Abnormal innermost toe bone ORCID:0000-0001-5208-3432 Absence or underdevelopment of the distal phalanges of the toes. doelkens 2009-05-29T01:52:41Z HP:0005735 HP:0005818 UMLS:C4020773 UMLS:C4021326 Absent/hypoplastic terminal phalanges of toes Absent/small outermost bones of toe Absent/underdeveloped outermost bones of toe human_phenotype Hypoplasia/agenesis of distal phalanges of toes HP:0010185 Aplasia/Hypoplasia of the distal phalanges of the toes Absence or underdevelopment of the distal phalanges of the toes. HPO:probinson Absent/small outermost bones of toe ORCID:0000-0001-5208-3432 Absent/underdeveloped outermost bones of toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:52:41Z UMLS:C4023977 Triangular shaped outermost bone of the toes human_phenotype HP:0010192 Triangular shaped distal phalanges of the toes Triangular shaped outermost bone of the toes ORCID:0000-0001-5208-3432 A partial or complete duplication of one or more distal phalanx of toe. doelkens 2009-05-29T01:52:41Z UMLS:C4021322 Duplication of outermost bone of toe Partial/complete duplication of the distal phalanges of the toes human_phenotype HP:0010193 Duplication of distal phalanx of toe A partial or complete duplication of one or more distal phalanx of toe. HPO:sdoelken Duplication of outermost bone of toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:53:35Z UMLS:C4023976 Absent/small middle bones of toe Absent/underdeveloped middle bones of toe human_phenotype HP:0010194 Aplasia/Hypoplasia of the middle phalanges of the toes Absent/small middle bones of toe ORCID:0000-0001-5208-3432 Absent/underdeveloped middle bones of toe ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:53:35Z UMLS:C4023972 Triangular shaped middle bones of toes human_phenotype HP:0010201 Triangular shaped middle phalanges of the toes Triangular shaped middle bones of toes ORCID:0000-0001-5208-3432 Partial or complete duplication of a middle phalanx of toe. doelkens 2009-05-29T01:53:35Z UMLS:C4021318 Partial/complete duplication of the middle bones of the toes Partial/complete duplication of the middle phalanges of the toes human_phenotype HP:0010202 Duplication of middle phalanx of toe Partial or complete duplication of a middle phalanx of toe. HPO:probinson Partial/complete duplication of the middle bones of the toes ORCID:0000-0001-5208-3432 Absence (agenesis) or underdevelopment of one or more of the proximal phalanges of the toes. doelkens 2009-05-29T01:54:18Z UMLS:C4021317 Absent/small innermost toe bones Absent/underdeveloped innermost toe bones Aplasia/Hypoplasia of the proximal phalanges of the toes human_phenotype HP:0010203 Aplasia/hypoplasia of proximal toe phalanx Absence (agenesis) or underdevelopment of one or more of the proximal phalanges of the toes. HPO:probinson Absent/small innermost toe bones ORCID:0000-0001-5208-3432 Absent/underdeveloped innermost toe bones ORCID:0000-0001-5208-3432 doelkens 2009-05-29T01:54:18Z UMLS:C4023969 Triangular shaped innermost toe bones human_phenotype HP:0010210 Triangular shaped proximal phalanges of the toes Triangular shaped innermost toe bones ORCID:0000-0001-5208-3432 Partial/complete duplication of a proximal phalanx of toe. doelkens 2009-05-29T01:54:18Z UMLS:C4021312 Duplication of innermost toe bones Partial/complete duplication of the proximal phalanges of the toes human_phenotype HP:0010211 Duplication of proximal phalanx of toe Partial/complete duplication of a proximal phalanx of toe. HPO:sdoelken Duplication of innermost toe bones ORCID:0000-0001-5208-3432 One or more bent (flexed) joints of the first (big) toe that cannot be straightened actively or passively. doelkens 2009-06-02T01:39:18Z UMLS:C4021311 Joint contracture of the big toe Joint contracture of the hallux human_phenotype HP:0010212 Flexion contracture of the hallux One or more bent (flexed) joints of the first (big) toe that cannot be straightened actively or passively. HPO:probinson Joint contracture of the big toe ORCID:0000-0001-5208-3432 Chronic loss of joint motion in the tarsometatarsal joint of the hallux due to structural changes in non-bony tissue. The tarsometatarsal joints of the feet are also called Lisfranc's joints. doelkens 2009-06-02T01:45:34Z UMLS:C4023968 human_phenotype HP:0010213 Contracture of the tarsometatarsal joint of the hallux Chronic loss of joint motion in the tarsometatarsal joint of the hallux due to structural changes in non-bony tissue. The tarsometatarsal joints of the feet are also called Lisfranc's joints. HPO:probinson The interphalangeal joint of the big toe cannot be straightened actively or passively. doelkens 2009-06-02T01:45:34Z UMLS:C4023967 human_phenotype HP:0010214 Contracture of the interphalangeal joint of the hallux The interphalangeal joint of the big toe cannot be straightened actively or passively. HPO:probinson The joint between the first metatarsal and the proximal phalanx of the first (big) toe cannot be straightened actively or passively. doelkens 2009-06-02T01:45:34Z UMLS:C4023966 human_phenotype HP:0010215 Contractures of the metatarsophalangeal joint of the hallux The joint between the first metatarsal and the proximal phalanx of the first (big) toe cannot be straightened actively or passively. HPO:probinson Any abnormality of the epiphysis of the fifth metacarpal bone. doelkens 2009-07-02T04:13:00Z UMLS:C4023958 Abnormality of the end part of the long bone of little finger Abnormality of the end part of the long bone of pinkie finger Abnormality of the end part of the long bone of pinky finger human_phenotype HP:0010226 Abnormality of the epiphysis of the 5th metacarpal Any abnormality of the epiphysis of the fifth metacarpal bone. HPO:curators Abnormality of the end part of the long bone of little finger ORCID:0000-0001-5208-3432 Abnormality of the end part of the long bone of pinkie finger ORCID:0000-0001-5208-3432 Abnormality of the end part of the long bone of pinky finger ORCID:0000-0001-5208-3432 Absence of one or more epiphyses of the phalanges of the fingers. doelkens 2009-07-06T03:31:52Z HP:0009359 UMLS:C4021310 Absent end part of fingers Absent epiphyses of the fingers human_phenotype HP:0010228 Absent epiphyses of the phalanges of the hand Absence of one or more epiphyses of the phalanges of the fingers. HPO:skoehler Absent end part of fingers ORCID:0000-0001-5208-3432 Abnormally large size of the epiphyses of the phalanges of the fingers with respect to age-dependent norms. doelkens 2009-07-06T03:31:52Z HP:0006023 HP:0009362 UMLS:C1865036 Enlarged end part of finger bones Enlarged epiphyses of the fingers Enlarged phalangeal epiphyses human_phenotype HP:0010231 Enlarged epiphyses of the phalanges of the hand Abnormally large size of the epiphyses of the phalanges of the fingers with respect to age-dependent norms. HPO:curators Enlarged end part of finger bones ORCID:0000-0001-5208-3432 A secondary ossification center in the phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. doelkens 2009-07-06T03:31:52Z HP:0009366 UMLS:C4021306 Pseudoepiphysis of the fingers human_phenotype HP:0010235 Pseudoepiphyses of the phalanges of the hand A secondary ossification center in the phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. HPO:curators Abnormally small size of the epiphyses of the phalanges of the fingers with respect to age-dependent norms. doelkens 2009-07-06T03:31:52Z HP:0009367 UMLS:C4021305 Small end part of finger bones Small epiphyses of the fingers human_phenotype HP:0010236 Small epiphyses of the phalanges of the hand Abnormally small size of the epiphyses of the phalanges of the fingers with respect to age-dependent norms. HPO:curators Small end part of finger bones ORCID:0000-0001-5208-3432 A triangular appearance of the epiphyses of the phalanges of the fingers of the hand. doelkens 2009-07-06T03:31:52Z HP:0009369 UMLS:C4021303 Delta-shaped epiphyses of the fingers Triangular end part of finger bones Triangular epiphyses of the fingers human_phenotype HP:0010238 Triangular epiphyses of the phalanges of the hand A triangular appearance of the epiphyses of the phalanges of the fingers of the hand. HPO:curators Triangular end part of finger bones ORCID:0000-0001-5208-3432 Congenital hypoplasia of one or more proximal phalanx of finger. doelkens 2009-07-06T04:00:44Z HP:0005670 HP:0006138 UMLS:C1860606 Hypoplasia of the proximal phalanges of the hand Short innermost finger bones Short proximal phalanges Short proximal phalanx of finger Shortening in proximal phalanges human_phenotype HP:0010241 Short proximal phalanx of finger Congenital hypoplasia of one or more proximal phalanx of finger. HPO:probinson Short innermost finger bones ORCID:0000-0001-5208-3432 Short proximal phalanx of finger Any anomaly of distal epiphysis of phalanx of finger. doelkens 2009-07-06T04:21:32Z UMLS:C4023956 Abnormality of the end part of the outermost bone of finger human_phenotype HP:0010243 Abnormality of the epiphyses of the distal phalanx of finger Any anomaly of distal epiphysis of phalanx of finger. HPO:probinson Abnormality of the end part of the outermost bone of finger ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:21:32Z UMLS:C4023955 Abnormality of the end part of the middle hand bones human_phenotype HP:0010244 Abnormality of the epiphyses of the middle phalanges of the hand Abnormality of the end part of the middle hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:21:32Z UMLS:C4023954 Abnormality of the end part of the innermost hand bones human_phenotype HP:0010245 Abnormality of the epiphyses of the proximal phalanges of the hand Abnormality of the end part of the innermost hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:23:06Z UMLS:C4023953 Absent end part of the outermost hand bones human_phenotype HP:0010246 Absent epiphyses of the distal phalanges of the hand Absent end part of the outermost hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:23:06Z UMLS:C4023950 Enlarged end part of the outermost hand bones human_phenotype HP:0010249 Enlarged epiphyses of the distal phalanges of the hand Enlarged end part of the outermost hand bones ORCID:0000-0001-5208-3432 A secondary ossification center in the distal phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. doelkens 2009-07-06T04:23:06Z UMLS:C4023947 human_phenotype HP:0010253 Pseudoepiphyses of the distal phalanges of the hand doelkens 2009-07-06T04:23:06Z UMLS:C4023946 Small end part of the outermost hand bones human_phenotype HP:0010254 Small epiphyses of the distal phalanges of the hand Small end part of the outermost hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:23:06Z UMLS:C4023944 Triangular end part of the outermost hand bones human_phenotype HP:0010256 Triangular epiphyses of the distal phalanges of the hand Triangular end part of the outermost hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:24:15Z UMLS:C4023943 Absent end part of the middle hand bones human_phenotype HP:0010257 Absent epiphyses of the middle phalanges of the hand Absent end part of the middle hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:24:15Z UMLS:C4023941 Enlarged end part of the middle hand bones human_phenotype HP:0010260 Enlarged epiphyses of the middle phalanges of the hand Enlarged end part of the middle hand bones ORCID:0000-0001-5208-3432 A secondary ossification center in the middle phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. doelkens 2009-07-06T04:24:15Z UMLS:C4023937 human_phenotype HP:0010264 Pseudoepiphyses of the middle phalanges of the hand doelkens 2009-07-06T04:24:15Z UMLS:C4023936 Small end part of the middle hand bones human_phenotype HP:0010265 Small epiphyses of the middle phalanges of the hand Small end part of the middle hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:24:15Z UMLS:C4023934 Triangular end part of the middle hand bones human_phenotype HP:0010267 Triangular epiphyses of the middle phalanges of the hand Triangular end part of the middle hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:25:12Z UMLS:C4023933 Absent end part of the innermost hand bones human_phenotype HP:0010268 Absent epiphyses of the proximal phalanges of the hand Absent end part of the innermost hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:25:12Z UMLS:C4023930 Enlarged end part of the innermost hand bones human_phenotype HP:0010271 Enlarged epiphyses of the proximal phalanges of the hand Enlarged end part of the innermost hand bones ORCID:0000-0001-5208-3432 A secondary ossification center in the proximal phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. doelkens 2009-07-06T04:25:12Z UMLS:C4023926 human_phenotype HP:0010275 Pseudoepiphyses of the proximal phalanges of the hand A secondary ossification center in the proximal phalanges of the hand that is distinct from the normal epiphysis that does not contribute to the longitudinal growth of a tubular bone. HPO:curators doelkens 2009-07-06T04:25:12Z UMLS:C4023925 Small end part of the innermost hand bones human_phenotype HP:0010276 Small epiphyses of the proximal phalanges of the hand Small end part of the innermost hand bones ORCID:0000-0001-5208-3432 doelkens 2009-07-06T04:25:12Z UMLS:C4023923 Triangular end part of the innermost hand bones human_phenotype HP:0010278 Triangular epiphyses of the proximal phalanges of the hand Triangular end part of the innermost hand bones ORCID:0000-0001-5208-3432 Stomatitis is an inflammation of the mucous membranes of any of the structures in the mouth. peter 2009-07-12T09:48:56Z MSH:D013280 SNOMEDCT_US:20607006 SNOMEDCT_US:61170000 UMLS:C0038362 UMLS:C0149704 Inflammation of the mouth Gingivostomatitis human_phenotype HP:0010280 Stomatitis Stomatitis is an inflammation of the mucous membranes of any of the structures in the mouth. HPO:probinson Inflammation of the mouth ORCID:0000-0001-5889-4463 Gingivostomatitis ORCID:0000-0001-5889-4463 A gap in the lower lip. peter 2009-07-12T09:50:34Z UMLS:C1856026 Cleft lower lip Cleft of the lower lip Lower labial cleft human_phenotype HP:0010281 Cleft lower lip A gap in the lower lip. HPO:probinson Cleft lower lip Cleft of the lower lip Lower labial cleft ORCID:0000-0001-5889-4463 Any abnormality of the salivary glands, the exocrine glands that produce saliva. peter 2009-07-12T10:38:51Z MSH:D012466 SNOMEDCT_US:10890000 UMLS:C0036093 UMLS:C0149772 Abnormality of the salivary glands human_phenotype Salivary gland disease HP:0010286 Abnormal salivary gland morphology Any abnormality of the salivary glands, the exocrine glands that produce saliva. HPO:probinson Abnormality of the salivary glands Salivary gland disease Any abnormality of the submandibular glands, which are the salivary glands that are located beneath the floor of the mouth, superior to the digastric muscles. peter 2009-07-12T10:41:17Z UMLS:C4023920 Abnormality of the submaxillary glands human_phenotype HP:0010287 Abnormality of the submandibular glands Any abnormality of the submandibular glands, which are the salivary glands that are located beneath the floor of the mouth, superior to the digastric muscles. HPO:curators Abnormality of the submaxillary glands ORCID:0000-0001-5889-4463 Absence or underdevelopment of the tongue. peter 2009-07-12T11:41:04Z UMLS:C4023916 UMLS:C4280384 Lingual aplasia/hypoplasia human_phenotype HP:0010295 Aplasia/Hypoplasia of the tongue Absence or underdevelopment of the tongue. HPO:curators Lingual aplasia/hypoplasia ORCID:0000-0001-5889-4463 Tongue with a median apical indentation or fork. peter 2009-07-12T11:47:28Z SNOMEDCT_US:84557007 UMLS:C0266111 UMLS:C4255098 Bifurcated tongue Cleft tongue Forked tongue Split tongue human_phenotype Snake tongue HP:0010297 Bifid tongue can be associated with ankyloglossia, but this should be assessed and coded separately. Small indentations of the tip of the tongue should not be coded as a bifid tongue. Bifid tongue Tongue with a median apical indentation or fork. PMID:19125428 Bifurcated tongue ORCID:0000-0001-5889-4463 Cleft tongue ORCID:0000-0001-5889-4463 Forked tongue ORCID:0000-0001-5889-4463 Split tongue Snake tongue ORCID:0000-0001-5889-4463 Any abnormality of dentin. peter 2009-07-12T12:11:14Z UMLS:C4021299 Abnormal dentin Abnormality of dentin Abnormality of dentine human_phenotype HP:0010299 Dentin is a calcified tissue of teeth that is covered by enamel on the crown and cementum on the root and surrounds the entire pulp. Abnormality of dentin Any abnormality of dentin. HPO:probinson Abnormal dentin HPO:skoehler Abnormality of dentin Abnormality of dentine ORCID:0000-0001-5889-4463 Any abnormality of the spinal meninges, the system of membranes (dura mater, the arachnoid mater, and the pia mater) which envelops the spinal cord. peter 2009-07-12T01:10:09Z UMLS:C4023914 Abnormality of the spinal meninges human_phenotype HP:0010303 Abnormal spinal meningeal morphology Any abnormality of the spinal meninges, the system of membranes (dura mater, the arachnoid mater, and the pia mater) which envelops the spinal cord. HPO:probinson An outpouching of the spinal meninges. peter 2009-07-12T01:11:53Z UMLS:C4023913 human_phenotype HP:0010304 Spinal meningeal diverticulum An outpouching of the spinal meninges. HPO:curators Reduced inferior to superior extent of the thorax. peter 2009-07-12T02:13:42Z SNOMEDCT_US:249670005 UMLS:C0426789 Shorter than typical length between neck and abdomen human_phenotype HP:0010306 Short thorax Reduced inferior to superior extent of the thorax. HPO:curators Shorter than typical length between neck and abdomen https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-6548-5200 Absence or underdevelopment of the breasts. peter 2009-07-12T02:31:49Z UMLS:C4023911 Absent/small breasts Absent/underdeveloped breasts human_phenotype HP:0010311 Aplasia/Hypoplasia of the breasts Absence or underdevelopment of the breasts. HPO:curators Absent/small breasts ORCID:0000-0001-5208-3432 Absent/underdeveloped breasts ORCID:0000-0001-5208-3432 The presence of hypertrophy of the breast. peter 2009-07-12T02:34:30Z MSH:C536821 SNOMEDCT_US:372281005 SNOMEDCT_US:372283008 SNOMEDCT_US:372285001 UMLS:C0020565 UMLS:C0392533 UMLS:C2225524 Breast enlargement Breasts enlarged Gigantomastia Hypertrophy of the breasts Large breast Macromastia human_phenotype HP:0010313 Breast hypertrophy The presence of hypertrophy of the breast. HPO:probinson Breast enlargement HPO:skoehler Breasts enlarged HPO:skoehler Gigantomastia ORCID:0000-0001-5208-3432 Hypertrophy of the breasts HPO:skoehler Large breast HPO:skoehler Macromastia ORCID:0000-0001-5208-3432 Absence or underdevelopment of the diaphragm. peter 2009-07-12T02:41:58Z UMLS:C4023910 Absent/small diaprhagm Absent/underdeveloped diaprhagm human_phenotype HP:0010315 Aplasia/Hypoplasia of the diaphragm Absence or underdevelopment of the diaphragm. HPO:curators Absent/small diaprhagm ORCID:0000-0001-5208-3432 Absent/underdeveloped diaprhagm ORCID:0000-0001-5208-3432 Absence or underdevelopment of the abdominal musculature. peter 2009-07-14T11:51:46Z UMLS:C4023909 Absent/small abdominal wall muscles Absent/underdeveloped abdominal wall muscles human_phenotype HP:0010318 Aplasia/Hypoplasia of the abdominal wall musculature Absence or underdevelopment of the abdominal musculature. HPO:curators Absent/small abdominal wall muscles ORCID:0000-0001-5208-3432 Absent/underdeveloped abdominal wall muscles ORCID:0000-0001-5208-3432 An anomaly of the little toe. doelkens 2009-07-16T11:37:12Z UMLS:C4023905 Abnormality of the little toe Abnormality of the pinkie toe Abnormality of the pinky toe human_phenotype HP:0010322 Abnormality of the 5th toe An anomaly of the little toe. HPO:probinson Abnormality of the little toe ORCID:0000-0001-5208-3432 Abnormality of the pinkie toe ORCID:0000-0001-5208-3432 Abnormality of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2009-07-16T11:41:49Z UMLS:C4023893 Abnormality of the end part of the little toe bone Abnormality of the end part of the pinkie toe bone Abnormality of the end part of the pinky toe bone human_phenotype HP:0010341 Abnormality of the epiphyses of the 5th toe Abnormality of the end part of the little toe bone ORCID:0000-0001-5208-3432 Abnormality of the end part of the pinkie toe bone ORCID:0000-0001-5208-3432 Abnormality of the end part of the pinky toe bone ORCID:0000-0001-5208-3432 doelkens 2009-07-16T11:41:49Z UMLS:C4023892 Abnormality of the little toe bones Abnormality of the pinkie toe bones Abnormality of the pinky toe bones human_phenotype HP:0010342 Abnormality of the phalanges of the 5th toe Abnormality of the little toe bones ORCID:0000-0001-5208-3432 Abnormality of the pinkie toe bones ORCID:0000-0001-5208-3432 Abnormality of the pinky toe bones ORCID:0000-0001-5208-3432 doelkens 2009-07-16T11:41:49Z UMLS:C4023891 Absent/small little toe Absent/small pinkie toe Absent/small pinky toe Absent/underdeveloped pinky toe human_phenotype HP:0010343 Aplasia/Hypoplasia of the 5th toe Absent/small little toe ORCID:0000-0001-5208-3432 Absent/small pinkie toe ORCID:0000-0001-5208-3432 Absent/small pinky toe ORCID:0000-0001-5208-3432 Absent/underdeveloped pinky toe ORCID:0000-0001-5208-3432 doelkens 2009-07-16T11:41:49Z UMLS:C4021291 Displacement of the 5th toe Displacement of the little toe Displacement of the pinkie toe Displacement of the pinky toe human_phenotype HP:0010344 Deviation of the 5th toe Displacement of the little toe ORCID:0000-0001-5208-3432 Displacement of the pinkie toe ORCID:0000-0001-5208-3432 Displacement of the pinky toe ORCID:0000-0001-5208-3432 One or more bent (flexed) joints of the fifth toe that cannot be straightened actively or passively. doelkens 2009-07-16T11:41:49Z UMLS:C4021290 Joint contractures of the 5th toe human_phenotype HP:0010345 Flexion contracture of the 5th toe One or more bent (flexed) joints of the fifth toe that cannot be straightened actively or passively. HPO:probinson Joint contractures of the 5th toe doelkens 2009-07-16T11:52:18Z UMLS:C4023867 Absent/small little toe bones Absent/small pinkie toe bones Absent/small pinky toe bones Absent/underdeveloped pinky toe bones human_phenotype HP:0010383 Aplasia/Hypoplasia of the phalanges of the 5th toe Absent/small little toe bones ORCID:0000-0001-5208-3432 Absent/small pinkie toe bones ORCID:0000-0001-5208-3432 Absent/small pinky toe bones ORCID:0000-0001-5208-3432 Absent/underdeveloped pinky toe bones ORCID:0000-0001-5208-3432 doelkens 2009-07-16T11:52:18Z UMLS:C4023863 Triangular shaped little toe bone Triangular shaped pinkie toe bone Triangular shaped pinky toe bone human_phenotype HP:0010390 Triangular shaped phalanges of the 5th toe Triangular shaped little toe bone ORCID:0000-0001-5889-4463 Triangular shaped pinkie toe bone ORCID:0000-0001-5889-4463 Triangular shaped pinky toe bone ORCID:0000-0001-5889-4463 Partial or complete duplication of one or more phalanx of little toe. doelkens 2009-07-16T11:52:18Z UMLS:C4020903 Duplication of the bones of the little toe Duplication of the bones of the pinkie toe Duplication of the bones of the pinky toe Duplication of the phalanges of the fifth toe Partial/complete duplication of the phalanges of the 5th toe human_phenotype HP:0010391 Duplication of the phalanges of the 5th toe Partial or complete duplication of one or more phalanx of little toe. HPO:probinson Duplication of the bones of the little toe ORCID:0000-0001-5208-3432 Duplication of the bones of the pinkie toe ORCID:0000-0001-5208-3432 Duplication of the bones of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2009-07-16T11:52:18Z UMLS:C4023862 Abnormality of the outermost bone of the little toe Abnormality of the outermost bone of the pinkie toe Abnormality of the outermost bone of the pinky toe human_phenotype HP:0010392 Abnormality of the distal phalanx of the 5th toe Abnormality of the outermost bone of the little toe ORCID:0000-0001-5208-3432 Abnormality of the outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Abnormality of the outermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2009-07-16T11:52:18Z UMLS:C4023861 Abnormality of the middle bone of the little toe Abnormality of the middle bone of the pinkie toe Abnormality of the middle bone of the pinky toe human_phenotype HP:0010393 Abnormality of the middle phalanx of the 5th toe Abnormality of the middle bone of the little toe ORCID:0000-0001-5208-3432 Abnormality of the middle bone of the pinkie toe ORCID:0000-0001-5208-3432 Abnormality of the middle bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2009-07-16T11:52:18Z UMLS:C4023860 Abnormality of the innermost bone of the little toe Abnormality of the innermost bone of the pinkie toe Abnormality of the innermost bone of the pinky toe human_phenotype HP:0010394 Abnormality of the proximal phalanx of the 5th toe Abnormality of the innermost bone of the little toe ORCID:0000-0001-5208-3432 Abnormality of the innermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Abnormality of the innermost bone of the pinky toe ORCID:0000-0001-5208-3432 A structural abnormality of the interventricular septum. doelkens 2009-07-27T11:59:56Z HP:0001628 Fyler:1815 UMLS:C4021264 Abnormal interventricular septum morphology Abnormality of the ventricular septum Ventricular septum abnormality human_phenotype HP:0010438 Abnormal ventricular septum morphology A structural abnormality of the interventricular septum. HPO:probinson Abnormal interventricular septum morphology ORCID:0000-0001-5208-3432 A congenital anomaly characterized by the presence of supernumerary fingers or toes. doelkens 2009-07-29T01:39:27Z HP:0006034 HP:0006046 HP:0006123 HP:0009605 Fyler:4103 MSH:D017689 SNOMEDCT_US:367506006 UMLS:C0152427 More than five fingers or toes on hands or feet human_phenotype HP:0010442 Polydactyly A congenital anomaly characterized by the presence of supernumerary fingers or toes. HPO:probinson More than five fingers or toes on hands or feet ORCID:0000-0002-6548-5200 A bifid or bifurcated appearance of the femur as seen on x-rays, possible appearing as a more or less severe bowing of the upper leg. Might be associated with hip dysplasia on the affected side. doelkens 2009-07-29T04:29:30Z UMLS:C4023824 Notched thighbone Split thighbone human_phenotype HP:0010443 Bifid femur A bifid or bifurcated appearance of the femur as seen on x-rays, possible appearing as a more or less severe bowing of the upper leg. Might be associated with hip dysplasia on the affected side. HPO:probinson Notched thighbone ORCID:0000-0001-5208-3432 Split thighbone ORCID:0000-0001-5208-3432 Absence or underdevelopment of the spleen. peter 2009-09-14T10:48:29Z UMLS:C4023823 Absent/small spleen Absent/underdeveloped spleen human_phenotype HP:0010451 Aplasia/Hypoplasia of the spleen Absence or underdevelopment of the spleen. HPO:curators Absent/small spleen ORCID:0000-0001-5208-3432 Absent/underdeveloped spleen ORCID:0000-0001-5208-3432 Abnormality of the female genital system. peter 2009-09-15T08:32:09Z UMLS:C4023820 human_phenotype HP:0010460 Abnormality of the female internal or external genitalia. Abnormality of the female genitalia Abnormality of the female genital system. HPO:probinson Abnormality of the male genital system. peter 2009-09-15T08:33:20Z UMLS:C4023819 Abnormal male genitals Abnormality of the male genitalia human_phenotype HP:0010461 Abnormality of the male genitalia Abnormality of the male genital system. HPO:probinson Abnormal male genitals Abnormality of the male genitalia Aplasia or developmental hypoplasia of the ovary. peter 2009-09-15T08:38:35Z UMLS:C4023818 Absent/small ovary Absent/underdeveloped ovary human_phenotype HP:0010462 Aplasia/Hypoplasia of the ovary Aplasia or developmental hypoplasia of the ovary. HPO:probinson Absent/small ovary ORCID:0000-0001-5208-3432 Absent/underdeveloped ovary ORCID:0000-0001-5208-3432 Absence or underdevelopment of the testes. peter 2009-09-15T09:28:46Z UMLS:C4023817 Absent/small testes Absent/underdeveloped testes human_phenotype HP:0010468 Aplasia/Hypoplasia of the testes Absence or underdevelopment of the testes. HPO:curators Absent/small testes ORCID:0000-0001-5208-3432 Absent/underdeveloped testes ORCID:0000-0001-5208-3432 The presence of more than two testes. peter 2009-09-15T09:34:18Z SNOMEDCT_US:17471001 UMLS:C0266430 Extra testes Polyorchidism human_phenotype HP:0010470 Supernumerary testes The presence of more than two testes. HPO:probinson Extra testes ORCID:0000-0001-5208-3432 Absence or underdevelopment of the urinary bladder. peter 2009-09-15T10:09:48Z UMLS:C4023813 Absent/small bladder Absent/underdeveloped bladder human_phenotype HP:0010476 Aplasia/Hypoplasia of the bladder Absence or underdevelopment of the urinary bladder. HPO:probinson Absent/small bladder ORCID:0000-0001-5208-3432 Absent/underdeveloped bladder ORCID:0000-0001-5208-3432 Abnormal increase in size of the upper limbs (due to an increase of the size of cells). peter 2009-09-16T09:23:57Z SNOMEDCT_US:298745009 UMLS:C0575518 Increased size of upper limb human_phenotype HP:0010484 Hypertrophy of the upper limb Abnormal increase in size of the upper limbs (due to an increase of the size of cells). HPO:curators Increased size of upper limb ORCID:0000-0001-5208-3432 An abnormally increased length of the metacarpal bones. peter 2009-09-17T10:25:37Z UMLS:C4021260 Elongated long bone of hand Increased length of metacarpals human_phenotype HP:0010493 Long metacarpals An abnormally increased length of the metacarpal bones. HPO:probinson Elongated long bone of hand ORCID:0000-0001-5208-3432 Abnormal increase in size of the lower limbs (due to an increase of the size of cells). peter 2009-09-17T11:08:38Z UMLS:C4023803 human_phenotype HP:0010496 Hypertrophy of the lower limb Abnormal increase in size of the lower limbs (due to an increase of the size of cells). HPO:curators An ability of the toe joints to move beyond their normal range of motion. peter 2009-09-19T10:15:12Z UMLS:C4023798 human_phenotype HP:0010510 Hypermobility of toe joints An ability of the toe joints to move beyond their normal range of motion. HPO:curators Toes that appear disproportionately long compared to the foot. peter 2009-09-19T10:40:43Z UMLS:C3150613 Increased length of toes Long toe Long toes human_phenotype HP:0010511 This finding must be distinguished from digits that are thin but of normal length and that of a short mid and hind foot with normal digit lengths. The affected digits should be specified. If only a subset of the digits of a limb is lengthened, the affected digits should be specified. Long toe Toes that appear disproportionately long compared to the foot. HPO:probinson PMID:19125433 Increased length of toes Long toe Long toes Calcification within the adrenal glands. peter 2009-09-19T03:34:26Z SNOMEDCT_US:12286000 UMLS:C0271750 human_phenotype HP:0010512 This condition may occur in a wide variety of pathologies, some serious and some with no obvious consequence. Adrenal hemorrhage may be detected as an incidental finding in children in radiographic studies of the abdomen. Etiologies include hemorrhage into the adrenals at or immediately after birth, neuroblastoma, ganglioneuroblastoma, cortical carcinoma, pheochromocytoma, and cysts. Adrenal calcification Calcification within the adrenal glands. HPO:probinson Deposition of calcium salts in the pituitary gland. peter 2009-09-19T04:09:21Z UMLS:C4023797 human_phenotype HP:0010513 Pituitary calcification Deposition of calcium salts in the pituitary gland. HPO:probinson Hypersecretion of one or more pituitary hormones. This can occur in conditions in which deficiency in the target organ leads to decreased hormonal feedback, or as a primary condition most usually in connection with a pituitary adenoma. peter 2009-09-19T04:14:54Z MSH:D006964 SNOMEDCT_US:10649000 UMLS:C0020506 human_phenotype HP:0010514 Hyperpituitarism Hypersecretion of one or more pituitary hormones. This can occur in conditions in which deficiency in the target organ leads to decreased hormonal feedback, or as a primary condition most usually in connection with a pituitary adenoma. HPO:probinson Absence or underdevelopment of the thymus. peter 2009-09-19T04:21:24Z UMLS:C3278004 UMLS:C4023796 Absent/small thymus Absent/underdeveloped thymus human_phenotype Thymic hypoplasia or aplasia HP:0010515 Aplasia/Hypoplasia of the thymus Absence or underdevelopment of the thymus. HPO:probinson Absent/small thymus ORCID:0000-0001-5208-3432 Absent/underdeveloped thymus ORCID:0000-0001-5208-3432 Thymic hypoplasia or aplasia HPO:skoehler An abnormal elevation of phytanic acid. peter 2009-10-20T07:19:29Z UMLS:C4023786 Elevated levels of phytanic acid human_phenotype HP:0010571 Phytanic acid (3,7,11,15-tetramethyl hexadecanoic acid) is a fatty acid that is derived from chlorophyll and present in the diet. The metabolism of phytanic acid involves alpha-oxidation in the peroxisome, which converts phytanic acid to pristanic acid. Peroxisomes involved in the catabolism of very long chain fatty acids and phytanic acid. Peroxisomal malfunctioning can lead to over-accumulation of very long chain fatty acids and phytanic acid, among other things. Elevated levels of phytanic acid An abnormal elevation of phytanic acid. HPO:curators Elevated levels of phytanic acid Any abnormality of the proximal epiphysis of the femur. sandra1 2009-10-21T01:28:23Z HP:0010589 UMLS:C4021252 Abnormality of the end part of the innermost thighbone Abnormality of the proximal femoral epiphysis human_phenotype HP:0010574 Note that the proximal epiphysis of the femur is often referred to as the capital femoral epiphysis from the Latin word caput for head. Abnormality of the epiphysis of the femoral head Any abnormality of the proximal epiphysis of the femur. HPO:sdoelken Abnormality of the end part of the innermost thighbone ORCID:0000-0001-5208-3432 The presence of developmental dysplasia of the femoral head. sandra1 2009-10-21T01:30:40Z Abnormality of femoral head development UMLS:C4021251 UMLS:C4280377 Dysplastic femoral head human_phenotype HP:0010575 Dysplasia of the femoral head The presence of developmental dysplasia of the femoral head. HPO:probinson Abnormality of femoral head development ORCID:0000-0001-5208-3432 A cystic lesion originating within the brain. sandra1 2009-10-22T01:38:49Z UMLS:C4021250 Cerebral cystic malformation human_phenotype HP:0010576 Intracranial cystic lesion A cystic lesion originating within the brain. HPO:probinson sandra1 2009-10-22T02:53:19Z UMLS:C4021862 Absent end part of bone human_phenotype HP:0010577 Absent epiphyses Absent end part of bone ORCID:0000-0001-5208-3432 Increased size of epiphyses. sandra1 2009-10-22T02:53:19Z HP:0003018 HP:0003055 HP:0005082 UMLS:C1833328 Large end part of bone Large epiphyses Widened, distorted epiphyses human_phenotype HP:0010580 Enlarged epiphyses Increased size of epiphyses. HPO:probinson Large end part of bone ORCID:0000-0001-5208-3432 sandra1 2009-10-22T02:53:19Z UMLS:C1841685 human_phenotype HP:0010584 Pseudoepiphyses Reduction in the size or volume of epiphyses. sandra1 2009-10-22T02:53:19Z HP:0005730 UMLS:C1846803 Small end part of bone human_phenotype HP:0010585 Small epiphyses Reduction in the size or volume of epiphyses. HPO:probinson Small end part of bone ORCID:0000-0001-5208-3432 sandra1 2009-10-22T02:53:19Z UMLS:C4023784 Triangular end part of bone human_phenotype HP:0010587 Triangular epiphyses Triangular end part of bone ORCID:0000-0001-5208-3432 Any abnormality of the distal epiphysis of the femur. sandra1 2009-10-22T03:00:23Z UMLS:C4023783 Abnormality of the end part of the outermost thighbone human_phenotype HP:0010590 Abnormality of the distal femoral epiphysis Any abnormality of the distal epiphysis of the femur. HPO:probinson Abnormality of the end part of the outermost thighbone ORCID:0000-0001-5208-3432 Any abnormality of the proximal epiphysis of the humerus. sandra1 2009-10-22T06:40:29Z UMLS:C4023775 Abnormality of the end part of the innermost long bone in upper arm human_phenotype HP:0010598 Abnormality of the proximal humeral epiphysis Any abnormality of the proximal epiphysis of the humerus. HPO:curators Abnormality of the end part of the innermost long bone in upper arm ORCID:0000-0001-5208-3432 Any abnormality of the distal epiphysis of the humerus. sandra1 2009-10-22T06:40:29Z UMLS:C4023774 Abnormality of the end part of the outermost long bone in upper arm human_phenotype HP:0010599 Abnormality of the distal humeral epiphysis Any abnormality of the distal epiphysis of the humerus. HPO:curators Abnormality of the end part of the outermost long bone in upper arm ORCID:0000-0001-5208-3432 Absence or underdevelopment of the anterior pituitary gland, also known as the adenohypophysis. peter 2009-12-05T03:03:17Z MSH:D010903 SNOMEDCT_US:62818001 UMLS:C0032008 UMLS:C4023771 Adenohypophysis human_phenotype HP:0010625 Anterior pituitary dysgenesis Absence or underdevelopment of the anterior pituitary gland, also known as the adenohypophysis. DDD:spark HPO:probinson Adenohypophysis ORCID:0000-0001-5208-3432 Underdevelopment of the anterior pituitary gland. peter 2009-12-05T03:04:48Z HP:0008238 UMLS:C0948740 UMLS:C1859775 Underdeveloped pituitary gland human_phenotype Hypoplasia of the pituitary gland HP:0010627 Anterior pituitary hypoplasia Underdevelopment of the anterior pituitary gland. DDD:spark HPO:probinson Underdeveloped pituitary gland ORCID:0000-0001-5208-3432 Any abnormality of a metatarsal bone epiphysis. peter 2009-12-06T05:58:36Z UMLS:C4021248 Abnormality of end part of long bone of foot Abnormality of the epiphyses of the metatarsals human_phenotype HP:0010630 Abnormality of metatarsal epiphysis Any abnormality of a metatarsal bone epiphysis. HPO:curators Abnormality of end part of long bone of foot ORCID:0000-0001-5208-3432 Any abnormality of the epiphyses of the feet. peter 2009-12-06T06:00:04Z UMLS:C4023769 Abnormality of the end part of the foot bone human_phenotype HP:0010631 Abnormality of the epiphyses of the feet Any abnormality of the epiphyses of the feet. HPO:curators Abnormality of the end part of the foot bone ORCID:0000-0001-5208-3432 Abnormality of the nasal cavity (the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures). doelkens 2009-12-17T04:56:17Z UMLS:C4023763 human_phenotype HP:0010640 Abnormality of the nasal cavity Abnormality of the nasal cavity (the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures). HPO:curators An abnormality of the Meninges, including any abnormality of the Dura mater, the Arachnoid mater, and the Pia mater. peter 2010-02-25T10:19:40Z UMLS:C4023758 Abnormality of the meninges human_phenotype HP:0010651 Abnormal meningeal morphology An abnormality of the Meninges, including any abnormality of the Dura mater, the Arachnoid mater, and the Pia mater. HPO:probinson An abnormality of the Dura mater. peter 2010-02-25T10:29:40Z UMLS:C4023757 Abnormality of the dura mater human_phenotype HP:0010652 Abnormal dura mater morphology An abnormality of the Dura mater. HPO:probinson An abnormality of the formation and mineralization of an epiphysis. doelkens 2010-02-25T09:43:04Z UMLS:C4021246 Abnormality of the mineralisation or ossification of the epiphyses human_phenotype Abnormal maturation of the end part of a bone HP:0010656 Abnormal epiphyseal ossification An abnormality of the formation and mineralization of an epiphysis. HPO:probinson Abnormal maturation of the end part of a bone ORCID:0000-0001-5208-3432 An abnormality of the formation and mineralization of any bone of the skeleton of hand. doelkens 2010-02-25T05:18:19Z HP:0005921 UMLS:C4021244 Abnormal ossification of hand bones Abnormality of the mineralisation and ossification of bones of the hand human_phenotype Abnormal maturation of the hand bones HP:0010660 Abnormal hand bone ossification An abnormality of the formation and mineralization of any bone of the skeleton of hand. HPO:probinson Abnormal maturation of the hand bones ORCID:0000-0001-5208-3432 An abnormality of the Diencephalon, which together with the cerebrum (telencephalon) makes up the forebrain. peter 2010-02-26T08:02:38Z UMLS:C4023752 human_phenotype HP:0010662 The diencephalon comprises the thalamus, hypothalamus, epithalamus, prethalamus or subthalamus and pretectum. Abnormality of the diencephalon An abnormality of the Diencephalon, which together with the cerebrum (telencephalon) makes up the forebrain. HPO:probinson An abnormality of the formation and mineralization of any bone of the skeleton of foot. sandra1 2010-02-28T05:27:47Z HP:0008370 HP:0009133 UMLS:C4020768 UMLS:C4021241 UMLS:C4280367 Abnormality of the mineralisation and ossification of bones of the feet human_phenotype Abnormal maturation of foot bones Abnormal ossification involving bones of the feet HP:0010675 Abnormal foot bone ossification An abnormality of the formation and mineralization of any bone of the skeleton of foot. HPO:probinson Abnormal maturation of foot bones ORCID:0000-0001-5208-3432 An abnormality of the distribution of hair growth. sdoelken 2010-04-20T09:53:15Z UMLS:C4023721 Abnormal distribution of hair Abnormal hair pattern human_phenotype HP:0010720 Abnormal hair pattern An abnormality of the distribution of hair growth. HPO:probinson Abnormal distribution of hair ORCID:0000-0001-5889-4463 Abnormal hair pattern A developmental defect characterized by absence of the retina. sdoelken 2010-04-20T11:09:59Z UMLS:C4023718 Absent retina human_phenotype HP:0010728 Aplasia of the retina A developmental defect characterized by absence of the retina. HPO:probinson Absent retina ORCID:0000-0001-5208-3432 Diminished length of a metatarsal bone, with resultant proximal displacement of the associated toe. doelkens 2010-04-22T04:30:18Z HP:0001779 HP:0001865 HP:0003092 HP:0004706 HP:0005754 UMLS:C1849020 Hypoplasia of the metatarsal bones Hypoplastic metatarsals Short long bone of foot Short metatarsal bone Short metatarsals Shortened metatarsals human_phenotype Short metatarsal bones HP:0010743 This is a subjective assessment and one generally compares the position of the MTP joint to that of the contralateral digit or the putatively shortened ray in proportion to the other rays. The affected digits should be specified. Short metatarsal Diminished length of a metatarsal bone, with resultant proximal displacement of the associated toe. HPO:probinson PMID:19125433 Short long bone of foot ORCID:0000-0001-5208-3432 Short metatarsal bones HPO:skoehler doelkens 2010-04-22T04:33:06Z UMLS:C4023715 Small toe bones human_phenotype HP:0010746 Hypoplasia of the phalanges of the toes Small toe bones ORCID:0000-0001-5208-3432 Positioning of a lacrimal punctum other than at the medial margins of the eyelid. sdoelken 2010-04-23T09:35:56Z UMLS:C4021230 Abnormal position of the lacrimal punctum human_phenotype HP:0010748 The openings of the tear ducts are normally located at the medial margin of each eyelid. The opening on the lower eyelid border is more visible than the opening on the upper eyelid border. Ectopic positions can include the upper eyelid, nasal bridge, or inferior to medial aspect of the lower lid. Ectopic lacrimal punctum Positioning of a lacrimal punctum other than at the medial margins of the eyelid. PMID:19125427 Aplasia of a toe. That is, absence of all phalanges of a non-hallux digit of the foot and the associated soft tissues. doelkens 2010-04-23T03:58:25Z HP:0008084 HP:0010108 HP:0011306 UMLS:C3553754 Absent toe Aplasia of toe human_phenotype Absent toes Aplasia of the toes HP:0010760 This descriptor does NOT require absence of the metatarsal. The definition excludes partial absent hallux. Absent toe Aplasia of a toe. That is, absence of all phalanges of a non-hallux digit of the foot and the associated soft tissues. HPO:probinson Absent toe Absent toes HPO:skoehler Deposition of calcium salts in a tissue or location in which calcification does not normally occur. doelkens 2010-04-27T09:52:59Z UMLS:C3806226 human_phenotype HP:0010766 Ectopic calcification Deposition of calcium salts in a tissue or location in which calcification does not normally occur. HPO:probinson The presence of an abnormally large pelvis. sdoelken 2010-04-29T11:03:39Z Large pelvis UMLS:C4019074 UMLS:C4072882 Large pelvis bone human_phenotype HP:0010779 Large pelvis bone The presence of an abnormally large pelvis. HPO:probinson Large pelvis HPO:skoehler Large pelvis bone A tumor (abnormal growth of tissue) of the uterus. sdoelken 2010-05-04T09:35:15Z Uterine cancer MSH:D014594 NCIT:C3262 SNOMEDCT_US:126908007 UMLS:C0042138 Uterine tumor human_phenotype Uterine neoplasia HP:0010784 Uterine neoplasm A tumor (abnormal growth of tissue) of the uterus. HPO:probinson Uterine cancer Uterine tumor ORCID:0000-0001-5208-3432 A tumor (abnormal growth of tissue) of the genital system. sdoelken 2010-05-04T09:47:50Z NCIT:C3262 UMLS:C0679347 UMLS:C4020767 Genital tumor human_phenotype Genital neoplasia HP:0010787 Genital neoplasm A tumor (abnormal growth of tissue) of the genital system. HPO:probinson Genital tumor ORCID:0000-0001-5208-3432 Any structural abormality of the fifth cranial nerve. peter 2010-07-10T03:51:21Z UMLS:C4021226 Abnormal trigeminal nerve morphology Abnormality of the fifth cranial nerve Abnormality of the nervus trigeminus human_phenotype HP:0010824 Abnormal fifth cranial nerve morphology Any structural abormality of the fifth cranial nerve. HPO:probinson Abnormality of the eleventh cranial nerve. peter 2010-07-10T03:54:53Z UMLS:C4021225 Abnormality of cranial nerve XI Abnormality of the accessory nerve human_phenotype HP:0010825 Abnormality of the eleventh cranial nerve Abnormality of the eleventh cranial nerve. HPO:probinson Abnormality of cranial nerve XI ORCID:0000-0001-5208-3432 Abnormality of the twelfth cranial nerve. peter 2010-07-10T03:58:00Z UMLS:C4021224 Abnormality of cranial nerve 12 Abnormality of cranial nerve xii Abnormality of the hypoglossal nerve human_phenotype HP:0010826 Abnormality of the twelfth cranial nerve Abnormality of the twelfth cranial nerve. HPO:probinson Abnormality of cranial nerve 12 ORCID:0000-0001-5889-4463 Abnormality of cranial nerve xii ORCID:0000-0001-5889-4463 Abnormality of the seventh cranial nerve sometimes also referred to as the facial nerve. peter 2010-07-10T04:04:55Z UMLS:C4021223 Abnormality of the facial nerve human_phenotype HP:0010827 Abnormality of the seventh cranial nerve Abnormality of the seventh cranial nerve sometimes also referred to as the facial nerve. HPO:probinson An incomplete closure of the abdominal wall. peter 2010-08-03T09:55:15Z UMLS:C0238577 Abdominal wall defect Congenital anterior abdominal wall defect human_phenotype HP:0010866 Abdominal wall defect An incomplete closure of the abdominal wall. HPO:probinson Abdominal wall defect An abnormality of the umbilical cord, which is the cord connecting the developing embryo or fetus to the placenta. peter 2010-09-13T08:24:04Z SNOMEDCT_US:90009001 UMLS:C0266785 Umbilical cord issue human_phenotype HP:0010881 Abnormality of the umbilical cord An abnormality of the umbilical cord, which is the cord connecting the developing embryo or fetus to the placenta. HPO:probinson Umbilical cord issue Any deviation from the normal concentration of a branched chain family amino acid in the blood circulation. peter 2010-11-11T02:53:04Z UMLS:C4023673 human_phenotype HP:0010892 Abnormal circulating branched chain amino acid concentration Any deviation from the normal concentration of a branched chain family amino acid in the blood circulation. HPO:probinson Any deviation from the normal concentration of phenylalanine in the blood circulation. peter 2010-11-11T03:23:30Z UMLS:C4023672 Abnormality of phenylalanine metabolism human_phenotype HP:0010893 Abnormal circulating phenylalanine concentration Any deviation from the normal concentration of phenylalanine in the blood circulation. HPO:probinson Any deviation from the normal concentration of a serine family amino acid in the blood circulation. peter 2010-11-30T05:21:41Z UMLS:C4023671 Abnormality of serine family amino acid metabolism human_phenotype HP:0010894 Abnormal circulating serine family amino acid concentration Any deviation from the normal concentration of a serine family amino acid in the blood circulation. HPO:probinson Any deviation from the normal concentration of glycine in the blood circulation. peter 2010-11-30T05:27:24Z UMLS:C4023670 human_phenotype HP:0010895 Abnormal circulating glycine concentration Any deviation from the normal concentration of glycine in the blood circulation. HPO:gcarletti Any deviation from the normal concentration of an aspartate family amino acid in the blood circulation. peter 2010-12-02T04:40:57Z UMLS:C4023667 human_phenotype HP:0010899 Abnormal circulating aspartate family amino acid concentration Any deviation from the normal concentration of an aspartate family amino acid in the blood circulation. HPO:probinson Any deviation from the normal concentration of methionine in the blood circulation. peter 2010-12-02T05:15:22Z UMLS:C4023665 Abnormality of methionine metabolism human_phenotype HP:0010901 Abnormal circulating methionine concentration Any deviation from the normal concentration of methionine in the blood circulation. HPO:probinson Any deviation from the normal concentration of a glutamine family amino acid in the blood circulation. peter 2010-12-03T04:30:22Z UMLS:C4023664 human_phenotype HP:0010902 Abnormal circulating glutamine family amino acid concentration Any deviation from the normal concentration of a glutamine family amino acid in the blood circulation. HPO:probinson Any deviation from the normal concentration of lysine in the blood circulation. peter 2010-12-08T08:05:55Z UMLS:C4023660 Abnormality of lysine metabolism human_phenotype HP:0010908 Abnormal circulating lysine concentration Any deviation from the normal concentration of lysine in the blood circulation. HPO:gcarletti Any deviation from the normal concentration of arginine in the blood circulation. peter 2010-12-08T08:25:05Z UMLS:C4023659 Abnormality of arginine metabolism human_phenotype HP:0010909 Arginine is a charged, aliphatic amino acid. Abnormal circulating arginine concentration Any deviation from the normal concentration of arginine in the blood circulation. HPO:probinson An increased concentration of valine in the blood. peter 2010-12-08T08:44:27Z MSH:C536524 SNOMEDCT_US:47719001 UMLS:C0268573 High blood valine concentration human_phenotype HP:0010910 Hypervalinemia An increased concentration of valine in the blood. HPO:gcarletti High blood valine concentration ORCID:0000-0001-5208-3432 An increased concentration of leucine in the blood. peter 2010-12-08T08:45:56Z SNOMEDCT_US:24013007 UMLS:C0268576 High blood leucine concentration human_phenotype HP:0010911 Normal leucine blood levels are around 120-160 micromole per liter. Hyperleucinemia An increased concentration of leucine in the blood. HPO:gcarletti High blood leucine concentration ORCID:0000-0001-5208-3432 Any deviation from the normal concentration of isoleucine in the blood circulation. peter 2010-12-08T08:47:47Z UMLS:C4023658 human_phenotype HP:0010912 Abnormal circulating isoleucine concentration Any deviation from the normal concentration of isoleucine in the blood circulation. HPO:probinson An increased concentration of isoleucine in the blood. peter 2010-12-08T08:49:42Z UMLS:C4023657 High blood isoleucine concentration human_phenotype HP:0010913 Normal isoleucine blood levels are around 60-80 micromole per liter. Hyperisoleucinemia An increased concentration of isoleucine in the blood. HPO:gcarletti High blood isoleucine concentration ORCID:0000-0001-5208-3432 Any deviation from the normal circulation of valine in the blood circulation. peter 2010-12-08T08:51:14Z UMLS:C4023656 Abnormality of valine metabolism human_phenotype HP:0010914 Abnormal circulating valine concentration Any deviation from the normal circulation of valine in the blood circulation. HPO:probinson Any deviation from the normal concentration of tyrosine in the blood circulation. peter 2010-12-08T09:13:53Z UMLS:C4023653 human_phenotype HP:0010917 Abnormal circulating tyrosine concentration Any deviation from the normal concentration of tyrosine in the blood circulation. HPO:probinson An abnormality of divalent inorganic cation homeostasis. peter 2011-01-06T07:47:18Z UMLS:C4023648 Abnormality of divalent inorganic cation homeostasis human_phenotype HP:0010927 Abnormal blood inorganic cation concentration An abnormality of divalent inorganic cation homeostasis. HPO:probinson An abnormality of cation homeostasis. peter 2011-01-06T10:36:04Z UMLS:C4023646 Abnormality of cation homeostasis human_phenotype HP:0010929 Abnormal blood cation concentration An abnormality of cation homeostasis. HPO:probinson An abnormality of monovalent inorganic cation homeostasis. peter 2011-01-06T10:38:38Z UMLS:C4023645 Abnormality of monovalent inorganic cation homeostasis human_phenotype HP:0010930 Abnormal blood monovalent inorganic cation concentration An abnormality of monovalent inorganic cation homeostasis. HPO:probinson An abnormal concentration of sodium. peter 2011-01-06T10:40:20Z UMLS:C4023644 Abnormal blood Na+ levels Abnormal circulating Na concentration Abnormality of sodium homeostasis human_phenotype HP:0010931 Abnormal blood sodium concentration An abnormal concentration of sodium. HPO:probinson Abnormal blood Na+ levels Abnormal circulating Na concentration An abnormality of a nucleobase metabolic process. peter 2011-01-06T10:46:17Z UMLS:C4020762 UMLS:C4023643 human_phenotype Abnormal nucleoside levels HP:0010932 This term is used to refers to abnormality in chemical reactions and pathways involving a nucleobase, a nitrogenous base that is a constituent of a nucleic acid, e.g. the purines: adenine, guanine, hypoxanthine, xanthine and the pyrimidines: cytosine, uracil, thymine. Abnormal circulating nucleobase concentration An abnormality of a nucleobase metabolic process. HPO:probinson An abnormality of the upper urinary tract. peter 2011-01-16T11:37:29Z UMLS:C4023641 Abnormality of the upper urinary tract human_phenotype HP:0010935 The upper urinary tract is a subdivision of urinary system which consists of the kidney and the ureters. Abnormality of the upper urinary tract An abnormality of the upper urinary tract. HPO:probinson Abnormality of the upper urinary tract An abnormality of the lower urinary tract. peter 2011-01-16T11:39:17Z UMLS:C4023640 human_phenotype HP:0010936 The lower urinary tract is a subdivision of urinary system which consists of the urinary bladder and the urethra. Abnormality of the lower urinary tract An abnormality of the lower urinary tract. HPO:probinson An abnormality of the nasal skeleton. peter 2011-01-16T02:19:38Z UMLS:C4023639 UMLS:C4280361 Abnormality of the nasal skeleton Anomaly of the nasal skeleton Deformity of the bones of the nose Deformity of the nasal skeleton Distortion of the bones of the nose Distortion of the nasal skeleton Malformation of the bones of the nose Malformation of the nasal skeleton human_phenotype HP:0010937 Abnormality of the nasal skeleton An abnormality of the nasal skeleton. HPO:probinson Abnormality of the nasal skeleton Anomaly of the nasal skeleton ORCID:0000-0001-5889-4463 Deformity of the bones of the nose ORCID:0000-0001-5889-4463 Deformity of the nasal skeleton ORCID:0000-0001-5889-4463 Distortion of the bones of the nose ORCID:0000-0001-5889-4463 Distortion of the nasal skeleton ORCID:0000-0001-5889-4463 Malformation of the bones of the nose ORCID:0000-0001-5889-4463 Malformation of the nasal skeleton ORCID:0000-0001-5889-4463 An abnormality of the external nose. peter 2011-01-16T02:21:10Z UMLS:C2164724 UMLS:C4023638 UMLS:C4280360 Abnormality of the external nose Anomaly of the external nose Deformity of the external nose Malformation of the external nose human_phenotype HP:0010938 Abnormality of the external nose An abnormality of the external nose. HPO:probinson Abnormality of the external nose Anomaly of the external nose ORCID:0000-0001-5889-4463 Deformity of the external nose ORCID:0000-0001-5889-4463 Malformation of the external nose ORCID:0000-0001-5889-4463 An abnormality of the renal pelvis. peter 2011-01-16T03:33:55Z UMLS:C4023633 Abnormality of the renal pelvis human_phenotype HP:0010944 Abnormal renal pelvis morphology An abnormality of the renal pelvis. HPO:probinson Mild pyelectasis is defined as a hypoechoic spherical or elliptical space within the renal pelvis that measures at least 5mm and not more than 10 mm. The measurement is taken on a transverse section through the fetal renal pelvis using the maximum anterior-to-posterior measurement. peter 2011-01-16T03:36:31Z MSH:D058536 SNOMEDCT_US:430035004 UMLS:C2317073 Fetal renal pelvic dilatation Foetal pyelectasis Mild fetal hydronephrosis human_phenotype HP:0010945 The renal pelvis is the part of the kidney that collects urine. Fetal pyelectasis is a prenatal ultrasound finding that is diagnosed with enlargement of the renal pelvis from 4 to 10 millimeters. In many cases, fetal pyelectasis resolves spontaneously. Note that dilatation of the renal pelvis to more than 10 mm is referred to as severe pyelectasis or hydronephrosis. Measurements less than 5mm are normal, should not be designated as pyelectasis, and should not be reported (PMID:16100637). Fetal pyelectasis Mild pyelectasis is defined as a hypoechoic spherical or elliptical space within the renal pelvis that measures at least 5mm and not more than 10 mm. The measurement is taken on a transverse section through the fetal renal pelvis using the maximum anterior-to-posterior measurement. HPO:probinson PMID:16100637 Foetal pyelectasis An abnormality of the fourth ventricle. peter 2011-01-17T12:58:00Z UMLS:C4023630 human_phenotype HP:0010950 The fourth ventricle is the cerebral ventricle that extends from the cerebral aqueduct to the obex, and is located within the pons and the upper part of the medulla oblongata. Abnormality of the fourth ventricle An abnormality of the fourth ventricle. HPO:probinson Underdevelopment of the right-sided structures of the heart. peter 2011-01-17T03:31:37Z SNOMEDCT_US:268180007 SNOMEDCT_US:39589002 UMLS:C0265856 UMLS:C0344963 Hypoplastic right heart syndrome Underdeveloped right heart human_phenotype HP:0010954 Hypoplastic right heart syndrome (HRHS) causes inadequate blood flow to the lungs postnatally and thus leads to cyanosis. HRHS involves pulmonary valve atresia, hypoplasia of the right ventricle, hypoplasia of the tricuspid valve, and a small, hypoplastic pulmonary artery. As the ductus arteriosus closes postnatally, infants with HRHS become critically ill. Hypoplastic right heart Underdevelopment of the right-sided structures of the heart. HPO:probinson Hypoplastic right heart syndrome ORCID:0000-0001-6908-9849 Underdeveloped right heart ORCID:0000-0001-6908-9849 Any deviation from the normal concentration of a long-chain fatty acid in the blood circulation. peter 2011-01-27T08:05:00Z UMLS:C4023624 HP:0010964 A long-chain fatty-acid is defined as an aliphatic monocarboxylic acid with a chain length of C13 to C18. Abnormal circulating long-chain fatty-acid concentration Any deviation from the normal concentration of a long-chain fatty acid in the blood circulation. HPO:probinson Any deviation from the normal concentration of phytanic acid in the blood circulation. peter 2011-01-27T08:07:48Z UMLS:C4023623 HP:0010965 Phytanic acid is a branched-chain saturated fatty acid consisting of hexadecanoic acid carrying methyl substituents at positions 3, 7, 11 and 15. Abnormal circulating phytanic acid level Any deviation from the normal concentration of phytanic acid in the blood circulation. HPO:probinson Any deviation from the normal concentration of a fatty acid anion in the blood circulation. peter 2011-01-27T09:17:48Z UMLS:C4021209 Abnormality of fatty acid anion human_phenotype HP:0010966 A fatty acid anion is the conjugate base of a fatty acid. Abnormal circulating fatty-acid anion concentration Any deviation from the normal concentration of a fatty acid anion in the blood circulation. HPO:probinson Any deviation from the normal concentration of carnitine in the blood circulation. peter 2011-01-27T09:19:42Z UMLS:C4020761 UMLS:C4021855 human_phenotype Carnitine levels abnormal HP:0010967 L-carnitine (3-hydroxy-4-N.trimethylammonium butyrate) plays a key role in facilitating the transport of long-chain fatty acids from the cytosol into the mitochondrial matrix, where they undergo 13-oxidation. Abnormal circulating carnitine concentration Any deviation from the normal concentration of carnitine in the blood circulation. HPO:gcarletti A functional abnormality of the immune system. peter 2011-02-07T04:28:55Z UMLS:C4023616 human_phenotype HP:0010978 Abnormality of immune system physiology A functional abnormality of the immune system. HPO:probinson MP:0001790 An abnormality of the abdominal musculature. peter 2011-02-09T08:05:11Z UMLS:C4023608 Abnormality of the abdominal musculature human_phenotype HP:0010991 Abnormal morphology of the abdominal musculature An abnormality of the abdominal musculature. HPO:probinson Any deviation from the normal concentration of a dicarboxylic acid in the blood circulation. peter 2011-02-10T02:01:02Z UMLS:C4023606 HP:0010995 A dicarboxylic acid is an oxoacid containing two carboxy groups. Abnormal circulating dicarboxylic acid concentration Any deviation from the normal concentration of a dicarboxylic acid in the blood circulation. HPO:probinson Any deviation from the normal concentration of a monocarboxylic acid in the blood circulation. peter 2011-02-10T02:20:42Z UMLS:C4023605 HP:0010996 Abnormal circulating monocarboxylic acid cocentration Any deviation from the normal concentration of a monocarboxylic acid in the blood circulation. HPO:gcarletti An abnormal increase of bone mineral density, that is, of the amount of matter per cubic centimeter of bones which is often referred to as osteosclerosis. Osteosclerosis can be detected on radiological examination as an increased whiteness (density) of affected bones. sdoelken 2011-02-13T11:57:32Z HP:0002796 HP:0004350 HP:0005711 HP:0005741 HP:0010738 MSH:D010026 SNOMEDCT_US:49347007 UMLS:C0029464 Increased bone density Increased bone mineral density Osteosclerosis Osteosclerosis of bones human_phenotype HP:0011001 This term may be merged with Increased bone density in the future or made obsolete. Increased bone mineral density An abnormal increase of bone mineral density, that is, of the amount of matter per cubic centimeter of bones which is often referred to as osteosclerosis. Osteosclerosis can be detected on radiological examination as an increased whiteness (density) of affected bones. HPO:probinson Increased bone density Increased bone mineral density Abnormally increased formation of dense trabecular bone tissue. Despite the increased density of bone tissue, osteopetrotic bones tend to be more fracture-prone than normal. sdoelken 2011-02-13T11:58:36Z MSH:D010022 SNOMEDCT_US:1926006 SNOMEDCT_US:367489004 UMLS:C0029454 Harder, denser, fracture-prone bones human_phenotype Albers-Schoenberg disease Albers-Schonberg disease Albers-Schönberg disease Marble bone disease HP:0011002 Osteopetrosis Abnormally increased formation of dense trabecular bone tissue. Despite the increased density of bone tissue, osteopetrotic bones tend to be more fracture-prone than normal. HPO:probinson Harder, denser, fracture-prone bones ORCID:0000-0002-6548-5200 An abnormality of the systemic arterial tree, which consists of the aorta and other systemic arteries. peter 2011-02-16T08:46:49Z HP:0002620 HP:0005114 Fyler:2600 SNOMEDCT_US:234119001 UMLS:C0151489 UMLS:C4021205 Abnormal systemic artery morphology Abnormality of the systemic arterial tree Systemic artery abnormality human_phenotype Arterial abnormalities HP:0011004 Abnormal systemic arterial morphology An abnormality of the systemic arterial tree, which consists of the aorta and other systemic arteries. HPO:probinson An abnormality of the neck musculature. peter 2011-02-19T11:15:01Z UMLS:C4023601 Abnormality of cervical musculature Abnormality of the musculature of the neck Neck muscle issue human_phenotype HP:0011006 Abnormal morphology of the musculature of the neck An abnormality of the neck musculature. HPO:probinson Abnormality of cervical musculature ORCID:0000-0001-5889-4463 Abnormality of the musculature of the neck Neck muscle issue A deviation from the normal concentration of a carbohydrate in the blood circulation. peter 2011-02-21T09:47:27Z UMLS:C4023599 human_phenotype HP:0011013 An abnormality of the metabolism (include abnormality of the concentration) of a carbohydrate, including monosaccharides, oligosaccharides and polysaccharides, and substances derived from them. Abnormal circulating carbohydrate concentration A deviation from the normal concentration of a carbohydrate in the blood circulation. HPO:probinson Abnormality of glucose homeostasis. peter 2011-02-21T10:37:21Z UMLS:C4023598 human_phenotype HP:0011014 An abnormality of any process involved in the maintenance of an internal steady state of glucose within an organism or cell. Abnormal glucose homeostasis Abnormality of glucose homeostasis. HPO:probinson An abnormality of the concentration of glucose in the blood. peter 2011-02-21T10:41:13Z UMLS:C4023597 Abnormality of blood glucose concentration human_phenotype HP:0011015 Abnormal blood glucose concentration An abnormality of the concentration of glucose in the blood. HPO:probinson An abnormality of the concentration of glucose in the urine. peter 2011-02-21T11:09:32Z UMLS:C4023596 human_phenotype HP:0011016 Abnormality of urine glucose concentration An abnormality of the concentration of glucose in the urine. HPO:gcarletti An abnormality in a cellular process. peter 2011-02-22T07:05:50Z HP:0025462 UMLS:C4023595 Abnormality of cell physiology human_phenotype HP:0011017 Abnormal cellular physiology An abnormality in a cellular process. HPO:probinson An abnormality of the gastrointestinal tract. peter 2011-03-01T07:52:06Z MSH:D004066 MSH:D005767 SNOMEDCT_US:119292006 SNOMEDCT_US:25374005 SNOMEDCT_US:53619000 UMLS:C0012242 UMLS:C0017178 UMLS:C4023588 Abnormality of the GI tract Abnormality of the gastrointestinal tract human_phenotype Digestive system disease Gastrointestinal disease HP:0011024 Abnormality of the gastrointestinal tract An abnormality of the gastrointestinal tract. HPO:probinson Abnormality of the GI tract Abnormality of the gastrointestinal tract Digestive system disease Gastrointestinal disease Abnormal functionality of the cardiovascular system. peter 2011-03-03T10:23:19Z UMLS:C4023587 Abnormality of cardiovascular system physiology human_phenotype HP:0011025 Abnormal cardiovascular system physiology Abnormal functionality of the cardiovascular system. HPO:probinson Aplasia or developmental hypoplasia of the vagina. peter 2011-03-02T06:17:46Z UMLS:C4023586 Absent/small vagina Absent/underdeveloped vagina human_phenotype HP:0011026 Aplasia/Hypoplasia of the vagina Aplasia or developmental hypoplasia of the vagina. HPO:probinson Absent/small vagina ORCID:0000-0001-5208-3432 Absent/underdeveloped vagina ORCID:0000-0001-5208-3432 An abnormality of the fallopian tube. peter 2011-03-02T06:36:01Z UMLS:C0281842 Abnormality of the fallopian tube human_phenotype HP:0011027 The Fallopian tubes (also known as oviducts, uterine tubes, and salpinges) are ducts that lead from the ovaries into the uterus. Abnormal fallopian tube morphology An abnormality of the fallopian tube. HPO:probinson An abnormality of blood circulation. peter 2011-03-03T10:25:21Z UMLS:C4020760 UMLS:C4023585 human_phenotype Blood circulation disorder HP:0011028 Abnormality of blood circulation An abnormality of blood circulation. HPO:probinson The presence of hemorrhage within the body. peter 2011-03-03T10:26:26Z UMLS:C1390214 Internal bleeding Internal haemorrhage human_phenotype HP:0011029 Internal hemorrhage The presence of hemorrhage within the body. HPO:probinson Internal bleeding ORCID:0000-0001-5208-3432 Internal haemorrhage An abnormality of the homeostasis (concentration) of transition element cation. peter 2011-03-04T07:59:31Z UMLS:C4023584 Abnormality of transition element cation homeostasis human_phenotype HP:0011030 Abnormal blood transition element cation concentration An abnormality of the homeostasis (concentration) of transition element cation. HPO:probinson An abnormality of the homeostasis (concentration) of iron cation. peter 2011-03-04T08:01:07Z UMLS:C4023583 human_phenotype HP:0011031 Abnormality of iron homeostasis An abnormality of the homeostasis (concentration) of iron cation. HPO:probinson An abnormality of the regulation of body fluids. peter 2011-03-05T09:09:27Z SNOMEDCT_US:1860003 SNOMEDCT_US:190902006 UMLS:C2364164 Abnormality of fluid regulation Fluid imbalance human_phenotype HP:0011032 Abnormality of fluid regulation An abnormality of the regulation of body fluids. HPO:probinson Abnormality of fluid regulation Fluid imbalance ORCID:0000-0001-6908-9849 An abnormality of the cortex of the kidney. peter 2011-03-06T11:31:39Z UMLS:C4023580 Abnormality of renal cortex morphology human_phenotype HP:0011035 Abnormal renal cortex morphology An abnormality of the cortex of the kidney. HPO:probinson An abnormality of the intrahepatic bile duct. peter 2011-03-07T07:54:11Z UMLS:C4023577 human_phenotype HP:0011040 Abnormality of the intrahepatic bile duct An abnormality of the intrahepatic bile duct. HPO:probinson Aplasia or developmental hypoplasia of the cervical vertebral column. peter 2011-03-09T08:29:34Z UMLS:C4023576 Absent/small cervical spine Absent/underdeveloped cervical spine human_phenotype HP:0011041 Aplasia/Hypoplasia of the cervical spine Aplasia or developmental hypoplasia of the cervical vertebral column. HPO:probinson Absent/small cervical spine ORCID:0000-0001-5208-3432 Absent/underdeveloped cervical spine ORCID:0000-0001-5208-3432 An abnormal concentration of potassium. peter 2011-03-09T11:00:32Z UMLS:C4023575 Abnormal blood K concentration Abnormality of potassium homeostasis human_phenotype HP:0011042 Abnormal blood potassium concentration An abnormal concentration of potassium. HPO:probinson Abnormal blood K concentration An abnormality of the structure or composition of the teeth. peter 2011-03-10T01:44:04Z UMLS:C4023557 Abnormality of tooth part Abnormality of tooth structure human_phenotype HP:0011061 Abnormality of dental structure An abnormality of the structure or composition of the teeth. HPO:ibailleulforestier Abnormality of tooth part ORCID:0000-0001-5889-4463 Abnormality of tooth structure ORCID:0000-0001-5889-4463 The presence of a supernumerary, i.e., extra, tooth or teeth. peter 2011-03-10T02:52:19Z HP:0000672 MSH:D014096 SNOMEDCT_US:266414008 SNOMEDCT_US:367534004 SNOMEDCT_US:8666004 UMLS:C0040457 Extra teeth Hyperdontia Increased number of teeth Increased tooth count Supernumerary teeth Supernumerary tooth Supplemental dentition Supplemental teeth Supernumary dentition Supernumary teeth human_phenotype More teeth than normal HP:0011069 The most frequent supernumerary tooth is a mesiodens, which occurs between the two maxillary central incisors. Often it fails to erupt, but creates a large anterior diastema, and would not be detected on physical examination (requires X-ray evaluation). This designation excludes coexistence of primary and permanent dentition due to delayed loss of the former. Note that this term does not refer to the situation in which two rows of teeth are seen at the time of eruption of permanent dentition before exfoliation of primary teeth, which can be a normal finding. Increased number of teeth The presence of a supernumerary, i.e., extra, tooth or teeth. HPO:ibailleulforestier Extra teeth ORCID:0000-0001-5889-4463 Hyperdontia ORCID:0000-0001-5889-4463 Increased number of teeth Increased tooth count ORCID:0000-0001-5889-4463 Supplemental dentition ORCID:0000-0001-5889-4463 Supplemental teeth ORCID:0000-0001-5889-4463 Supernumary dentition ORCID:0000-0001-5889-4463 Supernumary teeth ORCID:0000-0001-5889-4463 More teeth than normal ORCID:0000-0001-5889-4463 peter 2011-03-10T03:56:41Z MSH:C538215 SNOMEDCT_US:109493006 UMLS:C0399379 UMLS:C4082200 Absence of tooth root Agenesis of tooth root Aplasia of tooth root Missing tooth root Rootless teeth Teeth without roots human_phenotype Tooth with dentin dysplasia type i HP:0011072 Rootless teeth Absence of tooth root ORCID:0000-0001-5889-4463 Agenesis of tooth root ORCID:0000-0001-5889-4463 Aplasia of tooth root ORCID:0000-0001-5889-4463 Missing tooth root ORCID:0000-0001-5889-4463 Rootless teeth Teeth without roots ORCID:0000-0001-5889-4463 Tooth with dentin dysplasia type i ORCID:0000-0001-5889-4463 An abnormality of the outflow tract of the left ventricle. peter 2011-06-05T04:15:50Z SNOMEDCT_US:253545000 UMLS:C0344916 Abnormality of the left ventricular outflow tract human_phenotype HP:0011103 Abnormal left ventricular outflow tract morphology An abnormality of the outflow tract of the left ventricle. HPO:probinson An inflammation of the tonsils. peter 2011-06-10T07:46:38Z MSH:D014069 SNOMEDCT_US:90176007 UMLS:C0040425 Inflammation of tonsils HP:0011110 Tonsillitis HPO:skoehler An inflammation of the tonsils. HPO:probinson Inflammation of tonsils ORCID:0000-0001-5208-3432 Any morphological abnormality of the skin. peter 2011-06-12T10:03:23Z Fyler:4133 UMLS:C4023528 Abnormal skin morphology Abnormal skin structure human_phenotype HP:0011121 Abnormality of skin morphology Any morphological abnormality of the skin. HPO:probinson Abnormal skin morphology ORCID:0000-0001-5208-3432 Abnormal skin structure ORCID:0000-0001-5208-3432 Any abnormality of the physiological function of the skin. peter 2011-06-12T10:05:14Z UMLS:C4023527 Abnormality of skin physiology human_phenotype HP:0011122 Abnormality of skin physiology Any abnormality of the physiological function of the skin. HPO:probinson Abnormality of skin physiology The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes. peter 2011-06-12T10:06:04Z HP:0002727 HP:0007423 MP:0004947 MSH:D003872 SNOMEDCT_US:703938007 UMLS:C0011603 UMLS:C3875321 Abnormal tendency to infections of the skin Inflammatory abnormality of the skin Skin inflammation human_phenotype Dermatitis Inflammatory skin disease HP:0011123 Inflammatory abnormality of the skin The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes. HPO:probinson Inflammatory abnormality of the skin Skin inflammation An abnormality of the morphology of the epidermis. peter 2011-06-12T10:11:28Z UMLS:C4023526 human_phenotype HP:0011124 Abnormality of epidermal morphology An abnormality of the morphology of the epidermis. HPO:probinson Absence or developmental hypoplasia of the sweat glands. peter 2011-06-19T02:01:50Z UMLS:C4023520 Absent/small sweat glands Absent/underdeveloped sweat glands human_phenotype HP:0011135 Aplasia/Hypoplasia of the sweat glands Absence or developmental hypoplasia of the sweat glands. HPO:probinson Absent/small sweat glands ORCID:0000-0001-5208-3432 Absent/underdeveloped sweat glands ORCID:0000-0001-5208-3432 An abnormality of the skin adnexa (skin appendages), which are specialized skin structures located within the dermis and focally within the subcutaneous fatty tissue, comprising three histologically distinct structures: (1) the pilosebaceous unit (hair follicle and sebaceous glands); (2) the eccrine sweat glands; and (3) the apocrine glands. peter 2011-06-19T06:25:34Z UMLS:C4023518 Abnormal skin appendage human_phenotype HP:0011138 Abnormality of skin adnexa morphology An abnormality of the skin adnexa (skin appendages), which are specialized skin structures located within the dermis and focally within the subcutaneous fatty tissue, comprising three histologically distinct structures: (1) the pilosebaceous unit (hair follicle and sebaceous glands); (2) the eccrine sweat glands; and (3) the apocrine glands. HPO:probinson Abnormal skin appendage ORCID:0000-0001-5208-3432 Gastric duplication is a usually cystic malformation of gastrointestinal tract, usually attached to the greater curvature of the stomach and has no communication with the stomach. peter 2011-06-25T08:57:09Z UMLS:C4021201 Gastric duplication cyst human_phenotype HP:0011139 Gastric duplication usually presents as gastric outlet obstruction. They are usually spherical in form, do not communicate with the stomach, and are generally localized at the greater curvature. In some cases they may exhibit adhesion to the pancreas and even communicate with aberrant pancreatic ducts. Gastric duplication is more frequent in females. It is generally either diagnosed in infancy because of symptoms of gastric outlet obstruction or is an incidental finding in adulthood. Gastric duplication Gastric duplication is a usually cystic malformation of gastrointestinal tract, usually attached to the greater curvature of the stomach and has no communication with the stomach. HPO:probinson A spherical hollow structure with a smooth muscle coat, lined by a mucous membrane, and attached to any part of the gastrointestinal tract, from the base of the tongue to the anus. peter 2011-06-25T09:02:50Z SNOMEDCT_US:33257003 UMLS:C0266019 GI duplication human_phenotype HP:0011140 Gastrointestinal duplication A spherical hollow structure with a smooth muscle coat, lined by a mucous membrane, and attached to any part of the gastrointestinal tract, from the base of the tongue to the anus. HPO:probinson PMID:21218094 GI duplication An abnormal shape of occiput. peter 2011-12-03T10:14:06Z Abnormal shape of posterior head Abnormal shape of the back of the head UMLS:C4023459 Abnormal shape of posterior cranium Abnormal shape of posterior skull Abnormal shape of the back of the skull human_phenotype HP:0011217 Abnormal shape of the occiput An abnormal shape of occiput. HPO:probinson Abnormal shape of posterior head ORCID:0000-0001-5889-4463 Abnormal shape of the back of the head ORCID:0000-0001-5889-4463 Abnormal shape of posterior cranium ORCID:0000-0001-5889-4463 Abnormal shape of posterior skull ORCID:0000-0001-5889-4463 Abnormal shape of the back of the skull ORCID:0000-0001-5889-4463 An abnormal shape of the frontal part of the head. peter 2011-12-03T10:26:03Z UMLS:C4023458 Abnormal morphology of the frontal region Abnormal shape of the forehead Dysmorphic forehead Dysmorphic frontal region human_phenotype HP:0011218 Abnormal shape of the frontal region An abnormal shape of the frontal part of the head. HPO:probinson Abnormal morphology of the frontal region ORCID:0000-0001-5889-4463 Abnormal shape of the forehead ORCID:0000-0001-5889-4463 Dysmorphic forehead ORCID:0000-0001-5889-4463 Dysmorphic frontal region ORCID:0000-0001-5889-4463 Facial height (length) is more than two standard deviations below the mean (objective); or an apparent decrease in the height (length) of the face (subjective). peter 2011-12-07T09:01:18Z UMLS:C4023457 Decreased height of face Decreased length of face Decreased vertical dimension of face Short face Short facies Vertical Facial Deficiency Vertical deficiency of face Vertical facial insufficiency Vertical hypoplasia of face Vertical insufficiency of face Vertical shortening of face human_phenotype HP:0011219 Objective measurement of face height is made with sliding calipers from the nasion, just above the depth of the nasal root to the gnathion, the inferior border of the mandible, both in the midline. Note that short face is distinct from wide face. Short face Facial height (length) is more than two standard deviations below the mean (objective); or an apparent decrease in the height (length) of the face (subjective). PMID:19125436 Decreased height of face ORCID:0000-0001-5889-4463 Decreased length of face ORCID:0000-0001-5889-4463 Decreased vertical dimension of face ORCID:0000-0001-5889-4463 Short face Short facies ORCID:0000-0001-5889-4463 Vertical Facial Deficiency ORCID:0000-0001-5889-4463 Vertical deficiency of face ORCID:0000-0001-5889-4463 Vertical facial insufficiency ORCID:0000-0001-5889-4463 Vertical hypoplasia of face ORCID:0000-0001-5889-4463 Vertical insufficiency of face ORCID:0000-0001-5889-4463 Vertical shortening of face ORCID:0000-0001-5889-4463 peter 2011-12-30T02:51:16Z UMLS:C4023437 human_phenotype HP:0011277 Abnormality of the urinary system physiology An abnormality of calcium concentration in the urine. peter 2011-12-30T03:27:02Z UMLS:C4023434 Abnormality of urine Ca concentration Abnormality of urine Ca2+ concentration HP:0011280 Abnormality of urine calcium concentration An abnormality of calcium concentration in the urine. HPO:probinson Abnormality of urine Ca concentration https://orcid.org/0000-0001-7941-2961 Abnormality of urine Ca2+ concentration https://orcid.org/0000-0001-7941-2961 An abnormality of the hindbrain, also known as the rhombencephalon. peter 2012-01-01T01:22:36Z UMLS:C4021170 Abnormal shape of hindbrain Abnormality of the hindbrain human_phenotype HP:0011282 The hindbrain consists of two main structures: The pons and the cerebellum. Abnormality of hindbrain morphology An abnormality of the hindbrain, also known as the rhombencephalon. HPO:probinson Abnormal shape of hindbrain ORCID:0000-0001-5208-3432 An abnormality of the metencephalon. The metencephalon is the part of the hindbrain that consists of the pons and the cerebellum. peter 2012-01-01T01:24:14Z UMLS:C4023432 human_phenotype HP:0011283 Abnormality of the metencephalon An abnormality of the metencephalon. The metencephalon is the part of the hindbrain that consists of the pons and the cerebellum. HPO:probinson A morphological abnormality of a digit, i.e., of a finger or toe. peter 2012-02-11T07:16:22Z UMLS:C3550704 Abnormality of digit Abnormality of fingers or toes Digital anomalies human_phenotype HP:0011297 Abnormal digit morphology A morphological abnormality of a digit, i.e., of a finger or toe. HPO:probinson Abnormality of fingers or toes The total absence of the foot, with no bony elements distal to the tibia or fibula. hecht 2012-02-11T11:20:59Z SNOMEDCT_US:371197005 UMLS:C0265624 Absent foot Aplasia of the foot Apodia human_phenotype HP:0011301 Absent foot The total absence of the foot, with no bony elements distal to the tibia or fibula. PMID:19125433 Absent foot An abnormality of size or shape of the long bones. hecht 2012-02-12T02:31:03Z HP:0100713 HP:0100714 HP:0100715 UMLS:C4021165 Abnormal shape of long bone Abnormality of the tubular bones human_phenotype HP:0011314 Abnormality of long bone morphology An abnormality of size or shape of the long bones. HPO:probinson Abnormal shape of long bone ORCID:0000-0001-5208-3432 An abnormality of the fontanelle. peter 2012-02-25T02:34:36Z UMLS:C4020755 human_phenotype Anomaly of the fontanelles HP:0011328 The fontanelles are the regions in an infant's calvaria that are covered by a thick membrane that normally ossify in the first two years of life. Abnormality of fontanelles An abnormality of the fontanelle. HPO:probinson PMID:12825844 Any anomaly of a cranial suture, that is one of the six membrane-covered openings in the incompletely ossified skull of the fetus or newborn infant. peter 2012-02-25T03:33:56Z UMLS:C4023412 Abnormality of cranial sutures Abnormality of the bregma sutures Abnormality of the calvarium sutures Abnormality of the cranial sutures Abnormality of the skull suture human_phenotype HP:0011329 Abnormality of cranial sutures Any anomaly of a cranial suture, that is one of the six membrane-covered openings in the incompletely ossified skull of the fetus or newborn infant. HPO:probinson Abnormality of cranial sutures peter 2012-02-26T11:00:17Z UMLS:C4023408 Abnormality of mouth size Anomaly of mouth size human_phenotype HP:0011337 Abnormality of mouth size Abnormality of mouth size Anomaly of mouth size ORCID:0000-0001-5889-4463 An abnormality of the outline, configuration, or contour of the mouth. peter 2012-02-26T01:05:23Z Fyler:4874 UMLS:C4023407 Abnormality of mouth shape Anomaly of mouth shape Unusual mouth shape human_phenotype HP:0011338 Abnormality of mouth shape An abnormality of the outline, configuration, or contour of the mouth. DDD:jhurst Abnormality of mouth shape Anomaly of mouth shape ORCID:0000-0001-5889-4463 Unusual mouth shape ORCID:0000-0001-5889-4463 An abnormality of the skin that is not localized to any one particular region. peter 2012-03-01T01:55:07Z UMLS:C4021157 Generalised abnormality of skin Generalized abnormality of skin human_phenotype HP:0011354 Generalized abnormality of skin An abnormality of the skin that is not localized to any one particular region. DDD:cmoss Generalised abnormality of skin Generalized abnormality of skin A lesion of the skin that is located in a specific region rather than being generalized. peter 2012-03-01T02:37:43Z UMLS:C0850826 Localised skin lesion Localized skin lesion human_phenotype HP:0011355 Localized skin lesion A lesion of the skin that is located in a specific region rather than being generalized. DDD:cmoss Localised skin lesion Localized skin lesion An abnormal amount of hair. peter 2012-03-01T08:46:57Z HP:0002115 HP:0011357 UMLS:C4023397 UMLS:C4023401 Abnormal hair quantity Abnormality of hair density HP:0011362 Abnormal hair quantity An abnormal amount of hair. DDD:cmoss Abnormal hair quantity Absence of the inner ear due to a developmental defect. peter 2012-03-07T08:23:52Z SNOMEDCT_US:71973003 UMLS:C0266604 Absent inner ear Aplasia of the labyrinth Labyrinthine aplasia Michel deformity human_phenotype HP:0011372 Aplasia of the inner ear is usually diagnosed on MR or CT imaging. Aplasia of the inner ear Absence of the inner ear due to a developmental defect. DDD:dfitzpatrick Absent inner ear ORCID:0000-0001-5208-3432 Absence of the cochlea, a spiral shaped cavity in the inner ear, owing to a developmental defect. peter 2012-03-07T08:31:27Z UMLS:C4023390 Absent cochlea human_phenotype HP:0011375 Cochlear aplasia Absence of the cochlea, a spiral shaped cavity in the inner ear, owing to a developmental defect. HPO:dfitzpatrick Absent cochlea ORCID:0000-0001-5208-3432 An abnormality of the function of the inner ear. hecht 2012-03-09T04:58:30Z UMLS:C4023382 Functional abnormality of the inner ear human_phenotype HP:0011389 The inner ear comprises the cochlea, three semicircular canals and the vestibule (labyrinth), and is directly responsible for hearing. Additionally, the vestibule and semicircular canals function to maintain balance or equilibrium. Functional abnormality of the inner ear An abnormality of the function of the inner ear. DDD:dfitzpatrick Functional abnormality of the inner ear A structural anomaly of the internal part of the ear. hecht 2012-03-09T04:59:24Z UMLS:C4023381 human_phenotype HP:0011390 The inner ear contains the cochlea and the semicircular canals. Morphological abnormality of the inner ear A structural anomaly of the internal part of the ear. HPO:probinson hecht 2012-03-09T05:03:30Z UMLS:C4023380 human_phenotype HP:0011391 Morphological abnormality of the nerves of the inner ear Absence or underdevelopment of the cochlea, a spiral shaped cavity in the inner ear, owing to a developmental defect. hecht 2012-03-09T05:37:50Z UMLS:C4023378 Absent/small cochlea Absent/underdeveloped cochlea human_phenotype HP:0011395 Aplasia/Hypoplasia of the cochlea Absence or underdevelopment of the cochlea, a spiral shaped cavity in the inner ear, owing to a developmental defect. HPO:probinson Absent/small cochlea ORCID:0000-0001-5208-3432 Absent/underdeveloped cochlea ORCID:0000-0001-5208-3432 peter 2012-03-15T11:05:13Z UMLS:C4023372 human_phenotype HP:0011403 Abnormal umbilical cord blood vessels peter 2012-03-15T10:10:35Z SNOMEDCT_US:249174002 UMLS:C0426234 human_phenotype HP:0011415 Calcified placenta Increased length of the umbilical cord. peter 2012-03-15T10:12:55Z SNOMEDCT_US:237261008 UMLS:C0405028 Long umbilical cord human_phenotype HP:0011417 Long umbilical cord Increased length of the umbilical cord. DDD:hfirth Long umbilical cord An finding upon obstetric ultrasound examination performed at around 16 to 20 weeks of gestation that is abnormal but not clearly identifiable as a fetal anatomic malformation or growth restriction. Such findings are known as soft markers since they are associated with increased risk for fetal aneuploidy or other disorders. peter 2012-03-17T04:26:01Z UMLS:C4023366 Foetal ultrasound soft marker human_phenotype HP:0011425 The screening ultrasound at 16 to 20 weeks should evaluate 8 markers, 5 of which (thickened nuchal fold, echogenic bowel, mild ventriculomegaly, echogenic focus in the heart, and choroid plexus cyst) are associated with an increased risk of fetal aneuploidy, and in some cases with nonchromosomal problems, while 3 (single umbilical artery, enlarged cisterna magna, and pyelectasis) are only associated with an increased risk of nonchromosomal abnormalities when seen in isolation (PMID:16100637). Fetal ultrasound soft marker An finding upon obstetric ultrasound examination performed at around 16 to 20 weeks of gestation that is abnormal but not clearly identifiable as a fetal anatomic malformation or growth restriction. Such findings are known as soft markers since they are associated with increased risk for fetal aneuploidy or other disorders. PMID:16100637 Foetal ultrasound soft marker An abnormality of the medulla oblongata, the lower half of the brainstem. peter 2012-03-18T01:51:24Z UMLS:C4021148 Abnormality of the myencephalon human_phenotype HP:0011441 The medulla oblongata, which is often referred to simply as the medulla, comprises the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures. Abnormality of the medulla oblongata An abnormality of the medulla oblongata, the lower half of the brainstem. HPO:probinson A type of infection of the central nervous system that can be regarded as a sign of a pathological susceptibility to infection. peter 2012-03-18T05:57:29Z MSH:D002494 SNOMEDCT_US:128117002 UMLS:C0007684 Central nervous system infection human_phenotype HP:0011450 Unusual CNS infection Central nervous system infection ORCID:0000-0001-5208-3432 An abnormality of the function of the middle ear. peter 2012-03-19T09:33:03Z UMLS:C4021846 Functional abnormality of the middle ear human_phenotype HP:0011452 The middle ear comprises the tympanic cavity in the temporal bone of the skull behind the eardrum, and is separated from the outer ear by the ear drum. The tympanic cavity contains the auditory ossicles (malleus, incus, stapes) that vibrate when exposed to sound, forming a chain that extends to the oval window of the inner ear and whose main function is to amplify sound. Additionally, the middle ear connects to the back of the throat and nose through the Eustachian tube. Functional abnormality of the middle ear An abnormality of the function of the middle ear. HPO:probinson Functional abnormality of the middle ear Aplasia of the stapes. peter 2012-03-19T09:42:52Z SNOMEDCT_US:300178009 UMLS:C0576909 human_phenotype HP:0011456 Absent stapes Aplasia of the stapes. DDD:dfitzpatrick peter 2012-03-25T05:35:45Z UMLS:C0740651 human_phenotype HP:0011458 Abdominal symptom Absence or underdevelopment of the gallbladder. peter 2012-03-25T07:40:20Z UMLS:C4023344 Absent/small gallbladder Absent/underdeveloped gallbladder human_phenotype HP:0011466 Aplasia/Hypoplasia of the gallbladder Absence or underdevelopment of the gallbladder. HPO:probinson Absent/small gallbladder ORCID:0000-0001-5208-3432 Absent/underdeveloped gallbladder ORCID:0000-0001-5208-3432 A developmental defect in which the gallbladder fails to form. peter 2012-03-25T07:41:14Z MSH:C562564 SNOMEDCT_US:86507001 UMLS:C0266251 Absent gallbladder Agenesis of the gallbladder Aplasia of the gallbladder human_phenotype HP:0011467 Absent gallbladder A developmental defect in which the gallbladder fails to form. DDD:hfirth Absent gallbladder peter 2012-03-26T08:16:03Z UMLS:C4023341 Abnormal shape of small intestinal villus human_phenotype HP:0011472 Abnormality of small intestinal villus morphology Abnormal shape of small intestinal villus ORCID:0000-0001-5208-3432 An abnormality of the lacrimal punctum, an opening on the eyelid close to the medial canthus that drains tears from the conjunctival sac into the lacrimal duct in the same eyelid. peter 2012-04-01T09:08:05Z UMLS:C4023337 Abnormality of the lacrimal punctum human_phenotype HP:0011479 Abnormal lacrimal punctum morphology An abnormality of the lacrimal punctum, an opening on the eyelid close to the medial canthus that drains tears from the conjunctival sac into the lacrimal duct in the same eyelid. HPO:probinson An abnormality of the lacrimal duct, a duct that drain tears from the conjunctiva, via the lacrimal puncta, into the lacrimal sac. peter 2012-04-01T09:11:55Z UMLS:C1858567 Abnormality of the lacrimal canaliculus Abnormality of the lacrimal duct human_phenotype HP:0011481 Abnormal lacrimal duct morphology An abnormality of the lacrimal duct, a duct that drain tears from the conjunctiva, via the lacrimal puncta, into the lacrimal sac. HPO:probinson Abnormality of the lacrimal gland, i.e., of the almond-shaped gland that secretes the aqueous layer of the tear film for each eye. peter 2012-04-01T09:35:54Z UMLS:C4023336 Abnormality of the lacrimal gland human_phenotype HP:0011482 Abnormal lacrimal gland morphology Abnormality of the lacrimal gland, i.e., of the almond-shaped gland that secretes the aqueous layer of the tear film for each eye. HPO:probinson Abnormality of the corneal endothelium, that is, the single layer of cells on the inner surface of the cornea. peter 2012-04-02T10:18:50Z UMLS:C4023332 Abnormality of corneal endothelium human_phenotype HP:0011488 Abnormal corneal endothelium morphology Abnormality of the corneal endothelium, that is, the single layer of cells on the inner surface of the cornea. DDD:gblack Abnormality of Descemet's membrane, which is the basement membrane of the corneal endothelium. peter 2012-04-02T10:23:11Z UMLS:C4023330 Abnormality of Descemet's membrane human_phenotype HP:0011490 Abnormal Descemet membrane morphology Abnormality of Descemet's membrane, which is the basement membrane of the corneal endothelium. DDD:gblack An abnormality of the stroma of cornea, also known as the substantia propria of cornea. peter 2012-04-02T10:28:49Z UMLS:C4023328 human_phenotype HP:0011492 Abnormality of corneal stroma An abnormality of the stroma of cornea, also known as the substantia propria of cornea. DDD:ncarter HPO:probinson Abnormality of the corneal epithelium, that is of the epithelial tissue that covers the front of the cornea. peter 2012-04-03T07:10:49Z UMLS:C4023326 Abnormality of corneal epithelium human_phenotype HP:0011495 Abnormal corneal epithelium morphology Abnormality of the corneal epithelium, that is of the epithelial tissue that covers the front of the cornea. DDD:gblack Increased pigmentation of the fundus peter 2012-04-06T10:34:11Z UMLS:C4021146 Hyperpigmented fundi Hyperpigmented fundus human_phenotype HP:0011512 Hyperpigmentation of the fundus Increased pigmentation of the fundus DDD:ncarter ORCID:0000-0003-0986-4123 An iris cyst is composed of a single cell layer of epithelium and is filled with fluid. peter 2012-04-06T09:05:29Z SNOMEDCT_US:37761009 UMLS:C0271119 human_phenotype HP:0011523 Iris cyst An iris cyst is composed of a single cell layer of epithelium and is filled with fluid. DDD:gblack An abnormal shape of the lens. peter 2012-04-06T09:16:11Z UMLS:C4023314 Abnormality of lens shape human_phenotype HP:0011526 Abnormality of lens shape An abnormal shape of the lens. HPO:probinson Abnormality of lens shape An abnormality of the pulmonary situs, i.e., of the sidedness of the morphological right and left lungs, which is defined by characteristics such as the number of lobes per lung and the relationship of the pulmonary arteries to their bronchi. peter 2012-04-08T09:20:13Z UMLS:C4023271 Abnormality of pulmonary situs human_phenotype HP:0011615 Abnormal pulmonary situs morphology An abnormality of the pulmonary situs, i.e., of the sidedness of the morphological right and left lungs, which is defined by characteristics such as the number of lobes per lung and the relationship of the pulmonary arteries to their bronchi. DDD:dbrown A developmental defect of the pericardium with congenital onset. peter 2012-04-08T10:05:20Z UMLS:C4023261 human_phenotype HP:0011628 Congenital defect of the pericardium A developmental defect of the pericardium with congenital onset. DDD:dbrown No pericardium around the heart, occurring as a congenital defect, not the result of a surgical pericardectomy. peter 2012-04-08T10:06:22Z Fyler:1910 SNOMEDCT_US:253732001 UMLS:C0345140 Absent pericardium Congenital absence of the pericardium human_phenotype HP:0011629 Total absence of the pericardium No pericardium around the heart, occurring as a congenital defect, not the result of a surgical pericardectomy. DDD:dbrown Absent pericardium ORCID:0000-0001-5208-3432 Congenital absence of the pericardium ORCID:0000-0001-6908-9849 An abnormality of the coronary sinus, which is formed by the union of the great cardiac vein and the left marginal vein and terminates in the right atrium. The coronary sinus functions to o collect deoxygenated blood from the myocardium of the heart and drain it into the right atrium. peter 2012-04-09T09:02:09Z Fyler:2840 SNOMEDCT_US:253323000 UMLS:C0344680 Abnormality of the coronary sinus human_phenotype HP:0011642 Abnormal coronary sinus morphology An abnormality of the coronary sinus, which is formed by the union of the great cardiac vein and the left marginal vein and terminates in the right atrium. The coronary sinus functions to o collect deoxygenated blood from the myocardium of the heart and drain it into the right atrium. DDD:dbrown HPO:probinson A venous pouch within the left ventricular wall, with a neck opening into the coronary sinus. peter 2012-04-09T09:12:28Z SNOMEDCT_US:447661004 UMLS:C3163894 Diverticulum of the coronary sinus human_phenotype HP:0011644 Coronary sinus diverticulum A venous pouch within the left ventricular wall, with a neck opening into the coronary sinus. DDD:dbrown PMID:3138904 An abnormality of the pulmonary veins. peter 2012-04-11T08:45:48Z SNOMEDCT_US:111322000 SNOMEDCT_US:128585006 SNOMEDCT_US:199113001 UMLS:C0265914 Abnormality of lung veins HP:0011718 The right superior, right inferior, left superior, and left inferior pulmonary veins carry oxygenated blood to the left atrium. Abnormality of the pulmonary veins An abnormality of the pulmonary veins. HPO:probinson Abnormality of lung veins Defect or defects of the morphogenesis of the right heart identifiable at birth. peter 2012-04-11T08:56:19Z UMLS:C4023219 human_phenotype HP:0011723 Congenital malformation of the right heart An abnormality in the range and ease of motion of joints across their normal range. peter 2012-04-18T07:09:28Z UMLS:C4023216 human_phenotype HP:0011729 Abnormality of joint mobility An abnormality in the range and ease of motion of joints across their normal range. HPO:probinson Any structural anomaly of the adrenal glands. peter 2012-04-21T08:04:29Z UMLS:C4023213 human_phenotype HP:0011732 Abnormality of adrenal morphology Any structural anomaly of the adrenal glands. HPO:probinson A functional abnormality of the adrenal glands. peter 2012-04-21T08:05:42Z HP:0002855 UMLS:C4023212 human_phenotype HP:0011733 Abnormality of adrenal physiology A functional abnormality of the adrenal glands. HPO:probinson Absent development of the adrenal gland. peter 2012-04-21T09:46:49Z MSH:C538429 SNOMEDCT_US:702615004 SNOMEDCT_US:83190008 UMLS:C0266273 human_phenotype HP:0011743 Adrenal gland agenesis Absent development of the adrenal gland. DDD:spark An abnormality of the adenohypophysis, which is also known as the anterior lobe of the pituitary gland. peter 2012-04-22T11:17:00Z MSH:D010900 SNOMEDCT_US:399244003 UMLS:C0032002 UMLS:C4023206 human_phenotype Pituitary disease HP:0011747 Abnormality of the anterior pituitary An abnormality of the adenohypophysis, which is also known as the anterior lobe of the pituitary gland. DDD:spark An abnormality of the neurohypophysis, which is also known as the posterior lobe of the hypophysis. peter 2012-04-22T01:20:33Z UMLS:C4023204 Abnormality of the neurohypophysis human_phenotype HP:0011751 Abnormality of the posterior pituitary An abnormality of the neurohypophysis, which is also known as the posterior lobe of the hypophysis. DDD:spark HPO:probinson Abnormality of the neurohypophysis ORCID:0000-0001-6908-9849 Abnormal development of the neurohypophysis during embryonic growth and development. peter 2012-04-22T01:42:04Z UMLS:C4021123 Neurohypophysis dysplasia Posterior pituitary dysplasia human_phenotype HP:0011753 Posterior pituitary dysgenesis Abnormal development of the neurohypophysis during embryonic growth and development. DDD:spark Neurohypophysis dysplasia ORCID:0000-0001-6908-9849 Absence of the neurohypophysis owing to a developmental defect. peter 2012-04-22T01:55:35Z UMLS:C4023203 Neurohypophysis agenesis human_phenotype HP:0011756 Posterior pituitary agenesis Absence of the neurohypophysis owing to a developmental defect. DDD:spark Neurohypophysis agenesis ORCID:0000-0001-6908-9849 Underdevelopment of the neurohypophysis. peter 2012-04-22T01:56:23Z UMLS:C4023202 Neurohypophysis hypoplasia human_phenotype HP:0011757 Posterior pituitary hypoplasia Underdevelopment of the neurohypophysis. DDD:spark Neurohypophysis hypoplasia ORCID:0000-0001-6908-9849 A structural abnormality of the parathyroid gland. peter 2012-04-22T04:08:26Z UMLS:C4023199 human_phenotype HP:0011766 Abnormality of the parathyroid morphology A structural abnormality of the parathyroid gland. DDD:spark HPO:probinson A functional abnormality of the parathyroid gland. peter 2012-04-22T04:09:13Z Parathyroid issue UMLS:C4023198 Parathyroid dysfunction human_phenotype HP:0011767 Abnormality of the parathyroid physiology A functional abnormality of the parathyroid gland. DDD:spark HPO:probinson Parathyroid issue Parathyroid dysfunction Abnormal embryonic development of the parathyroid gland. peter 2012-04-22T04:20:41Z UMLS:C4023197 human_phenotype HP:0011768 Parathyroid dysgenesis Abnormal embryonic development of the parathyroid gland. DDD:spark A structural abnormality of the thyroid gland. peter 2012-04-22T05:54:57Z UMLS:C4023195 Abnormal shape of thyroid gland Abnormality of thyroid morphology HP:0011772 Abnormal thyroid morphology A structural abnormality of the thyroid gland. DDD:spark Abnormal shape of thyroid gland ORCID:0000-0001-5208-3432 Neoplasm categorized according to the anatomical site of origin of the neoplasm. peter 2012-04-22T07:00:13Z UMLS:C4023185 human_phenotype HP:0011793 Neoplasm by anatomical site Neoplasm categorized according to the anatomical site of origin of the neoplasm. DDD:rscott peter 2012-04-23T07:27:57Z UMLS:C4023183 Abnormality of facial soft tissue Anomaly of facial soft tissue Deformity of facial soft tissue Malformation of facial soft tissue human_phenotype HP:0011799 Abnormality of facial soft tissue Abnormality of facial soft tissue Anomaly of facial soft tissue ORCID:0000-0001-5889-4463 Deformity of facial soft tissue ORCID:0000-0001-5889-4463 Malformation of facial soft tissue ORCID:0000-0001-5889-4463 Posterior positions and/or vertical shortening of the infraorbital and perialar regions, or increased concavity of the face and/or reduced nasolabial angle. peter 2012-04-24T07:46:05Z HP:0040199 Small midface UMLS:C1853242 UMLS:C2673410 UMLS:C4280320 UMLS:C4280321 Decreased size of midface Flat midface Hypoplasia of midface Midface deficiency Midface hypoplasia Midface retrusion Midface, flat Retrusive midface Underdevelopment of midface Decreased projection of midface human_phenotype Hypotrophic midface HP:0011800 Midface retrusion Posterior positions and/or vertical shortening of the infraorbital and perialar regions, or increased concavity of the face and/or reduced nasolabial angle. DDD:jclayton-smith PMID:19125436 Small midface ORCID:0000-0001-5889-4463 Decreased size of midface ORCID:0000-0001-5889-4463 Midface deficiency ORCID:0000-0001-5889-4463 Midface hypoplasia HPO:skoehler Midface retrusion Retrusive midface ORCID:0000-0001-5208-3432 ORCID:0000-0001-5889-4463 Underdevelopment of midface ORCID:0000-0001-5889-4463 Decreased projection of midface ORCID:0000-0001-5889-4463 Hypotrophic midface ORCID:0000-0001-5889-4463 Visually assessable vertical indentation, cleft, or depression of the nasal bridge, ridge and tip. peter 2012-04-25T08:09:58Z MSH:C535441 SNOMEDCT_US:204521002 UMLS:C0221363 UMLS:C4280318 UMLS:C4280319 Bifid nasal bridge Indentation or clefting of the nose human_phenotype Cleft nasal bridge Cleft nose Indented bridge of nose HP:0011803 This is a bundled term, but as it is useful in practice it is kept here. If it is only an indentation or cleft of the nasal tip, this should be coded as Bifid nasal tip. Bifid nose Visually assessable vertical indentation, cleft, or depression of the nasal bridge, ridge and tip. PMID:19152422 Bifid nasal bridge ORCID:0000-0001-5889-4463 Indentation or clefting of the nose https://orcid.org/0000-0002-6548-5200 Cleft nasal bridge ORCID:0000-0001-5889-4463 Cleft nose ORCID:0000-0001-5889-4463 Indented bridge of nose ORCID:0000-0001-5889-4463 A functional abnormality of a skeletal muscle. peter 2012-04-25T02:00:15Z UMLS:C4023182 Abnormality of muscle physiology Issue with muscle function human_phenotype HP:0011804 Abnormal muscle physiology A functional abnormality of a skeletal muscle. HPO:probinson Issue with muscle function A structural abnormality of a skeletal muscle. peter 2012-04-25T02:00:34Z HP:0003735 UMLS:C4023181 Abnormal muscle morphology Abnormality of muscle morphology Abnormally shaped muscle Issue with muscle structure human_phenotype HP:0011805 Abnormal skeletal muscle morphology A structural abnormality of a skeletal muscle. HPO:probinson Abnormally shaped muscle ORCID:0000-0001-5208-3432 Issue with muscle structure An abnormality of one or more of the set of bones that make up the facial skeleton. peter 2012-04-29T04:37:30Z SNOMEDCT_US:433096001 UMLS:C2315229 Abnormality of facial skeleton Anomaly of facial skeleton Abnormality of facial bones Anomaly of facial bones Deformity of facial skeleton Deformity of the facial bones Malformation of facial bones Malformation of facial skeleton human_phenotype HP:0011821 The facial skeleton comprises the mandible, maxilla, frontal bone, nasal bones, and zygoma, as well as the inferior nasal concha, the lacrimal bones, the palatine bone, and the vomer. Abnormality of facial skeleton An abnormality of one or more of the set of bones that make up the facial skeleton. DDD:awilkie Abnormality of facial skeleton Anomaly of facial skeleton ORCID:0000-0001-5889-4463 Abnormality of facial bones ORCID:0000-0001-5889-4463 Anomaly of facial bones ORCID:0000-0001-5889-4463 Deformity of facial skeleton ORCID:0000-0001-5889-4463 Deformity of the facial bones ORCID:0000-0001-5889-4463 Malformation of facial bones ORCID:0000-0001-5889-4463 Malformation of facial skeleton ORCID:0000-0001-5889-4463 Abnormality of the oral mucosa. peter 2012-05-01T10:43:40Z UMLS:C4023170 Abnormality of lining of mouth Abnormality of mucosa of mouth Abnormality of oral mucosa Abnormality of oral mucous membrane human_phenotype HP:0011830 Abnormal oral mucosa morphology Abnormality of the oral mucosa. HPO:probinson Abnormality of lining of mouth ORCID:0000-0001-5889-4463 Abnormality of mucosa of mouth ORCID:0000-0001-5889-4463 Abnormality of oral mucous membrane ORCID:0000-0001-5889-4463 An abnormality of the form, structure, or size of the skeletal system. peter 2012-05-07T08:08:37Z UMLS:C4023165 Abnormally shaped skeletal human_phenotype HP:0011842 Abnormality of skeletal morphology An abnormality of the form, structure, or size of the skeletal system. HPO:probinson Abnormally shaped skeletal ORCID:0000-0001-5208-3432 An abnormality of the function of the skeletal system. peter 2012-05-07T08:09:43Z UMLS:C4023164 human_phenotype HP:0011843 Abnormality of musculoskeletal physiology An abnormality of the function of the skeletal system. HPO:probinson An abnormality of the appendicular skeletal system, consisting of the of the limbs, shoulder and pelvic girdles. peter 2012-05-07T08:12:26Z UMLS:C4023163 human_phenotype HP:0011844 Abnormal appendicular skeleton morphology An abnormality of the appendicular skeletal system, consisting of the of the limbs, shoulder and pelvic girdles. HPO:probinson Any anomaly in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. peter 2012-05-15T07:39:58Z MP:0008271 UMLS:C4023161 UMLS:C4280317 human_phenotype Abnormal bone maturation HP:0011849 All bones are formed by the replacement by osteocytes of mesenchyme-derived connective tissue. Intramembranous ossification refers to the direct replacement of primitive mesenchyme with bone, and is responsible for bones such as the calvarium (e.g., frontals, parietals, interparietal) and the clavicula. In endochondral ossification, the mesenchyme differentiates into a cartilaginous intermediate, which serves as a template (anlange) that is subsequently removed and replaced by bone. Most bones are formed via endochondral ossification, including those at the base of the skull, the vertebral column, pectoral and pelvic regions and long bones of the extremities. A reduction in the amount of mineralized bone compared with that expected for a given developmental age. In clinicakl parlance, reduced ossification and delayed ossification are often used synonymously, but in principle a bone delayed ossification in a child can display normal ossification at a later developmental stage. The HPO will therefore treat poor, reduced, and decreased officiation as synonymous, and delayed ossification as a specific kind of reduced ossification. Abnormal bone ossification Any anomaly in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance. HPO:probinson PMID:18157903 MP:0008271 Abnormal bone ossification Abnormal bone maturation ORCID:0000-0001-5208-3432 Any structural anomaly of the connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity. peter 2012-05-27T01:32:04Z UMLS:C4023158 human_phenotype HP:0011862 Abnormal bone collagen fibril morphology Any structural anomaly of the connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity. HPO:probinson MP:0011642 Bleeding from vessels of the various tissues of the eye. peter 2012-06-02T10:44:39Z MSH:D005130 SNOMEDCT_US:417244000 SNOMEDCT_US:93478000 UMLS:C0015402 Bleeding from the eye Haemorrhage of the eye human_phenotype HP:0011885 Hemorrhage of the eye Bleeding from vessels of the various tissues of the eye. DDD:akelly Bleeding from the eye ORCID:0000-0001-5208-3432 Haemorrhage of the eye Hemorrhage from the vessels of the choroid. peter 2012-06-02T10:50:39Z MSH:D002832 SNOMEDCT_US:122003 UMLS:C0008522 Choroid haemorrhage Choroidal hemorrhage human_phenotype HP:0011887 Choroid hemorrhage Hemorrhage from the vessels of the choroid. HPO:probinson Choroid haemorrhage An anomaly of a metacarpophalangeal joint. peter 2012-06-03T11:03:36Z UMLS:C4023132 Abnormality of the knuckle human_phenotype HP:0011911 Abnormality of metacarpophalangeal joint An anomaly of a metacarpophalangeal joint. HPO:probinson Abnormality of the knuckle An anomaly of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. peter 2012-06-05T08:51:23Z UMLS:C4023131 human_phenotype HP:0011912 Abnormality of the glenoid fossa An anomaly of the glenoid fossa, also known as the glenoid cavity, which is the articular surface of the scapula that articulates with the head of the humerus. HPO:probinson Abnormal calcification in the cardiovascular system. peter 2012-06-05T10:35:58Z UMLS:C4023128 human_phenotype HP:0011915 Cardiovascular calcification Abnormal calcification in the cardiovascular system. HPO:probinson Underdevelopment (hypoplasia) of the fifth toe. peter 2012-06-08T08:25:00Z UMLS:C4021111 Short fifth toe Short little toe Short pinkie toe Short pinky toe human_phenotype HP:0011917 Short 5th toe Underdevelopment (hypoplasia) of the fifth toe. HPO:probinson Short little toe ORCID:0000-0001-5208-3432 Short pinkie toe ORCID:0000-0001-5208-3432 Short pinky toe ORCID:0000-0001-5208-3432 One or more digit that appears disproportionately short compared to the hand/foot, whereby either the entire digit or a specific phalanx is shortened. peter 2012-06-10T09:18:42Z UMLS:C1860176 UMLS:C4023124 Short digit human_phenotype Very short digits HP:0011927 Note that the term brachydactyly is reserved for specific patterns of short digits, see HP:0001156. Short digit One or more digit that appears disproportionately short compared to the hand/foot, whereby either the entire digit or a specific phalanx is shortened. HPO:probinson Short digit Very short digits HPO:skoehler Developmental hypoplasia (shortening) of proximal phalanx of toe. peter 2012-06-10T10:06:30Z UMLS:C4023123 Short innermost toe bone human_phenotype HP:0011928 Short proximal phalanx of toe Developmental hypoplasia (shortening) of proximal phalanx of toe. HPO:probinson Short innermost toe bone ORCID:0000-0001-5208-3432 An infection of the upper or lower respiratory tract. peter 2012-06-21T08:26:36Z MSH:D012141 SNOMEDCT_US:275498002 UMLS:C0035243 Respiratory infection Respiratory tract infection human_phenotype Respiratory infections HP:0011947 Respiratory tract infection An infection of the upper or lower respiratory tract. HPO:probinson Respiratory infection Respiratory tract infection Respiratory infections HPO:skoehler Any deviation from the normal concentration of citrulline in the blood circulation. peter 2012-07-18T08:21:59Z UMLS:C4023103 human_phenotype HP:0011965 Citrulline is an alpha-amino acid that is a key intermediate in the urea cycle. Abnormal circulating citrulline concentration Any deviation from the normal concentration of citrulline in the blood circulation. HPO:probinson An increased concentration of citrulline in the blood. peter 2012-07-18T08:23:22Z UMLS:C4023102 human_phenotype HP:0011966 Elevated plasma citrulline An increased concentration of citrulline in the blood. HPO:probinson An abnormality of the interatrial septum. peter 2012-07-19T11:34:27Z Fyler:2002 SNOMEDCT_US:253363004 UMLS:C0344722 Abnormal interatrial septum morphology Abnormality of the atrial septum human_phenotype HP:0011994 Abnormal atrial septum morphology An abnormality of the interatrial septum. HPO:probinson Abnormal interatrial septum morphology ORCID:0000-0001-5208-3432 Elevated concentration of galactose in the urine. peter 2012-07-26T10:31:35Z SNOMEDCT_US:71690006 UMLS:C0268157 Increased urinary galactose level human_phenotype HP:0012023 Galactosuria Elevated concentration of galactose in the urine. HPO:probinson Increased urinary galactose level ORCID:0000-0001-5208-3432 Elevated concentration of galactose in the blood. peter 2012-07-26T10:35:58Z MSH:D005693 SNOMEDCT_US:190745006 SNOMEDCT_US:190749000 UMLS:C0016952 UMLS:C4023071 human_phenotype Galactosemia HP:0012024 Hypergalactosemia is used here to mean the increased concentration of galactose in the blood. Note that the word galactosemia is occasionally used with the same meaning but more commonly denotes the disease entity called galactosemia caused by mutations in the galactose-1-phosphate uridyltransferase gene (MIM:230400). Hypergalactosemia Elevated concentration of galactose in the blood. HPO:probinson Deviation from the normal concentration of ornithine in the blood circulation. peter 2012-07-26T10:48:59Z UMLS:C4023070 human_phenotype HP:0012025 Ornithine is an amino acid produced in the urea cycle by the splitting off of urea from arginine. Ornithine is a naturally occurring, non-proteinogenic amino acid found in meat, fish, dairy and eggs. Abnormal circulating ornithine concentration Deviation from the normal concentration of ornithine in the blood circulation. HPO:probinson Increased concentration of ornithine in the blood. peter 2012-07-26T10:49:54Z MSH:D015799 SNOMEDCT_US:276426004 SNOMEDCT_US:33985005 UMLS:C0599035 High blood ornithine levels human_phenotype HP:0012026 Hyperornithinemia Increased concentration of ornithine in the blood. HPO:probinson High blood ornithine levels ORCID:0000-0001-5208-3432 An abnormal concentration of a hormone in the urine. peter 2012-07-27T01:29:51Z UMLS:C4023069 Abnormality of urine hormone level human_phenotype HP:0012029 Abnormal urine hormone level An abnormal concentration of a hormone in the urine. HPO:probinson Excretion of urine with an acid pH, i.e., having an increased hydrogen ion concentration. SNOMEDCT_US:21806007 UMLS:C0278026 Acidic urine HP:0012072 Aciduria Excretion of urine with an acid pH, i.e., having an increased hydrogen ion concentration. HPO:probinson Acidic urine An abnormally increased size of the cerebellum compared to other brain structures. peter 2012-08-18T05:29:26Z UMLS:C3278024 human_phenotype HP:0012081 Enlarged cerebellum An abnormally increased size of the cerebellum compared to other brain structures. HPO:probinson An anomaly in the surface contour of mitochondria. peter 2012-09-08T11:02:39Z UMLS:C4023050 human_phenotype HP:0012087 Abnormal mitochondrial shape An anomaly in the surface contour of mitochondria. HPO:probinson MP:0011633 peter 2012-08-20T09:16:38Z UMLS:C4023049 Abnormality of pancreas morphology Abnormally shaped pancreas human_phenotype HP:0012090 Abnormal pancreas morphology Abnormally shaped pancreas ORCID:0000-0001-5208-3432 An anomaly of the function of the pancreas. peter 2012-08-20T09:17:10Z UMLS:C4023048 human_phenotype HP:0012091 Abnormality of pancreas physiology An anomaly of the function of the pancreas. HPO:probinson A functional anomaly of the acinar gland portion of the pancreas that secretes digestive enzymes. peter 2012-08-20T09:17:46Z UMLS:C4021103 Abnormal exocrine pancreatic function human_phenotype HP:0012092 Abnormality of exocrine pancreas physiology A functional anomaly of the acinar gland portion of the pancreas that secretes digestive enzymes. HPO:probinson Abnormal exocrine pancreatic function HPO:skoehler A function abnormality of the endocrine pancreas. peter 2012-08-20T09:18:18Z UMLS:C4023047 human_phenotype HP:0012093 Abnormality of endocrine pancreas physiology A function abnormality of the endocrine pancreas. HPO:probinson A deviation from the normal size of the pancreas. peter 2012-08-20T09:19:08Z UMLS:C4023046 Abnormal pancreas size human_phenotype HP:0012094 Abnormal pancreas size A deviation from the normal size of the pancreas. HPO:probinson Abnormal pancreas size A deviation from the normal number of mitochondria per cell. peter 2012-09-08T11:03:33Z UMLS:C4023043 human_phenotype HP:0012102 Abnormal mitochondrial number A deviation from the normal number of mitochondria per cell. HPO:probinson An anomaly of the mitochondrion, the membranous cytoplasmic organelle the interior of which is subdivided by cristae. The mitochondrion is a self replicating organelle that is the site of tissue respiration. peter 2012-09-08T11:05:06Z UMLS:C4020732 UMLS:C4023042 human_phenotype Mitochondrial abnormalities HP:0012103 Abnormality of the mitochondrion An anomaly of the mitochondrion, the membranous cytoplasmic organelle the interior of which is subdivided by cristae. The mitochondrion is a self replicating organelle that is the site of tissue respiration. HPO:probinson Mitochondrial abnormalities HPO:skoehler Underdevelopment of the pons. peter 2012-09-10T05:35:36Z UMLS:C1848529 Pontine hypoplasia human_phenotype HP:0012110 Hypoplasia of the pons Underdevelopment of the pons. HPO:probinson An abnormality of the concentration of a glucocorticoid in the blood. hecht 2012-09-16T04:22:26Z UMLS:C4023038 human_phenotype HP:0012111 Abnormality of circulating glucocorticoid level An abnormality of the concentration of a glucocorticoid in the blood. HPO:probinson Inflammation of the liver. hecht 2012-09-16T05:03:29Z MSH:D006505 SNOMEDCT_US:128241005 UMLS:C0019158 Liver inflammation human_phenotype HP:0012115 Hepatitis Inflammation of the liver. HPO:probinson Liver inflammation An decrease in the level of triglycerides in the blood. peter 2012-09-20T06:39:11Z UMLS:C0542037 Decreased circulating Tg levels Decreased plasma Tg levels Low blood triglyceride levels human_phenotype HP:0012153 Hypotriglyceridemia An decrease in the level of triglycerides in the blood. HPO:probinson Decreased circulating Tg levels Decreased plasma Tg levels Low blood triglyceride levels ORCID:0000-0001-5208-3432 A developmental defect resulting in the presence of fewer than the normal number of digits. peter 2013-02-16T10:44:40Z UMLS:C3887496 human_phenotype HP:0012165 Oligodactyly A developmental defect resulting in the presence of fewer than the normal number of digits. HPO:probinson Any structural anomaly of the kidney. peter 2013-03-14T07:41:11Z HP:0000792 HP:0004726 HP:0004735 HP:0008712 Fyler:4512 SNOMEDCT_US:44513007 UMLS:C0266292 Abnormal kidney morphology Abnormally shaped kidney Kidney malformation Kidney structure issue Renal malformation Structural anomalies of the renal tract Structural kidney abnormalities Structural renal anomalies human_phenotype HP:0012210 Abnormal renal morphology Any structural anomaly of the kidney. HPO:probinson Abnormal kidney morphology ORCID:0000-0001-5208-3432 Abnormally shaped kidney ORCID:0000-0001-5208-3432 Kidney malformation Kidney structure issue Structural kidney abnormalities An abnormal functionality of the kidney. peter 2013-03-14T07:43:34Z HP:0000082 HP:0000087 HP:0005566 HP:0008646 SNOMEDCT_US:39539005 UMLS:C0151746 Abnormal kidney function Abnormal renal function Abnormality of renal physiology Kidney function issue Renal functional abnormality human_phenotype HP:0012211 Abnormal renal physiology An abnormal functionality of the kidney. HPO:probinson Abnormal kidney function ORCID:0000-0001-5208-3432 Abnormal renal function HPO:skoehler Kidney function issue A structural or developmental anomaly of any of the tissues involved in the genital system. peter 2013-04-02T07:02:20Z UMLS:C4021096 Abnormal genital system morphology human_phenotype HP:0012243 Abnormal reproductive system morphology A structural or developmental anomaly of any of the tissues involved in the genital system. HPO:probinson MP:0002160 A structural anomaly of the respiratory system. peter 2013-04-07T09:11:09Z Fyler:4235 UMLS:C4022992 human_phenotype HP:0012252 Abnormal respiratory system morphology A structural anomaly of the respiratory system. HPO:probinson Any structural anomaly of the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi. peter 2013-04-07T09:12:48Z UMLS:C4022991 human_phenotype HP:0012253 Abnormal respiratory epithelium morphology Any structural anomaly of the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi. HPO:probinson MP:0010942 An abnormally reduced concentration of glycine in the blood. peter 2013-04-07T03:54:41Z UMLS:C4022973 Low blood glycine levels human_phenotype HP:0012277 Hypoglycinemia An abnormally reduced concentration of glycine in the blood. HPO:probinson Low blood glycine levels ORCID:0000-0001-5208-3432 Any deviation from the normal concentration of serine in the blood circulation. peter 2013-04-07T03:57:10Z UMLS:C4022972 human_phenotype HP:0012278 Abnormal circulating serine concentration Any deviation from the normal concentration of serine in the blood circulation. HPO:probinson Reduced concentration of serine in the blood. peter 2013-04-07T03:57:25Z UMLS:C4022971 Low blood serine levels human_phenotype HP:0012279 Hyposerinemia Reduced concentration of serine in the blood. HPO:probinson Low blood serine levels ORCID:0000-0001-5208-3432 An abnormal functionality of the hypothalamus. peter 2013-04-09T07:51:07Z UMLS:C4022968 human_phenotype HP:0012285 The hypothalamus is linked vascularly with the anterior lobe of the pituitary gland and thereby controls the secretion of pituitary hormones. Abnormal hypothalamus physiology An abnormal functionality of the hypothalamus. HPO:probinson Any structural anomaly of the hypothalamus. peter 2013-04-09T07:53:16Z HP:0002443 UMLS:C4021095 Abnormal shape of hypothalamus Abnormality of hypothalamus morphology Abnormality of the hypothalamus human_phenotype HP:0012286 The hypothalamus is a cone-shaped cerebral structure that projects downward, ending in the pituitary (infundibular) stalk, a tubular connection to the pituitary gland. It is linked vascularly with the anterior lobe of the pituitary gland and thereby controls the secretion of pituitary hormones. Abnormal hypothalamus morphology Any structural anomaly of the hypothalamus. HPO:probinson Abnormal shape of hypothalamus ORCID:0000-0001-5208-3432 An abnormal pigmentation pattern of the external genitalia. peter 2013-04-11T06:02:08Z UMLS:C4022965 human_phenotype HP:0012293 Abnormal genital pigmentation An abnormal pigmentation pattern of the external genitalia. HPO:probinson Abnormality of the occipital bone of the skull. peter 2013-04-11T06:21:12Z UMLS:C4022964 human_phenotype HP:0012294 Abnormality of the occipital bone Abnormality of the occipital bone of the skull. HPO:probinson Increased length of the middle phalanx of finger. peter 2013-04-12T05:46:43Z UMLS:C4022960 Long middle bone of finger human_phenotype HP:0012298 Long middle phalanx of finger Increased length of the middle phalanx of finger. HPO:probinson Long middle bone of finger ORCID:0000-0001-5208-3432 Increased length of the distal phalanx of finger. peter 2013-04-12T05:48:52Z UMLS:C4021865 Long outermost bone of finger human_phenotype HP:0012299 Long distal phalanx of finger Increased length of the distal phalanx of finger. HPO:probinson Long outermost bone of finger ORCID:0000-0001-5208-3432 An anomaly of the process of rib bone formation. peter 2013-08-10T09:31:03Z UMLS:C4022957 human_phenotype Abnormal maturation of rib bones HP:0012306 Abnormal rib ossification An anomaly of the process of rib bone formation. HPO:probinson Abnormal maturation of rib bones ORCID:0000-0001-5208-3432 Lack of skin pigmentation (coloring) of the abdomen. peter 2013-08-10T08:21:54Z UMLS:C4022956 human_phenotype HP:0012319 Absent pigmentation of the abdomen Lack of skin pigmentation (coloring) of the abdomen. HPO:probinson Lack of skin pigmentation (coloring) of the arms and legs. peter 2013-08-10T08:22:30Z UMLS:C4022955 human_phenotype HP:0012320 Absent pigmentation of the limbs Lack of skin pigmentation (coloring) of the arms and legs. HPO:probinson An anomaly of the celiac artery. peter 2013-08-12T08:47:21Z UMLS:C4022954 Abnormal coeliac artery morphology Abnormality of the celiac artery human_phenotype HP:0012326 The celiac artery (celiac trunk or truncus coeliacus) is the first major branch of the abdominal aorta. Abnormal celiac artery morphology An anomaly of the celiac artery. HPO:probinson Abnormal coeliac artery morphology A structural abnormality of the autonomic nervous system. peter 2013-09-13T07:52:31Z UMLS:C4022953 human_phenotype HP:0012331 Abnormal autonomic nervous system morphology A structural abnormality of the autonomic nervous system. HPO:probinson A functional abnormality of the autonomic nervous system. peter 2013-09-13T07:53:55Z HP:0002271 HP:0002387 HP:0002459 HP:0007310 UMLS:C4022952 Autonomic dysfunction Autonomic dysregulation Dysautonomia human_phenotype HP:0012332 Abnormal autonomic nervous system physiology A functional abnormality of the autonomic nervous system. HPO:probinson An abnormality of the metabolism of folic acid, which is also known as vitamin B9. peter 2013-09-13T08:38:06Z UMLS:C4022951 human_phenotype HP:0012335 Abnormality of folate metabolism An abnormality of the metabolism of folic acid, which is also known as vitamin B9. HPO:probinson An anomaly in the processes involved in the maintenance of an internal equilibrium. peter 2013-09-13T09:23:23Z MP:0001764 UMLS:C4022950 human_phenotype HP:0012337 Abnormal homeostasis An anomaly in the processes involved in the maintenance of an internal equilibrium. HPO:probinson MP:0001764 Abnormal homeostasis A decreased concentration of potassium(1+) in the urine. peter 2013-10-03T10:21:51Z SNOMEDCT_US:54781007 UMLS:C0268024 Decreased urinary K Hypokaluria Low urine potassium levels human_phenotype HP:0012364 Decreased urinary potassium A decreased concentration of potassium(1+) in the urine. HPO:probinson Decreased urinary K Low urine potassium levels ORCID:0000-0001-5208-3432 An abnormally decreased phosphate concentration in the urine. peter 2013-10-03T10:25:06Z SNOMEDCT_US:91632005 UMLS:C0268077 Low urine phosphate levels human_phenotype HP:0012365 Hypophosphaturia An abnormally decreased phosphate concentration in the urine. HPO:probinson Low urine phosphate levels ORCID:0000-0001-5208-3432 A structural anomaly of the globe of the eye, or bulbus oculi. peter 2013-10-13T03:44:43Z HP:0000489 HP:0012374 Fyler:4863 UMLS:C4022925 Abnormal eye structure Abnormality of the globe Abnormally shaped eye HP:0012372 previously: Abnormal globe morphology Abnormal eye morphology A structural anomaly of the globe of the eye, or bulbus oculi. HPO:probinson Abnormal eye structure Abnormally shaped eye ORCID:0000-0001-5208-3432 A functional anomaly of the eye. peter 2013-10-13T03:45:37Z UMLS:C4022924 Abnormal eye physiology human_phenotype HP:0012373 Abnormal eye physiology A functional anomaly of the eye. HPO:probinson Abnormal eye physiology An altered ability of any enzyme or their cofactors to act as catalysts. This term includes changes due to altered levels of an enzyme. peter 2013-10-15T08:58:55Z UMLS:C4022922 human_phenotype HP:0012379 Abnormal enzyme/coenzyme activity An altered ability of any enzyme or their cofactors to act as catalysts. This term includes changes due to altered levels of an enzyme. HPO:probinson MP:0005584 The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers or toes cannot be extended to 180 degrees by either active or passive extension. hecht 2013-10-20T08:08:19Z SNOMEDCT_US:29271008 UMLS:C0685409 Permanent flexion of the finger or toe human_phenotype HP:0012385 Camptodactyly The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers or toes cannot be extended to 180 degrees by either active or passive extension. HPO:probinson Permanent flexion of the finger or toe orcid.org/0000-0002-6548-5200 An abnormality of the partial pressure of oxygen or carbon dioxide in the arterial blood. peter 2013-11-10T04:59:20Z SNOMEDCT_US:312391003 UMLS:C0476337 Abnormal blood gas level human_phenotype HP:0012415 Abnormal blood gas level An abnormality of the partial pressure of oxygen or carbon dioxide in the arterial blood. HPO:probinson Abnormal blood gas level An inflammation of the choroid and retina. peter 2013-11-11T08:10:29Z MSH:D002825 SNOMEDCT_US:46627006 UMLS:C0008513 human_phenotype HP:0012424 Chorioretinitis is a form of posterior uveitis. Note that the term Chorioretinitis suggests that the origin of the process is predominantly in the choroid while Retinitis suggests that the process is mainly in the retina. Chorioretinitis An inflammation of the choroid and retina. ORCID:0000-0001-5208-3432 PMID:16196117 A structural anomaly of the gallbladder. peter 2013-11-23T01:13:40Z UMLS:C4022904 Abnormal gallbladder structure Abnormal shape of gallbladder HP:0012437 Abnormal gallbladder morphology A structural anomaly of the gallbladder. HPO:probinson Abnormal gallbladder structure Abnormal shape of gallbladder ORCID:0000-0001-5208-3432 A functional anomaly of the gallbladder. peter 2013-11-23T01:17:00Z UMLS:C4022903 human_phenotype HP:0012438 Abnormal gallbladder physiology A functional anomaly of the gallbladder. HPO:probinson A functional abnormality of the biliary tree. peter 2013-11-23T02:14:51Z UMLS:C4022902 human_phenotype HP:0012439 Abnormal biliary tract physiology A functional abnormality of the biliary tree. HPO:probinson A structural abnormality of the biliary tree. peter 2013-11-23T02:15:33Z UMLS:C4021086 Anomaly of the biliary tract human_phenotype HP:0012440 Abnormal biliary tract morphology A structural abnormality of the biliary tree. HPO:probinson A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain. peter 2013-11-23T02:38:00Z UMLS:C4021085 Abnormal shape of brain Abnormality of the brain human_phenotype HP:0012443 Abnormality of brain morphology A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain. HPO:probinson Abnormal shape of brain ORCID:0000-0001-5208-3432 Abnormality of the brain An increased level of iron in liver tissues. peter 2013-11-24T12:54:57Z UMLS:C4022891 Increased iron concentration in liver Increased liver iron level human_phenotype HP:0012465 This abnormality can be measured by liver biopsy or by hepatic magnetic resonance imaging. Elevated hepatic iron concentration An increased level of iron in liver tissues. HPO:probinson PMID:10922422 PMID:14668426 Increased iron concentration in liver ORCID:0000-0001-5208-3432 Increased liver iron level HPO:skoehler An anomaly of cerebral veins. peter 2013-11-28T08:01:32Z UMLS:C4022888 human_phenotype HP:0012480 Abnormality of cerebral veins An anomaly of cerebral veins. HPO:probinson Inflammation of the spinal cord. peter 2013-11-29T08:10:12Z MSH:D009187 SNOMEDCT_US:41370002 UMLS:C0026975 Inflammation of spinal cord human_phenotype HP:0012486 Myelitis Inflammation of the spinal cord. HPO:probinson Inflammation of spinal cord ORCID:0000-0001-5208-3432 Inflammation of adipose tissue. peter 2013-11-29T09:28:11Z MSH:D015434 SNOMEDCT_US:22125009 UMLS:C0030326 Inflammation of adipose tissue Inflammation of fat tissue human_phenotype HP:0012490 Panniculitis most commonly affects the skin and characterized by reddened subcutaneous nodules. Panniculitis Inflammation of adipose tissue. HPO:probinson Inflammation of adipose tissue ORCID:0000-0001-5208-3432 Inflammation of fat tissue ORCID:0000-0001-5208-3432 An anomaly of the pituitary gland. peter 2013-11-30T09:34:21Z MSH:D010900 SNOMEDCT_US:399244003 UMLS:C0032002 disorder of pituitary gland human_phenotype HP:0012503 Abnormality of the pituitary gland An anomaly of the pituitary gland. HPO:probinson A deviation from the normal size of the pituitary gland. peter 2013-11-30T09:36:04Z UMLS:C4022874 human_phenotype HP:0012504 Abnormal size of pituitary gland A deviation from the normal size of the pituitary gland. HPO:probinson An abnormally increased size of the pituitary gland. peter 2013-11-30T09:36:45Z SNOMEDCT_US:237718009 UMLS:C0342422 human_phenotype HP:0012505 Enlarged pituitary gland An abnormally increased size of the pituitary gland. ORCID:0000-0001-5208-3432 An abnormally decreased size of the pituitary gland. peter 2013-11-30T09:37:34Z UMLS:C4022873 human_phenotype HP:0012506 Small pituitary gland An abnormally decreased size of the pituitary gland. ORCID:0000-0001-5208-3432 An anomaly of the circle of Willis, also known as the cerebral arterial circle. peter 2013-12-09T07:03:02Z UMLS:C4022868 Abnormality of the cerebral arterial circle human_phenotype HP:0012518 The circle of Willis is a circulatory anastomosis in the brain comprised of the anterior cerebral arteries, the anterior communicating artery, the internal carotid arteries, the posterior cerebral arteries, and the posterior communicating arteries. Abnormal circle of Willis morphology An anomaly of the circle of Willis, also known as the cerebral arterial circle. HPO:probinson Abnormality of the cerebral arterial circle ORCID:0000-0001-6908-9849 A structural anomaly of the nephron. peter 2014-01-16T12:49:04Z UMLS:C4022838 Abnormality of the nephron human_phenotype HP:0012575 Abnormal nephron morphology A structural anomaly of the nephron. Eurenomics:fschaefer An abnormality in the concentration of electrolytes in the urine. peter 2014-01-16T05:44:11Z UMLS:C4022833 Urinary electrolyte imbalance HP:0012591 Abnormal urinary electrolyte concentration An abnormality in the concentration of electrolytes in the urine. PMID:25215103 An abnormal concentration of potassium(1+) in the urine. peter 2014-01-16T06:11:59Z UMLS:C4022829 Abnormal urine K concentration HP:0012598 Abnormal urine potassium concentration An abnormal concentration of potassium(1+) in the urine. Eurenomics:fschaefer Abnormal urine K concentration An abnormal phosphate concentration in the urine. peter 2014-01-16T06:14:49Z UMLS:C4022828 HP:0012599 Abnormal urine phosphate concentration An abnormal phosphate concentration in the urine. Eurenomics:ewuehl An abnormal concentration of sodium in the urine. peter 2014-01-16T06:19:27Z UMLS:C4022825 Abnormal urine Na concentration Abnormal urine Na+ levels human_phenotype HP:0012603 Abnormal urine sodium concentration An abnormal concentration of sodium in the urine. Eurenomics:fschaefer An abnormally decreased sodium concentration in the urine. peter 2014-01-16T06:22:09Z UMLS:C4022824 Low urine sodium levels human_phenotype HP:0012604 Hyponatriuria An abnormally decreased sodium concentration in the urine. Eurenomics:ewuehl Low urine sodium levels ORCID:0000-0001-5208-3432 An increased concentration of sodium(1+) in the urine. peter 2014-01-16T06:22:44Z HP:0003608 UMLS:C3671887 Increased urinary sodium human_phenotype HP:0012605 Hypernatriuria An increased concentration of sodium(1+) in the urine. Eurenomics:ewuehl An abnormal concentration of magnesium the urine. peter 2014-01-17T11:37:50Z UMLS:C4022823 Abnormal urine magnesium concentration HP:0012607 Abnormal urine magnesium concentration An abnormal concentration of magnesium the urine. Eurenomics:ewuehl Abnormal urine magnesium concentration An increased concentration of magnesium the urine. peter 2014-01-17T11:38:51Z UMLS:C2673443 human_phenotype HP:0012608 Hypermagnesiuria An increased concentration of magnesium the urine. Eurenomics:fschaefer An decreased concentration of magnesium the urine. peter 2014-01-17T11:39:31Z UMLS:C3203528 Decreased urine magnesium Low urine magnesium levels human_phenotype HP:0012609 Hypomagnesiuria An decreased concentration of magnesium the urine. Eurenomics:fschaefer Decreased urine magnesium Low urine magnesium levels ORCID:0000-0001-5208-3432 An anomalous finding in the examination of the urine for cells. peter 2014-01-17T12:01:16Z SNOMEDCT_US:310439007 UMLS:C0587955 human_phenotype HP:0012614 Abnormal urine cytology An anomalous finding in the examination of the urine for cells. Eurenomics:ewuehl A developmental anomaly associated with the failure of rectum, vagina, and bladder to separate. peter 2014-01-17T12:27:06Z UMLS:C4022816 human_phenotype HP:0012620 Cloacal abnormality A developmental anomaly associated with the failure of rectum, vagina, and bladder to separate. HPO:probinson A functional anomaly of the nervous system. peter 2014-01-19T08:02:46Z UMLS:C4022811 Abnormality of nervous system physiology human_phenotype HP:0012638 Abnormal nervous system physiology A functional anomaly of the nervous system. HPO:probinson A structural anomaly of the nervous system. peter 2014-01-19T08:03:08Z Fyler:4135 Fyler:4300 UMLS:C4022810 Abnormal nervous system morphology Abnormal shape of nervous system Abnormality of nervous system morphology human_phenotype HP:0012639 Abnormal nervous system morphology A structural anomaly of the nervous system. HPO:probinson Abnormal nervous system morphology ORCID:0000-0001-5208-3432 Abnormal shape of nervous system ORCID:0000-0001-5208-3432 Increase in size of a peripheral nerve. This finding can be appreciated by palpation along the axis of the nerve. peter 2014-02-01T12:44:16Z UMLS:C2675074 human_phenotype Enlarged peripheral nerves HP:0012645 This feature can be appreciated by imaging studies (magnetic resonancy tomography), by palpation along the axis of a nerve, and by biopsy, and may be caused by axonal swelling or by myelin thickening. The differential diagnosis of enlarged peripheral nerves includes leprosy, hereditary motor and sensory neuropathy type 1 (about 30% of patients), but not type 2 (the axonal form), some other polyneuropathies, neurofibromatosis, and nerve tumors. A good review is available in Practical Neurology, 2003,3:40-45 by Michael Donaghy (no pubmed id). Enlarged peripheral nerve Increase in size of a peripheral nerve. This finding can be appreciated by palpation along the axis of the nerve. HPO:probinson Enlarged peripheral nerves HPO:skoehler Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. peter 2014-02-01T01:25:42Z UMLS:C4022805 Abnormal inflammatory response human_phenotype HP:0012647 Abnormal inflammatory response Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. MONARCH:mhaendel Abnormal inflammatory response An abnormal reduction in the inflammatory response to injury or infection. peter 2014-02-01T01:29:24Z UMLS:C4022804 Decreased inflammatory response human_phenotype HP:0012648 Decreased inflammatory response An abnormal reduction in the inflammatory response to injury or infection. MONARCH:mhaendel Decreased inflammatory response A abnormal increase in the inflammatory response to injury or infection. peter 2014-02-01T01:29:58Z UMLS:C4022803 human_phenotype HP:0012649 Increased inflammatory response A abnormal increase in the inflammatory response to injury or infection. MONARCH:mhaendel An abnormal build up of iron (Fe) in brain tissue. hecht 2014-03-13T07:22:40Z UMLS:C4021076 Brain iron deposition Iron accumulation in brain human_phenotype HP:0012675 Iron accumulation in brain An abnormal build up of iron (Fe) in brain tissue. HPO:probinson Iron accumulation in brain An anomaly of the pineal gland,a small endocrine gland in the brain that produces melatonin. peter 2014-03-22T12:46:36Z UMLS:C4022783 human_phenotype HP:0012680 Abnormality of the pineal gland An anomaly of the pineal gland,a small endocrine gland in the brain that produces melatonin. HPO:probinson A structural abnormality of the pineal gland. peter 2014-03-22T12:50:21Z UMLS:C4022782 human_phenotype HP:0012681 The pineal gland typically measures 7 x 6 x 3mm in size and is located in a groove between the laterally placed thalamic bodies. Abnormality of pineal morphology A structural abnormality of the pineal gland. UToronto:htrang Accumulation of calcium salts in the pineal gland. peter 2014-03-22T12:51:57Z UMLS:C1398718 human_phenotype HP:0012682 This feature can be appreciated on skull radiography. Pineal gland calcification Accumulation of calcium salts in the pineal gland. HPO:probinson An abnormal increase or decrease in the quantity of three-dimensional space taken up by the pineal gland. peter 2014-03-22T01:08:48Z UMLS:C4022781 human_phenotype HP:0012684 This feature is typically assessed by magnetic resonance tomography of the brain. Abnormal pineal volume An abnormal increase or decrease in the quantity of three-dimensional space taken up by the pineal gland. UToronto:htrang An abnormal reduction in the quantity of three-dimensional space taken up by the pineal gland. peter 2014-03-22T01:10:12Z UMLS:C4022780 human_phenotype HP:0012685 Decreased pineal volume An abnormal reduction in the quantity of three-dimensional space taken up by the pineal gland. PMID:24456088 UToronto:htrang An abnormal elevation in the quantity of three-dimensional space taken up by the pineal gland. peter 2014-03-22T01:11:33Z UMLS:C4022779 human_phenotype HP:0012686 Increased pineal volume An abnormal elevation in the quantity of three-dimensional space taken up by the pineal gland. UToronto:htrang A functional abnormality of the pineal gland. peter 2014-03-22T01:15:36Z UMLS:C4022778 human_phenotype HP:0012688 Abnormality of pineal physiology A functional abnormality of the pineal gland. UToronto:htrang A structural abnormality of a diaphysis of the leg. peter 2014-03-22T06:14:15Z UMLS:C4022767 Anomaly of shaft of long bone of lower limb human_phenotype HP:0012699 Anomaly of lower limb diaphyses A structural abnormality of a diaphysis of the leg. UToronto:htrang Anomaly of shaft of long bone of lower limb ORCID:0000-0001-5208-3432 A functional anomaly of the large intestine. peter 2014-03-22T06:20:38Z UMLS:C4022766 human_phenotype HP:0012700 Abnormal large intestine physiology A functional anomaly of the large intestine. HPO:probinson Abnormality in the space in the meninges beneath the arachnoid membrane and above the pia mater that contains the cerebrospinal fluid. peter 2014-03-22T07:45:24Z UMLS:C4022765 Abnormality of the subarachnoid space human_phenotype HP:0012703 Abnormal subarachnoid space morphology Abnormality in the space in the meninges beneath the arachnoid membrane and above the pia mater that contains the cerebrospinal fluid. UToronto:htrang Abnormal structure of the gastrointestinal tract. peter 2014-03-23T01:09:02Z UMLS:C4021073 Abnormal shape of the digestive system Morphological abnormality of the GI tract Morphological anomaly of the digestive system human_phenotype HP:0012718 Morphological abnormality of the gastrointestinal tract Abnormal structure of the gastrointestinal tract. HPO:probinson Abnormal shape of the digestive system ORCID:0000-0001-5208-3432 Morphological abnormality of the GI tract Abnormal functionality of the gastrointestinal tract. peter 2014-03-23T01:10:47Z UMLS:C4022755 Functional abnormality of the GI tract GI dysfunction human_phenotype HP:0012719 Functional abnormality of the gastrointestinal tract Abnormal functionality of the gastrointestinal tract. HPO:probinson Functional abnormality of the GI tract GI dysfunction https://orcid.org/0000-0001-5208-3432 A vascular malformation resulting from a developmental error of venous tissue composed of dysmorphic channels lined by flattened endothelium and exhibiting slow turnover. A venous malformation may present as a blue patch on the skin ranging to a soft blue mass. Venous malformations are easily compressible and usually swell in thewhen venous pressure increases (e.g., when held in a dependent position or when a child cries). They may be relatively localized or quite extensive within an anatomic region. peter 2014-03-23T01:20:33Z SNOMEDCT_US:297222002 UMLS:C2937220 Venous malformations human_phenotype HP:0012721 Venous malformations are always present at birth, and usually involve the skin of the face, limbs, or trunk. Venous malformation A vascular malformation resulting from a developmental error of venous tissue composed of dysmorphic channels lined by flattened endothelium and exhibiting slow turnover. A venous malformation may present as a blue patch on the skin ranging to a soft blue mass. Venous malformations are easily compressible and usually swell in thewhen venous pressure increases (e.g., when held in a dependent position or when a child cries). They may be relatively localized or quite extensive within an anatomic region. HPO:probinson Venous malformations HPO:skoehler An abnormality of the anus or rectum. peter 2014-03-23T02:48:00Z MSH:D000071056 SNOMEDCT_US:33225004 UMLS:C3495676 human_phenotype HP:0012732 Anorectal anomaly An abnormality of the anus or rectum. HPO:probinson Excessive fat around the stomach and abdomen. peter 2014-03-23T05:00:05Z MSH:D056128 SNOMEDCT_US:248311001 UMLS:C0311277 Abdominal obesity Central obesity human_phenotype HP:0012743 Abdominal obesity Excessive fat around the stomach and abdomen. HPO:probinson Abdominal obesity Central obesity HPO:skoehler Failure of the femur to develop. peter 2014-03-23T05:14:34Z SNOMEDCT_US:47276000 UMLS:C0265629 Absent femur Absent thighbone Aplasia of the femur human_phenotype HP:0012744 Femoral aplasia Failure of the femur to develop. HPO:probinson Absent thighbone ORCID:0000-0001-5208-3432 A deviation from normal size of the placenta. peter 2014-04-07T12:11:29Z UMLS:C4022732 human_phenotype HP:0012767 Abnormal placental size A deviation from normal size of the placenta. HPO:probinson A structural anomaly of the ciliary body. peter 2014-04-07T04:00:10Z UMLS:C4022726 Abnormality of the ciliary body human_phenotype HP:0012776 Abnormal ciliary body morphology A structural anomaly of the ciliary body. CINEAS:asollie Chronic loss of joint motion in a finger due to structural changes in non-bony tissue. peter 2014-04-20T04:09:34Z UMLS:C1857304 Flexion deformity of finger human_phenotype HP:0012785 Note that the term camptodactyly refers to a painless flexion contracture of the proximal interphalangeal (PIP) joint and not to a finger joint contracture in general. Flexion contracture of finger Chronic loss of joint motion in a finger due to structural changes in non-bony tissue. HPO:probinson An anomaly of the process of formation of bone in the humerus. peter 2014-04-24T10:23:43Z UMLS:C4022722 Abnormal maturation of long bone in upper arm human_phenotype HP:0012791 Abnormal humeral ossification An anomaly of the process of formation of bone in the humerus. HPO:probinson Abnormal maturation of long bone in upper arm ORCID:0000-0001-5208-3432 A lack of bone mineralization of one or more body of thoracic vertebra. peter 2014-04-24T11:05:14Z UMLS:C4022721 human_phenotype HP:0012792 Absent ossification of thoracic vertebral bodies HPO:skoehler A lack of bone mineralization of one or more body of thoracic vertebra. HPO:probinson Underdevelopment of part or all of the female external reproductive organs (which include the mons pubis, labia majora, labia minora, Bartholin glands, and clitoris). peter 2014-05-27T08:14:55Z UMLS:C4022715 Underdeveloped female external genitalia human_phenotype HP:0012815 Hypoplastic female external genitalia Underdevelopment of part or all of the female external reproductive organs (which include the mons pubis, labia majora, labia minora, Bartholin glands, and clitoris). HPO:probinson Underdeveloped female external genitalia ORCID:0000-0001-6908-9849 Inflammation of the myocardium. hecht 2014-05-28T09:01:32Z MSH:D009205 SNOMEDCT_US:50920009 UMLS:C0027059 Inflammation of heart muscle human_phenotype HP:0012819 Myocarditis can be caused by a variety of bacterial and viral infections. Enteroviruses, especially coxsackievirus B, are often associated with acute myocarditis. However, with the advent of genetic analysis, adenovirus and parvovirus B19 have also been found to be frequent causes of myocarditis. Exposure to drug treatment, physical stimuli such as radiation and heat, metabolic disorders, immune disorders, and pregnancy are also causes of myocarditis. Many cases of myocarditis are idiopathic. Myocarditis presents with non-specific symptoms including chest pain, dyspnoea, and palpitations, and thus often mimics more common disorders such as coronary artery disease. In some patients, cardiac MRI and endomyocardial biopsy can help identify myocarditis, predict risk of cardiovascular events, and guide treatment. Myocarditis Inflammation of the myocardium. HPO:probinson PMID:21304213 PMID:22185868 PMID:22361396 Inflammation of heart muscle https://orcid.org/0000-0002-6548-5200 Bleeding from the small intestine. hecht 2014-06-07T09:12:22Z SNOMEDCT_US:70375006 UMLS:C0520561 Small intestinal bleeding Small intestinal hemorrhage human_phenotype HP:0012849 Small intestinal bleeding Bleeding from the small intestine. HPO:probinson Small intestinal bleeding An abnormal functionality of the male genital system. hecht 2014-06-09T11:20:46Z UMLS:C4020716 human_phenotype Abnormal male genital system physiology HP:0012874 Abnormal male reproductive system physiology An abnormal functionality of the male genital system. HPO:probinson An anomaly of the neck of the uterus (lower part of the uterus), called the uterine cervix. hecht 2014-06-11T09:40:02Z UMLS:C4022694 human_phenotype HP:0012888 Abnormality of the uterine cervix An anomaly of the neck of the uterus (lower part of the uterus), called the uterine cervix. HPO:probinson Hypertrophy of one or more muscles innervated by the facial nerve (the seventh cranial nerve). peter 2014-06-23T10:58:42Z UMLS:C4022691 UMLS:C4280307 Increased size of facial muscles Large facial muscles human_phenotype Hyperplasia of facial muscles HP:0012892 Facial muscle hypertrophy Hypertrophy of one or more muscles innervated by the facial nerve (the seventh cranial nerve). UToronto:htrang Increased size of facial muscles ORCID:0000-0001-5889-4463 Large facial muscles ORCID:0000-0001-5889-4463 Hyperplasia of facial muscles ORCID:0000-0001-5889-4463 Muscle hypertrophy affecting the muscles of the neck. peter 2014-06-23T10:59:17Z Increased size of neck muscles UMLS:C4022690 UMLS:C4280306 Hypertrophy of cervical muscles Large neck muscles Overgrowth of neck muscles human_phenotype Hyperplasia of neck muscles HP:0012893 Neck muscle hypertrophy Muscle hypertrophy affecting the muscles of the neck. UToronto:htrang Increased size of neck muscles ORCID:0000-0001-5889-4463 Hypertrophy of cervical muscles ORCID:0000-0001-5889-4463 Large neck muscles ORCID:0000-0001-5889-4463 Overgrowth of neck muscles ORCID:0000-0001-5889-4463 Hyperplasia of neck muscles ORCID:0000-0001-5889-4463 Muscle hypertrophy affecting the scapular muscles. peter 2014-06-23T11:00:11Z UMLS:C4022688 human_phenotype HP:0012895 Scapular muscle hypertrophy Muscle hypertrophy affecting the scapular muscles. UToronto:htrang A coloboma of the ciliary body. UMLS:C4072884 Ciliary body coloboma 2016-08-12T11:24:56Z HPO:probinson Abnormal vascular morphology A structural anomaly of the tiny blood vessels that connect arterioles with venules and whose walls act as semipermeable membranes that mediate the diffusion of fluids and gases between the blood circulation and body tissues. 2016-08-12T11:42:27Z HPO:probinson Abnormal capillary morphology A functional anomaly of the tiny blood vessels that connect arterioles with venules and whose walls act as semipermeable membranes that mediate the diffusion of fluids and gases between the blood circulation and body tissues. 2016-08-12T11:56:48Z HPO:probinson Abnormal capillary physiology 2016-08-27T13:44:32Z HPO:probinson Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus. Abnormality of the digestive system A functional anomaly of the digestive system. 2016-08-27T13:58:05Z HPO:probinson Abnormality of digestive system physiology A structural anomaly of the digestive system. 2016-08-27T13:58:23Z HPO:probinson Abnormality of digestive system morphology A collection of pus within a testicle. Ultrasonographic features include shaggy, irregular walls, intratesticular location, low-level internal echoes, and occasionally, hypervascular margins. 2016-09-21T11:02:09Z HPO:probinson Testicular abscess Intratesticular abscess A collection of pus within a testicle. Ultrasonographic features include shaggy, irregular walls, intratesticular location, low-level internal echoes, and occasionally, hypervascular margins. PMID:11598263 A circumscribed area of pus or necrotic debris in lung parenchyma, which leads to a cavity, and after formation of bronchopulmonary fistula, can manifest as an air-fluid level inside the cavity. 2016-09-25T14:30:50Z HPO:probinson Lung abscess A circumscribed area of pus or necrotic debris in lung parenchyma, which leads to a cavity, and after formation of bronchopulmonary fistula, can manifest as an air-fluid level inside the cavity. PMID:26366400 A circumscribed area of pus or necrotic debris in the parenchyma of the spleen. 2016-09-26T09:11:25Z HPO:probinson Splenic abscesses generally occur in patients with neoplasia, immunodeficiency, trauma, metastatic infection, splenic infarct or diabetes. Splenic abscess A circumscribed area of pus or necrotic debris in the parenchyma of the spleen. PMID:21319348 A circumscribed area of pus or necrotic debris in the parenchyma of the pancreas. 2016-09-26T11:01:28Z HPO:probinson Pancreas abscess Pancreatic abscess Passage of many stools containing blood. 2016-10-15T13:58:14Z HPO:probinson Blood in stool Bloody stool Bloody bowel movement Bloody diarrhea Bloody diarrhoea Diarrhea that contains bright red or maroon-colored blood may be referred to as hematochezia, while melena is used to describe black, tarry, and smelly diarrhea. Bloody diarrhea Blood in stool Bloody stool Bloody bowel movement Bloody diarrhea Bloody diarrhoea Structural abnormality of the hypothalamus related to defective development. 2016-10-28T06:41:35Z HPO:probinson Hypothalamic dysgenesis Note that the term hypothalamic dysgenesis is generally used to refer to a morphological abnormality of the hypothalamus that is of presumed developmental (rather than acquired) origin. Dysgenesis of the hypothalamus A functional anomaly of the hepatobiliary system 2016-12-04T12:05:04Z HPO:probinson Abnormality of hepatobiliary system physiology A hollow mass located in the skin that is surrounded by an epithelium-lined wall and is well demarcated from the adjacent tissue. Cysts are often said to be sac-like and may contain serous liquid or semisolid material. 2016-12-17T13:11:37Z HPO:probinson In contrast to cysts, vesicles, pustules and bullae do not have a complete epithelial lining and are therefore less well demarcated. Cutaneous cyst Any physiological abnormality of the esophagus. 2016-12-18T13:39:06Z HPO:probinson Abnormality of oesophagus physiology Functional abnormality of the esophagus Abnormality of esophagus physiology Abnormality of oesophagus physiology An anomaly of arterial function. 2017-02-03T12:08:38Z HPO:probinson Abnormal arterial physiology An anomaly of the margin of the cornea overlapped by the sclera. 2017-02-12T23:58:19Z HPO:probinson Abnormality of the corneal limbus An anomaly of cellular morphology or physiology. 2017-02-13T00:29:35Z HPO:probinson Abnormal cellular phenotype Any anomaly of the structure of the spleen. 2017-04-23T10:55:52Z HPO:probinson Abnormal spleen morphology Any anomaly of the function of the spleen. 2017-04-23T10:56:59Z HPO:probinson Abnormal spleen physiology Any anomaly of the structure of the larynx. 2017-04-23T12:44:49Z HPO:probinson Abnormal larynx morphology Any anomaly of the function of the larynx. 2017-04-23T12:46:36Z HPO:probinson Abnormal larynx physiology Any anomaly of the morphology of the bronchi. 2017-04-23T12:50:43Z HPO:probinson HP:0002109 Abnormality of the bronchi Abnormal bronchus morphology Any anomaly of the function of the bronchi. 2017-04-23T12:51:32Z HPO:probinson Abnormal bronchus physiology Inflammation (due to infection or irritation) of the pharynx. 2017-04-24T00:03:24Z HPO:probinson Pharyngitis Any deviation from the normal range of concentration of a metabolite in the cerebrospinal fluid. 2017-05-05T10:24:32Z HPO:probinson Abnormal CSF metabolite level Any anomaly of cell structure. 2017-05-07T11:14:54Z HPO:probinson Abnormal cell morphology Any structural anomaly of the bladder. 2017-05-14T17:07:03Z HPO:probinson Abnormality of bladder morphology A congenital anomaly characterized by the presence of two bladders. 2017-05-14T17:16:59Z HPO:probinson Bladder duplication A congenital anomaly characterized by the presence of two bladders. PMID:25657554 Any structural anomaly of the principal vein draining blood from the upper portion of the body and delivering it to the right ventricle of the heart. 2017-12-15T23:00:56Z HPO:probinson Fyler:2820 Abnormal superior vena cava morphology Any structural anomaly of the principal vein draining blood from the upper portion of the body and delivering it to the right ventricle of the heart. MP:0006064 Any structural anomaly of the principal vein draining blood from the lower portion of the body. 2017-12-15T23:02:17Z HPO:probinson Fyler:2810 Abnormal inferior vena cava morphology Any structural anomaly of the principal vein draining blood from the lower portion of the body. MP:0006063 Any structural abnormality of the left atrium. 2017-12-15T23:54:09Z HPO:probinson Fyler:3010 Abnormal left atrium morphology Any structural abnormality of the right atrium. 2017-12-15T23:56:01Z HPO:probinson Fyler:1770 Abnormal right atrium morphology 2019-04-08T22:41:54Z HPO:probinson Abscess A structural abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder. 2019-04-26T17:40:47Z HPO:probinson Abnormal ureter morphology A functional abnormality of the ureter. The ureter is the duct by which urine passes from the kidney to the bladder. 2019-04-26T17:43:08Z HPO:probinson Abnormal ureter physiology Congenital absence of the cervix. SNOMEDCT_US:37687000 UMLS:C0266404 Absent cervix Aplasia of the cervix Cervical aplasia Cervical agenesis Absent cervix ORCID:0000-0001-5208-3432 UMLS:C4020714 UMLS:C4022678 Abnormal female reproductive system physiology Abnormal female genital system physiology Abnormal female reproductive system physiology Abnormal female reproductive system physiology Abnormal female genital system physiology Incomplete duplication of the ureter. UMLS:C3887498 Bifid ureter Incomplete duplication of the ureter. PMID:23513084 A bent (flexed) finger or toe joint that cannot be straightened actively or passively. It is thus a chronic loss of joint motion due to structural changes in muscle, tendons, ligaments, or skin that prevents normal movement of joints. UMLS:C1839864 Flexion contracture of digit A collection of pus, immune cells, and other material in the brain. MSH:D001922 SNOMEDCT_US:441806004 UMLS:C0006105 Brain abscess Brain abscess usually results from a bacterial or fungal infection. Brain abscess Brain abscess An anomaly of the inner mucous membrane of the uterus. UMLS:C4022620 Abnormality of the endometrium An anomaly of the inner mucous membrane of the uterus. HPO:probinson A structural anomaly of the liver located predominantly in the hepatocytes as opposed to stromal cells. UMLS:C4022605 Abnormal liver parenchyma morphology A structural anomaly of the liver located predominantly in the hepatocytes as opposed to stromal cells. HPO:probinson PMID:11157536 Inflammation of the biliary ductal system, affecting the intrahepatic or extrahepatic portions, or both. MSH:D002761 SNOMEDCT_US:82403002 UMLS:C0008311 Bile duct inflammation Cholangitis is characterized by biliary epithelial damage with inflammatory cell infiltration. Some cholangitis is also associated with ductal and periductal fibrosis. Cholangitis Inflammation of the biliary ductal system, affecting the intrahepatic or extrahepatic portions, or both. HPO:probinson PMID:21994886 Bile duct inflammation Abnormality of vascular function. UMLS:C4022603 Abnormal vascular physiology Abnormality of vascular function. HPO:probinson Abnormalities of the overall muscle bulk based on clinical observation. UMLS:C4022563 Abnormality of muscle size Abnormality of muscle size Abnormalities of the overall muscle bulk based on clinical observation. Neuromics:vstraub Abnormality of muscle size Thrombosis of the portal vein and/or its tributaries, which include the splenic vein and the superior and inferior mesenteric veins. SNOMEDCT_US:17920008 UMLS:C0155773 Blood clot in portal vein Portal vein thrombosis (PVT) can occur within the main portal vein, or it can occur in the branches of the portal vein within the liver itself. It can be an occluding thrombus or nonoccluding, with a clot present but continued blood flow through the vessel. The sequela of a long-standing PVT is cavernous formation of the portal vein, which represents bridging collaterals around the occlusion. Portal vein thrombosis Thrombosis of the portal vein and/or its tributaries, which include the splenic vein and the superior and inferior mesenteric veins. HPO:probinson PMID:21960890 Blood clot in portal vein ORCID:0000-0001-6908-9849 An obstruction in the veins of the liver caused by a blood clot (thrombosis). MSH:D006502 SNOMEDCT_US:38739001 UMLS:C0019154 Blood clot in liver vein Hepatic venous thrombosis Hepatic vein thrombosis An obstruction in the veins of the liver caused by a blood clot (thrombosis). HPO:probinson Blood clot in liver vein ORCID:0000-0001-5208-3432 The term splanchnic vein thrombosis encompasses Budd-Chiari syndrome (hepatic vein thrombosis), extrahepatic portal vein obstruction (EHPVO), and mesenteric vein thrombosis; the word splanchnic is used to refer to the visceral organs (of the abdominal cavity). UMLS:C4022560 Blood clot in splanchnic vein Splanchnic vein thrombosis The term splanchnic vein thrombosis encompasses Budd-Chiari syndrome (hepatic vein thrombosis), extrahepatic portal vein obstruction (EHPVO), and mesenteric vein thrombosis; the word splanchnic is used to refer to the visceral organs (of the abdominal cavity). HPO:probinson PMID:20532730 Blood clot in splanchnic vein ORCID:0000-0001-6908-9849 Lack of recognizable penile structures. HP:0040316 SNOMEDCT_US:204908001 SNOMEDCT_US:59981001 UMLS:C0555231 Absent penis Aphallia Aplasia of the penis Penis aplasia Absence of the penis is always accompanied by abnormal position of the meatus (usually in the perineum, sometimes in the rectum), may be accompanied by Cryptorchidism, and is often associated with non-genital anomalies, which all should be coded separately. Absent penis should be differentiated from a penis concealed within pre-pubic fat tissue. Absent penis Lack of recognizable penile structures. HPO:probinson PMID:23650202 Absent penis A deviation from the normal number of vertebrae in the spinal column. UMLS:C4022523 Abnormal number of vertebrae A deviation from the normal number of vertebrae in the spinal column. HPO:probinson UMLS:C4022522 Decreased number of vertebrae An increase in the vertical distance between adjacent vertebral bodies, observed as an increase in the intervertebral disc space. UMLS:C4022513 Increased intervertebral space An increase in the vertical distance between adjacent vertebral bodies, observed as an increase in the intervertebral disc space. HPO:probinson A closed sac located in the spleen. SNOMEDCT_US:79040006 UMLS:C0272407 Cyst on spleen Splenic cyst A closed sac located in the spleen. HPO:probinson PMID:24794024 Cyst on spleen ORCID:0000-0001-5208-3432 A closed fluid filled sac originating from the mesentary. MSH:D008639 SNOMEDCT_US:253802003 SNOMEDCT_US:27970007 UMLS:C0025467 A mesenteric cyst is defined as any cyst located in the mesentery; it may or may not extend into the retroperitoneum, which has a recognizable lining of endothelium or mesothelial cell. Mesenteric cyst can occur anywhere in the mesentery of gastrointestinal tract from duodenum to rectum. Mesenteric cysts can be simple or multiple, unilocular or multilocular, and they may contain hemorrhagic, serous, chylous, or infected fluid. They can range in size from a few millimetres to few cm in diameter, however, at times may be so large that it may mimic tubercular ascites. Mesenteric cyst A closed fluid filled sac originating from the mesentary. HPO:probinson PMID:24936122 UMLS:C4072991 Yellow/white lesions of the retina Any cystic lesion associated with the umbilical cord. UMLS:C4073114 Umbilical cord cysts can be single or multiple. Most usually, a solitary umbilical cyst is observed. They can be classified as (i) true cysts if they have an epithelial lining (allentoic cyst or omphalomesenteric duct cyst) or false cysts if they do not have an epithelial lining (umbilical cord pseudocyst). Umbilical cord cyst Any cystic lesion associated with the umbilical cord. PMID:10206815 PMID:12666213 A structural anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. UMLS:C4073120 Abnormal ocular adnexa morphology Any structural anomaly of the heart and great vessels. HP:0001632 HP:0002564 HP:0002565 UMLS:C4049796 Cardiovascular malformations HP:0030680 Abnormality of cardiovascular system morphology Inflammation of the vagina that can result from a spectrum of conditions that cause vaginal and sometimes vulvar symptoms, such as itching, burning, irritation, odor, and vaginal discharge. MSH:D014627 SNOMEDCT_US:30800001 UMLS:C0042267 Vulvovaginitis The most common infectious causes of vaginitis are bacterial vaginosis, vulvovaginal candidiasis, and trichomoniasis. Physicians traditionally diagnose vaginitis using the combination of symptoms, physical examination, pH of vaginal fluid, microscopy, and the whiff test. Vaginitis Increase in size of the right atrium. Fyler:1771 Fyler:2859 SNOMEDCT_US:67751000119106 UMLS:C0748427 Dilated right atrium Enlarged heart right atrium Right atrial dilatation This feature can be appreciated on chext radiography, MRI, or CT. Right atrial enlargement Increase in size of the right atrium. HPO:probinson A fluid-filled sac (cyst) located within the central nervous system. MSH:D020863 SNOMEDCT_US:277333006 UMLS:C0349606 CNS cyst Cyst of the central nervous system Cysts of CNS are usually maldevelopmental in nature, but in some cases are acquired. The recognition of these cysts radiologically and confirmation by pathology is essential for prognostic purposes. Central nervous system cyst A fluid-filled sac (cyst) located within the central nervous system. HPO:probinson PMID:11593239 PMID:24455569 CNS cyst Any structural anomaly of the tongue. UMLS:C4280755 Abnormal tongue morphology Increase in size of the tonsils, small collections of lymphoid tissue facing into the aerodigestive tract on either side of the back part of the throat. SNOMEDCT_US:46689006 UMLS:C0272386 Enlargment of tonsils Tonsillar hypertrophy tonsils large/hypertrophy Enlarged tonsils Increase in size of the tonsils, small collections of lymphoid tissue facing into the aerodigestive tract on either side of the back part of the throat. HPO:probinson Lack of observable tonsillar tissue. SNOMEDCT_US:249393008 SNOMEDCT_US:300277007 UMLS:C0576999 Hypoplastic tonsils Tonsillar hypoplasia Absent tonsils Lack of observable tonsillar tissue. HPO:probinson An anomaly of venous function. UMLS:C4280744 Abnormality of venous physiology An anomaly of venous function. HPO:probinson A functional anomaly of that portion of the cardiosvascular system that carries deoxygenated blood from the heart to the lungs and returns oxygenated blood back to the heart. UMLS:C4280730 Abnormal pulmonary circulation Abnormality of respiratory circulation Abnormality of pulmonary circulation A functional anomaly of that portion of the cardiosvascular system that carries deoxygenated blood from the heart to the lungs and returns oxygenated blood back to the heart. HPO:probinson Supernumerary clitoris. The word bifid indicates the presence of a split clitoris, as opposed to a supernumerary clitoris, which could be described as duplicated clitoris. Duplicated clitoris A structural anomaly affecting a blood vessel involved in the circulation of the heart, i.e., the superior or inferior vena cava, the pulmonary arteries, the pulmonary veins, and the aorta. 2017-04-18T13:00:44Z robinp Abnormal morphology of the great vessels 2017-04-18T13:14:14Z robinp Abnormal aortic physiology An abnormality of the structure of the pulmonary artery. 2017-04-18T13:29:12Z robinp Abnormal pulmonary artery morphology An abnormality of the structure of the pulmonary veins. 2017-04-18T13:38:34Z robinp Fyler:3000 Abnormal pulmonary vein morphology An abnormality of the function of the pulmonary veins. 2017-04-18T13:38:42Z robinp Abnormal pulmonary vein physiology A chronic deviation from normal pressure in the systemic arterial system. 2017-04-18T13:55:40Z robinp Abnormal systemic BP Abnormal systemic blood pressure Abnormal systemic BP An elevation in bone density in one or more tarsal bones of the foot. Sclerosis is normally detected on a radiograph as an area of increased opacity. 2017-05-27T14:41:39Z peter Tarsal sclerosis 2017-05-28T22:32:58Z peter Abnormal ovarian morphology Any anomaly of ovarian function. 2017-05-28T22:33:50Z peter Abnormal ovarian physiology Any anomaly of the structure of an organ ofthe endocrine system. 2017-05-28T23:11:43Z peter Abnormal endocrine morphology Any anomaly of the function of the endocrine system. 2017-05-28T23:12:36Z peter Abnormal endocrine physiology Any anomaly of the structure of the breast. 2017-06-30T15:41:38Z robinp Abnormal breast morphology Any anomaly of the function of the breast. 2017-06-30T15:42:09Z robinp Abnormal breast physiology Any anomaly of the structure of the humerus. 2017-05-30T01:22:39Z peter Abnormal humerus morphology Any anomaly of the structure of the uterus 2017-05-30T02:52:38Z peter Abnormal uterus morphology Increase in size of the left atrium. 2017-08-13T21:38:04Z peter Fyler:3011 Fyler:3020 Enlarged heart left atrium Left atrial enlargement An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in an artery that is located within the skull (intracranial). 2017-08-26T21:30:38Z peter Intracranial arterial calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in the internal carotid artery. 2017-08-26T21:32:35Z peter Internal carotid artery calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in a cerebral artery. 2017-08-26T21:34:47Z peter Cerebral artery calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in a carotid artery. 2017-08-26T21:52:52Z peter Carotid artery calcification An accumulation of calcium and phosphate in arteries with mineral deposits in the intimal or medial layer of the vessel wall in the external carotid artery. 2017-08-26T21:53:48Z peter External carotid artery calcification A maladaptive personality trait characterized by moderate or greater impairment in personality (self /interpersonal) functioning. 2017-09-17T16:30:45Z peter The emergence of the self in childhood and adolescence is based on experience and perception, which then becomes organized into identity, which organizes further experience and perception. Identity is related to the individual's selfsameness and continuity in time. Impairment in personality functioning A maladaptive personality trait characterized by moderate or greater impairment in personality (self /interpersonal) functioning. PMID:23902698 Any anomaly of the pigmentation of the fundus, the posterior part of the eye including the retina and optic nerve. 2017-12-01T11:02:43Z peter Alterations in pigmentation of the fundus are typically not a result of changes in the retina. The variable pigmentation within both RPE and choroid combine to change profoundly the appearance of the normal fundus between individuals. This is partly a racial characteristic and partly genetic. Abnormality of fundus pigmentation 2017-12-17T21:04:26Z peter Abnormal faeces composition Abnormal feces composition Abnormal stool composition Abnormal faeces composition Any structural anomaly of the ear. 2017-12-18T00:20:14Z peter Fyler:4867 Abnormal ear morphology Any functional anomaly of the ear. 2017-12-18T00:20:24Z peter Abnormal ear physiology A developmental defect in which the coronary sinus fails to form. 2018-01-28T12:02:56Z peter Fyler:2841 Absent coronary sinus A developmental defect in which the coronary sinus fails to form. HPO:nvasilevsky PMID:24551710 Any deviation from the normal concentration of glycerol in the blood. 2018-02-25T14:28:46Z peter Abnormal circulating glycerol level Bleeding within the fundus of the eye. 2018-03-07T15:30:14Z peter Fundus haemorrhage Fundus hemorrhage Fundus haemorrhage A functional anomaly of the mouth (which is also known as the oral cavity). 2018-04-29T14:50:56Z peter The physiological functions of the mouth include salivary gland secretory function, mastication (chewing) and preparation of food for swallowing. Abnormal oral physiology Any structural anomaly of the mouth, which is also known as the oral cavity. 2018-04-29T14:55:47Z peter Abnormal oral morphology A functional abnormality affecting one or more of the cranial nerves, which emerge directly from the brain stem. 2018-06-23T13:49:43Z peter Abnormal cranial nerve physiology Any deviation from the normal concentration of a carbohydrate in the urine. 2018-07-08T12:53:24Z peter Carbohydrates, also known as saccharides, comprise mono-, d-, and oligosaccharides (substances from endogenous metabolism or from exogenous sources such as diet). Most saccharides except glucose are readily excreted in the urine, reflecting dieteray consuption. Increased sacchardie levels may indicate an enzyme defect or other disease if a certain type of saccharide or a certain profile is found. Abnormal urine carbohydrate level Any deviation from the normal concentration of a carboxylic acid in the urine. 2018-07-08T13:01:16Z peter Carboxylic acid refers to an organic compound that contains a carboxyl group (-COOH). Abnormal urine carboxylic acid level An anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. 2018-09-03T00:17:49Z peter Abnormality of the ocular adnexa A functional anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. 2018-09-03T00:18:45Z peter Abnormal ocular adnexa physiology Underdevelopment of the carotid canal, which normally is a circular aperture in the temporal bone of the skull through which the internal carotid artery and the carotid plexus of nerves traverse. 2018-09-16T10:47:06Z peter Hypoplastic carotid canal A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystis jirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections. 2018-11-04T22:23:03Z peter Unusual infection A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystis jirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections. PMID:22052638 Any functional abnormality of the part of the nervous system that consists of the nerves and ganglia outside of the brain and spinal cord. 2018-11-17T16:57:55Z peter Abnormal peripheral nervous system physiology An unusual infection classified by the affected body part. 2018-12-09T12:17:59Z peter Unusual infection by anatomical site 2018-12-09T14:04:29Z peter An elevated circulating concentration of folic acid, which is also known as vitamin B9. Increased blood folate concentration An abnormal level of an analyte measured in the blood. 2019-01-12T13:45:59Z peter Abnormal circulating metabolite concentration Any deviation from the normal concentration of a metabolite in cerebrospinal fluid. 2019-01-20T15:49:06Z peter Abnormal CSF metabolite concentration Abnormal cerebrospinal fluid metabolite concentration Abnormal CSF metabolite concentration Any structural anomaly of the sebaceous glands. 2019-01-26T14:26:26Z peter Sebaceous glands are found all over the human body except on the palms of the hands and soles of the feet. The glands are numerous on the face and scalp and are sparse in areas such as the back. They can number as many as 400-900 glands/cm2 on the face. Sebaceous glands are usually found in association with a hair follicle, which, together, is referred to as a pilosebaceous unit. The sebaceous gland is located in association with the upper portion of the hair follicle, where it is not affected by the hair cycle. Sebaceous glands can be unilobular or multilobular. Although a majority of sebaceous glands are part of a pilosebaceous unit, some glands can be found without an associated hair follicle. Sebaceous glands secrete sebum, which contains cholesterol, cholesteryl esters, squalene, fatty acids, diglycerides and triglycerides, and wax esters. Abnormal sebaceous gland morphology Any structural anomaly of the sebaceous glands. PMID:17975220 Any deviation from the normal concentration of a metabolite in a tissue. 2019-01-27T11:56:39Z peter Abnormal tissue metabolite concentration An abnormality in the function of the chemical reactions related to processes including conversion of food to enter, synthesis of proteins, lipids, nucleic acids, and carbohydrates, or the elimination of waste products. 2019-01-27T12:48:52Z peter Abnormal metabolism 2019-01-27T16:44:33Z peter Abnormal immune system morphology Abnormal increase in blood pressure. An individual measurement of increased blood pressure does not necessarily imply hypertension. In practical terms, multiple measurements are recommended to diagnose the presence of hypertension. 2019-01-27T20:07:59Z peter Increased BP Increased blood pressure Abnormal increase in blood pressure. An individual measurement of increased blood pressure does not necessarily imply hypertension. In practical terms, multiple measurements are recommended to diagnose the presence of hypertension. PMID:9137951 Increased BP Increased level of phenylalanine in urine. 2019-02-23T16:46:17Z peter Increased level of phenylalanine in urine Phenylalaninuria Increased level of phenylalanine in urine. PMID:18566668 UCDenver:tjcallahan An abnormally low blood pH (usually defined as less than 7.35). 2019-02-23T18:37:21Z peter When describing acid-base abnormalities, acidosis and alkalosis refer to physiological processes that lower or raise the pH, respectively, while acidemia and alkalemia simply describe the state of an abnormal blood pH. This distinction is important: a patient with acidemia could have both a respiratory and metabolic acidosis as well as a concurrent metabolic alkalosis. Acidemia An abnormally low blood pH (usually defined as less than 7.35). PMID:24381489 An abnormally high blood pH (usually defined as 7.41 or above). 2019-02-23T18:42:24Z peter When describing acid-base abnormalities, acidosis and alkalosis refer to physiological processes that lower or raise the pH, respectively, while acidemia and alkalemia simply describe the state of an abnormal blood pH. This distinction is important: a patient with acidemia could have both a respiratory and metabolic acidosis as well as a concurrent metabolic alkalosis. Alkalemia An abnormally high blood pH (usually defined as 7.41 or above). PMID:24381489 A round circumscribed space within a lung that is surrounded by an epithelial or fibrous wall of variable thickness. A cyst usually has a thin and regular wall (less than 2 mm) and contains air, although some may contain fluid. 2019-03-03T17:31:21Z peter Lung cyst The thin wall of cystic lesions differentiates them from cavitary processes, which have thicker and irregular walls and will not be discussed in this article. On chest radiographs, findings of a cyst are often subtle, consisting of lucencies and sometimes linear opacities. An air-fluid level can improve the visibility of a cyst and may suggest infection. For the investigation of cysts, CT is substantially more sensitive than chest radiography, showing a cyst as a ringlike lucency surrounded by a thin wall. Pulmonary cyst A round circumscribed space within a lung that is surrounded by an epithelial or fibrous wall of variable thickness. A cyst usually has a thin and regular wall (less than 2 mm) and contains air, although some may contain fluid. PMID:20028879 Pulmonary bullae are rounded focal regions of emphysema with a thin wall which measure more than 1 cm in diameter. They are often subpleural in location and are typically larger in the apices. In some cases, bullae can be very large and result in compression of adjacent lung tissue. A giant bulla is arbitrarily defined as one that occupies at least one third of the volume of a hemithorax. When large, bullae can simulate pneumothorax. The most common cause is paraseptal emphysema but bullae may also be seen in association with centrilobular emphysema. 2019-03-03T17:45:09Z peter Pulmonary bullae Blebs and bullae are commonly subpleural and are mostly seen in both upper lobes in patients with coexisting centrilobular and paraseptal emphysema. Pulmonary bulla Pulmonary bullae are rounded focal regions of emphysema with a thin wall which measure more than 1 cm in diameter. They are often subpleural in location and are typically larger in the apices. In some cases, bullae can be very large and result in compression of adjacent lung tissue. A giant bulla is arbitrarily defined as one that occupies at least one third of the volume of a hemithorax. When large, bullae can simulate pneumothorax. The most common cause is paraseptal emphysema but bullae may also be seen in association with centrilobular emphysema. PMID:18195376 PMID:20028879 PMID:24106540 Pulmonary bullae Abnormal coloring of the lip, whereby the lip discolored, blotchy, or darker or lighter than normal. 2019-03-08T11:06:30Z peter Abnormal lip pigmentation Underdevelopment of the ureter. 2019-04-04T09:26:25Z peter Hypoplasia of the ureter Ureter hypoplasia Ureteral hypoplasia Underdevelopment of the ureter. ORCID:0000-0001-5208-3432 Any structural anomaly of the renal tubular epithelial cells (RTEC), a layer of cells in the outer layer of the renal tubule. These cells play a role in the absorption of substances such as glucose and amino from the primary urine. peter Abnormal renal tubular epithelial morphology An encapsulated collection of pus and necrotic material within the renal parenchyma. The destruction of renal parenchyma is associated with suppurative/neutrophil-rich inflammation and necrosis. peter Renal abscess Renal parenchymal abcess Most renal abscesses are caused by gram-negative bacteria and are commonly caused by ascending infection associated with urologic abnormality, obstruction or calculi. Intrarenal abscess An encapsulated collection of pus and necrotic material within the renal parenchyma. The destruction of renal parenchyma is associated with suppurative/neutrophil-rich inflammation and necrosis. KPMP:arosenberg PMID:27998164 A deviation of urine pH from the normal range of 4.5 to 7.8. peter Urine pH typically is 5 as a result of daily net acid excretion. The interpretation of the urine pH depends on the medical context. Abnormal urine pH A neoplasm that affects the female reproductive system. peter NCIT:C3053 Female reproductive system neoplasm Any structural anomaly of the fetal part of the placenta, which is known as the chorion. peter Abnormal chorion morphology Any structural anomaly of the fetal part of the placenta, which is known as the chorion. PMID:18755720 Absence or underdevelopment of the thyroid gland. peter Aplasia/Hypoplasia of the thyroid gland An elevated level of an aromatic amino acid in the urine. peter Increased aromatic amino acid level in urine An abnormally increased level of tyrosine in the urine. peter Increased tyrosine in urine Tyrosinuria An elevated level of an glutamine family amino acid in the urine. peter Increased glutamine family amino acid level in urine peter An elevated level of an aspartate family amino acid in the urine. Increased aspartate family amino acid level in urine An increased level in the urine of an alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids. peter Elevated urinary non-proteinogenic amino acid level Increased urinary non-proteinogenic amino acid level An increased level of a serine family amino acid in the urine. peter Increased serine family amino acid in urine An elevated level of a proteinogenic amino acid in the urine. These are the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. peter Increased proteinogenic amino acid level in urine An elevated level of a proteinogenic amino acid in the blood circulation. These are the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. 2020-08-29T11:59:15Z peter Abnormal circulating proteinogenic amino acid concentration Any deviation from the normal concentration in the blood circulation of an alpha-amino acid which is not a member of the group of 23 proteinogenic amino acids. 2020-08-29T12:04:47Z peter Abnormal circulating non-proteinogenic amino acid concentration Inflammation of the lining of the upper small intestine (duodenum). 2020-09-03T12:01:20Z peter The diagnosis of duodenitis is made when there is infiltration by inflammatory cells with changes in villous architecture and surface and crypt epithelium. Duodenitis can be graded according to the amount of neutrophilic and plasma cell infiltration, villous height, Brunner's gland hyperplasia with prolapse into the lamina propria and gastric metaplasia. Duodenitis Inflammation of the lining of the upper small intestine (duodenum). PMID:16679353 An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body. 2020-09-05T13:35:03Z peter Abnormality of the musculoskeletal system A structural anomaly of the pharynx. 2020-09-20T11:17:40Z peter Abnormal pharynx morphology A functional anomaly of the pharynx. 2020-09-20T11:18:32Z peter Abnormal pharynx physiology Any structural anomaly of a blood vessel (artery, arteriole, capillary, venule, or vein). 2020-12-01T11:42:14Z peter Abnormal blood vessel morphology Any deviation from the normal concentration of a metabolite in urine. 2020-12-01T12:00:51Z peter As water reabsorption in kidneys affect urinary solute concentrations, various methods are applied to normalize the measured concentration. Frequently, concentrations are reported as a ratio to urinary creatinine. The HPO terms in this subhierarchy therefore use the word 'level' to indicate that appropriate normalization has been performed before concluding that the amount of the indicated metabolite is abnormal. Abnormal urine metabolite level HPO:skoehler UMLS:C4022500 Abnormality of corneal shape Lack of skin pigmentation (coloring) of the chest. HPO:skoehler UMLS:C4022498 Lack of skin coloring on chest human_phenotype Absent pigmentation of chest Lack of skin pigmentation (coloring) of the chest. HPO:skoehler Lack of skin coloring on chest ORCID:0000-0001-5208-3432 HPO:skoehler UMLS:C4022493 Decreased mitochondrial number HPO:skoehler UMLS:C4022492 Increased mitochondrial number HPO:skoehler UMLS:C4022483 Chorioretinal hypopigmentation HPO:skoehler UMLS:C4022482 Chorioretinal hyperpigmentation HPO:skoehler UMLS:C4022480 Absent/small 5th long bone of foot Absent/underdeveloped 5th long bone of foot Aplasia/Hypoplasia of the fifth metatarsal bone Absent/small 5th long bone of foot ORCID:0000-0001-5208-3432 Absent/underdeveloped 5th long bone of foot ORCID:0000-0001-5208-3432 HPO:skoehler UMLS:C4022473 Underdeveloped diaphragm Hypoplasia of the diaphragm Underdeveloped diaphragm ORCID:0000-0001-5208-3432 HPO:skoehler UMLS:C4021858 Abnormality of nasal hair Abnormality of nose hair Abnormality of nasal hair Abnormality of nasal hair Abnormality of nose hair ORCID:0000-0001-5889-4463 HPO:skoehler UMLS:C4022461 Calcification of ribs HPO:skoehler UMLS:C4022459 Decreased fat tissue Decreased adipose tissue Decreased fat tissue ORCID:0000-0001-5208-3432 HPO:skoehler SNOMEDCT_US:445144002 UMLS:C0239337 UMLS:C4073131 Abnormal limbs Abnormality of limbs Limb anomaly Dysmelia Abnormality of limbs Abnormal limbs HPO:skoehler Abnormality of limbs Limb anomaly https://orcid.org/0000-0001-5208-3432 Dysmelia HPO:probinson HPO:skoehler UMLS:C4022456 Abnormality of limb bone Abnormality of limb bone Abnormality of limb bone HPO:skoehler HP:0040066 UMLS:C4022455 UMLS:C4022457 Abnormal morphology of bones of the lower limbs Abnormal shape of bones of the lower limbs Abnormality of lower limb bone Abnormal lower limb bone morphology Abnormal shape of bones of the lower limbs Abnormality of lower limb bone HPO:skoehler UMLS:C4022454 UMLS:C4022458 Abnormal morphology of bones of the upper limbs Abnormal shape of bones of the upper limbs Abnormality of upper limb bone Abnormal upper limb bone morphology Abnormal shape of bones of the upper limbs Abnormality of upper limb bone HPO:skoehler UMLS:C4022452 Abnormality of forearm bone Abnormality of forearm bone Abnormality of forearm bone HPO:skoehler UMLS:C4022451 Abnormal shape of of forearm bone Abnormal forearm bone morphology Abnormal shape of of forearm bone ORCID:0000-0001-5208-3432 HPO:skoehler MSH:D007018 SNOMEDCT_US:74728003 UMLS:C0020635 Hypopituitarism Any deviation from the normal concentration of folate in the blood circulation. HPO:skoehler UMLS:C4021037 Abnormal serum folate Abnormality of folate in blood Folate is an essential water-soluble vitamin (vitamin B9) that is found in green leafy vegetables, cereals, legumes, and fruit. As a major methyl group donor, it plays an important role in one-carbon metabolism and is involved in DNA, RNA, and protein synthesis, in addition to its significant role in energy production and normal cell division. Low blood folate concentration is associated with an increased risk for neural tube defects during pregnancy. Abnormal blood folate concentration Abnormal serum folate HPO:skoehler An abnormality of the tympanic membrane HPO:skoehler UMLS:C4022447 Abnormality of the eardrum The tympanic membrane is considered to be the border of middle and outer ear. Abnormality of the tympanic membrane Abnormality of the eardrum ORCID:0000-0001-5208-3432 A deviation from the normal concentration of cobalamin (vitamin B12) in the blood. Vitamin B12 is one of the eight B vitamins. HPO:skoehler UMLS:C4021032 Abnormal serum cobalamin level Abnormal vitamin B12 level A deviation from the normal concentration of cobalamin (vitamin B12) in the blood. Vitamin B12 is one of the eight B vitamins. HPO:probinson HPO:skoehler UMLS:C0235760 Abnormal serum iron concentration HPO:skoehler UMLS:C4022420 Abnormal liver iron concentration Abnormal liver iron level Abnormal hepatic iron concentration Abnormal liver iron concentration ORCID:0000-0001-5208-3432 Abnormal liver iron level HPO:skoehler HPO:skoehler UMLS:C4022416 Dicarboxylic acidemia An increased amount of carboxylic acid in the urine. HPO:skoehler UMLS:C4022413 Elevated urinary carboxylic acid UMLS:C4073132 Abnormal shape of pelvis bone Abnormal pelvis bone morphology Abnormal shape of pelvis bone ORCID:0000-0001-5208-3432 HPO:skoehler UMLS:C4073139 Abnormality of lingual muscle Abnormality of the tongue muscle Abnormality of the tongue muscle Abnormality of lingual muscle ORCID:0000-0001-5889-4463 Abnormality of the tongue muscle HPO:skoehler UMLS:C4073140 Abnormality of extrinsic lingual muscle Abnormality of extrinsic muscle of tongue Abnormality of extrinsic lingual muscle ORCID:0000-0001-5889-4463 MSH:D006472 SNOMEDCT_US:22490002 UMLS:C0029163 Oral bleeding Oral hemorrhage Oral bleeding Oral bleeding Oral hemorrhage ORCID:0000-0001-5889-4463 An abnormally increased head circumference in a growing child. Head circumference is measured with a nonelastic tape and comprises the distance from above the eyebrows and ears and around the back of the head. The measured HC is then plotted on an appropriate growth chart. UMLS:C4083076 Increased head circumference Increased head circumference Increased head circumference An abnormally reduced head circumference in a growing child. Head circumference is measured with a nonelastic tape and comprises the distance from above the eyebrows and ears and around the back of the head. The measured HC is then plotted on an appropriate growth chart. Microcephaly is defined as a head circumference (HC) that is great than two standard deviations below the mean of age- and gender-matched population based samples. Severe microcephaly is defined with an HC that is three standard deviations below the mean. SNOMEDCT_US:271611007 UMLS:C0424688 Decreased head circumference Although HC measures skull size, it typically also reflects overall brain volume and has been described as a widely used proxy of neural growth and brain size. Brain size outside of normal values is an important risk factor for cognitive and motor delay. Microcephaly at birth has been termed primary microcephaly and that acquired after birth is secondary microcephaly. Decreased head circumference An abnormally reduced head circumference in a growing child. Head circumference is measured with a nonelastic tape and comprises the distance from above the eyebrows and ears and around the back of the head. The measured HC is then plotted on an appropriate growth chart. Microcephaly is defined as a head circumference (HC) that is great than two standard deviations below the mean of age- and gender-matched population based samples. Severe microcephaly is defined with an HC that is three standard deviations below the mean. PMID:26505062 Decreased head circumference UMLS:C4280723 Abnormal size of the dental root UMLS:C4280722 Hypoplasia of the dental root Bleeding occuring within a muscle SNOMEDCT_US:95422003 UMLS:C0151702 Muscle haemorrhage Muscle hemorrhage Bleeding occuring within a muscle PMID:27231694 Muscle haemorrhage UMLS:C4280696 Abnormal size of the clitoris UMLS:C4280695 Increased size of the clitoris UMLS:C4280694 Decreased size of the clitoris UMLS:C4280693 Aplasia/Hypoplasia of the clitoris Absence or underdevelopment of the nasopharyngeal adenoids. UMLS:C4280290 Adenoids small or absent Aplastic/Hypoplastic nasopharyngeal adenoids A deviation in the size of nasopharyngeal adenoids. UMLS:C4280692 Abnormal size of nasopharyngeal adenoids A deviation in the size of nasopharyngeal adenoids. ORCID:0000-0001-7941-2961 Underdevelopment of the nasopharyngeal adenoids. UMLS:C4280691 Underdeveloped nasopharyngeal adenoids Hypoplastic nasopharyngeal adenoids An abnormal decrease in the size of nasopharyngeal adenoids. UMLS:C4280689 Decreased size of nasopharyngeal adenoids An abnormal decrease in the size of nasopharyngeal adenoids. ORCID:0000-0001-7941-2961 An abnormal increase in the size of nasopharyngeal adenoids. SNOMEDCT_US:111591002 SNOMEDCT_US:276442006 UMLS:C0149825 UMLS:C0455938 Adenoid hypertrophy Adenoids large Increased size of nasopharyngeal adenoids UMLS:C4280687 Upper limb muscle hypertrophy An abnormal resistance to glucose, i.e., a reduction in the ability to maintain glucose levels in the blood stream within normal limits following oral or intravenous administration of glucose. MP:0005291 UMLS:C0151671 Decreased glucose tolerance Glucose tolerance decreased Impaired glucose tolerance An abnormal resistance to glucose, i.e., a reduction in the ability to maintain glucose levels in the blood stream within normal limits following oral or intravenous administration of glucose. HPO:probinson A structural anomaly of the muscles of the trunk and head. ORCID:0000-0002-5316-1399 Abnormality of axial muscles Abnormal axial muscle morphology Duplication of tongue Tongue duplicated Tongue duplication Duplicated tongue An increased concentration of glycerol in the urine. Increased urinary glycerol Increased concentration of glycerol in the blood. Pseudohypertriglyceridemia In glycerol kinase deficiency, the increased glycerol concentration has been noted to cause false-positive results of hypertriglyceridemia, a phenomenon called pseudohypertriglyceridemia. Hyperglycerolemia Increased concentration of glycerol in the blood. PMID:23415440 Low serum iron Decreased serum iron Tubular lumnal dilatation/prominence lined by simple layer of cuboidal-to-flat tublar epihelial cells. Renal tubule cyst Renal tubular cyst Tubular lumnal dilatation/prominence lined by simple layer of cuboidal-to-flat tublar epihelial cells. ORCID:0000-0002-0736-9199 HPO:skoehler UMLS:C4022400 Abnormality of peripheral nerves HPO:skoehler SNOMEDCT_US:238090007 UMLS:C0342892 Hypolipidemia Defect or defects of the morphogenesis of the left heart identifiable at birth. HPO:skoehler UMLS:C4022397 Congenital malformation of the left heart HPO:skoehler HP:0100722 UMLS:C4022395 Abnormality of the mediastinum HPO:skoehler UMLS:C4022394 Abnormality of the thoracic cavity HPO:skoehler UMLS:C4073166 Abnormality of jaw muscles Abnormality of jaw muscles Abnormality of jaw muscles An anomaly of the size of the testicle (the male gonad). UMLS:C4073180 Abnormality of the testis size UMLS:C4073181 Aplasia/hypoplasia involving bones of the extremities UMLS:C4073182 Decreased carnitine level in liver Inflammation in any serous cavity. Serositis Inflammation in any serous cavity. HPO:skoehler Hip joint hypermobility Any morphological abnormality of the cervical vertebral column. SNOMED_CT:298391004 Abnormal cervical spine morphology A tumor (abnormal growth of tissue) of the breast. doelkens 2010-05-14T09:45:09Z HP:0010623 MSH:D001943 NCIT:C3262 SNOMEDCT_US:126926005 UMLS:C1458155 Breast tumor Tumours of the breast human_phenotype Neoplasia of the breast HP:0100013 Neoplasm of the breast A tumor (abnormal growth of tissue) of the breast. HPO:probinson Breast tumor ORCID:0000-0001-5208-3432 Tumours of the breast Folds of membranous tissue (peritoneum, mesothelium) attached to the wall of the abdomen and enclosing viscera. Examples include the mesentery for the small intestine; the transverse mesocolon, which attaches the transverse portion of the colon to the back wall of the abdomen; and the mesosigmoid, which enfolds the sigmoid portion of the colon. Cells of the same embryologic origin also surround the other organs of the body such as the lungs (pleura) or the heart (pericardium). doelkens 2010-05-25T11:20:36Z UMLS:C4022389 human_phenotype Abnormality of the mesentery HP:0100016 Abnormality of mesentery morphology Folds of membranous tissue (peritoneum, mesothelium) attached to the wall of the abdomen and enclosing viscera. Examples include the mesentery for the small intestine; the transverse mesocolon, which attaches the transverse portion of the colon to the back wall of the abdomen; and the mesosigmoid, which enfolds the sigmoid portion of the colon. Cells of the same embryologic origin also surround the other organs of the body such as the lungs (pleura) or the heart (pericardium). HPO:sdoelken doelkens 2010-06-24T10:00:02Z UMLS:C4022344 Absent end part of the little toe bone Absent end part of the pinkie toe bone Absent end part of the pinky toe bone human_phenotype HP:0100077 Absent epiphyses of the 5th toe Absent end part of the little toe bone ORCID:0000-0001-5208-3432 Absent end part of the pinkie toe bone ORCID:0000-0001-5208-3432 Absent end part of the pinky toe bone ORCID:0000-0001-5208-3432 doelkens 2010-06-24T10:00:02Z UMLS:C4022341 Enlarged end part of the little toe bone Enlarged end part of the pinkie toe bone Enlarged end part of the pinky toe bone human_phenotype HP:0100080 Enlarged epiphyses of the 5th toe Enlarged end part of the little toe bone ORCID:0000-0001-5208-3432 Enlarged end part of the pinkie toe bone ORCID:0000-0001-5208-3432 Enlarged end part of the pinky toe bone ORCID:0000-0001-5208-3432 doelkens 2010-06-24T10:00:02Z UMLS:C4022337 human_phenotype HP:0100084 Pseudoepiphyses of the 5th toe doelkens 2010-06-24T10:00:02Z UMLS:C4022336 Small end part of the little toe bone Small end part of the pinkie toe bone Small end part of the pinky toe bone human_phenotype HP:0100085 Small epiphyses of the 5th toe Small end part of the little toe bone ORCID:0000-0001-5208-3432 Small end part of the pinkie toe bone ORCID:0000-0001-5208-3432 Small end part of the pinky toe bone ORCID:0000-0001-5208-3432 doelkens 2010-06-24T10:00:02Z UMLS:C4022334 Triangular end part of the little toe bone Triangular end part of the pinkie toe bone Triangular end part of the pinky toe bone human_phenotype HP:0100087 Triangular epiphyses of the 5th toe Triangular end part of the little toe bone ORCID:0000-0001-5208-3432 Triangular end part of the pinkie toe bone ORCID:0000-0001-5208-3432 Triangular end part of the pinky toe bone ORCID:0000-0001-5208-3432 doelkens 2010-06-24T10:02:41Z UMLS:C4022324 Abnormality of the end part of the outermost bone of the little toe Abnormality of the end part of the outermost bone of the pinkie toe Abnormality of the end part of the outermost bone of the pinky toe human_phenotype HP:0100097 Abnormality of the epiphysis of the distal phalanx of the 5th toe Abnormality of the end part of the outermost bone of the little toe ORCID:0000-0001-5208-3432 Abnormality of the end part of the outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Abnormality of the end part of the outermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T10:02:41Z UMLS:C4022323 Abnormality of the end part of the middle bone of the little toe Abnormality of the end part of the middle bone of the pinkie toe Abnormality of the end part of the middle bone of the pinky toe human_phenotype HP:0100098 Abnormality of the epiphysis of the middle phalanx of the 5th toe Abnormality of the end part of the middle bone of the little toe ORCID:0000-0001-5208-3432 Abnormality of the end part of the middle bone of the pinkie toe ORCID:0000-0001-5208-3432 Abnormality of the end part of the middle bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T10:02:41Z UMLS:C4022322 Abnormality of the end part of the innermost bone of the little toe Abnormality of the end part of the innermost bone of the pinkie toe Abnormality of the end part of the innermost bone of the pinky toe human_phenotype HP:0100099 Abnormality of the epiphysis of the proximal phalanx of the 5th toe Abnormality of the end part of the innermost bone of the little toe ORCID:0000-0001-5208-3432 Abnormality of the end part of the innermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Abnormality of the end part of the innermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:03:31Z UMLS:C4022219 Absent end part of the outermost bone of the little toe Absent end part of the outermost bone of the pinkie toe Absent end part of the outermost bone of the pinky toe human_phenotype HP:0100202 Absent epiphysis of the distal phalanx of the 5th toe Absent end part of the outermost bone of the little toe ORCID:0000-0001-5208-3432 Absent end part of the outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Absent end part of the outermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:03:31Z UMLS:C4022216 Enlarged end part of the outermost bone of the little toe Enlarged end part of the outermost bone of the pinkie toe Enlarged end part of the outermost bone of the pinky toe human_phenotype HP:0100205 Enlarged epiphysis of the distal phalanx of the 5th toe Enlarged end part of the outermost bone of the little toe ORCID:0000-0001-5208-3432 Enlarged end part of the outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Enlarged end part of the outermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:03:31Z UMLS:C4022212 human_phenotype HP:0100209 Pseudoepiphysis of the distal phalanx of the 5th toe doelkens 2010-06-24T05:03:31Z UMLS:C4022211 Small end part of the outermost bone of the little toe Small end part of the outermost bone of the pinkie toe Small end part of the outermost bone of the pinky toe human_phenotype HP:0100210 Small epiphysis of the distal phalanx of the 5th toe Small end part of the outermost bone of the little toe ORCID:0000-0001-5208-3432 Small end part of the outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Small end part of the outermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:03:31Z UMLS:C4022209 Triangular end part of the outermost bone of the little toe Triangular end part of the outermost bone of the pinkie toe Triangular end part of the outermost bone of the pinky toe human_phenotype HP:0100212 Triangular epiphysis of the distal phalanx of the 5th toe Triangular end part of the outermost bone of the little toe ORCID:0000-0001-5208-3432 Triangular end part of the outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Triangular end part of the outermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:04:00Z UMLS:C4022208 Absent end part of the middle bone of the little toe Absent end part of the middle bone of the pinkie toe Absent end part of the middle bone of the pinky toe human_phenotype HP:0100213 Absent epiphysis of the middle phalanx of the 5th toe Absent end part of the middle bone of the little toe ORCID:0000-0001-5208-3432 Absent end part of the middle bone of the pinkie toe ORCID:0000-0001-5208-3432 Absent end part of the middle bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:04:00Z UMLS:C4022205 Enlarged end part of the middle bone of the little toe Enlarged end part of the middle bone of the pinkie toe Enlarged end part of the middle bone of the pinky toe human_phenotype HP:0100216 Enlarged epiphysis of the middle phalanx of the 5th toe Enlarged end part of the middle bone of the little toe ORCID:0000-0001-5208-3432 Enlarged end part of the middle bone of the pinkie toe ORCID:0000-0001-5208-3432 Enlarged end part of the middle bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:04:00Z UMLS:C4022201 human_phenotype HP:0100220 Pseudoepiphysis of the middle phalanx of the 5th toe doelkens 2010-06-24T05:04:00Z UMLS:C4022200 Small end part of the middle bone of the little toe Small end part of the middle bone of the pinkie toe Small end part of the middle bone of the pinky toe human_phenotype HP:0100221 Small epiphysis of the middle phalanx of the 5th toe Small end part of the middle bone of the little toe ORCID:0000-0001-5208-3432 Small end part of the middle bone of the pinkie toe ORCID:0000-0001-5208-3432 Small end part of the middle bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:04:00Z UMLS:C4022198 Triangular end part of the middle bone of the little toe Triangular end part of the middle bone of the pinkie toe Triangular end part of the middle bone of the pinky toe human_phenotype HP:0100223 Triangular epiphysis of the middle phalanx of the 5th toe Triangular end part of the middle bone of the little toe ORCID:0000-0001-5208-3432 Triangular end part of the middle bone of the pinkie toe ORCID:0000-0001-5208-3432 Triangular end part of the middle bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:04:53Z UMLS:C4022197 Absent end part of the innermost bone of the little toe Absent end part of the innermost bone of the pinkie toe Absent end part of the innermost bone of the pinky toe human_phenotype HP:0100224 Absent epiphysis of the proximal phalanx of the 5th toe Absent end part of the innermost bone of the little toe ORCID:0000-0001-5208-3432 Absent end part of the innermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Absent end part of the innermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:04:53Z UMLS:C4022194 Enlarged end part of the innermost bone of the little toe Enlarged end part of the innermost bone of the pinkie toe Enlarged end part of the innermost bone of the pinky toe human_phenotype HP:0100227 Enlarged epiphysis of the proximal phalanx of the 5th toe Enlarged end part of the innermost bone of the little toe ORCID:0000-0001-5208-3432 Enlarged end part of the innermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Enlarged end part of the innermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:04:53Z UMLS:C4022190 human_phenotype HP:0100231 Pseudoepiphysis of the proximal phalanx of the 5th toe doelkens 2010-06-24T05:04:53Z UMLS:C4022189 Small end part of the innermost bone of the little toe Small end part of the innermost bone of the pinkie toe Small end part of the innermost bone of the pinky toe human_phenotype HP:0100232 Small epiphysis of the proximal phalanx of the 5th toe Small end part of the innermost bone of the little toe ORCID:0000-0001-5208-3432 Small end part of the innermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Small end part of the innermost bone of the pinky toe ORCID:0000-0001-5208-3432 doelkens 2010-06-24T05:04:53Z UMLS:C4022187 Triangular end part of the innermost bone of the little toe Triangular end part of the innermost bone of the pinkie toe Triangular end part of the innermost bone of the pinky toe human_phenotype HP:0100234 Triangular epiphysis of the proximal phalanx of the 5th toe Triangular end part of the innermost bone of the little toe ORCID:0000-0001-5208-3432 Triangular end part of the innermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Triangular end part of the innermost bone of the pinky toe ORCID:0000-0001-5208-3432 Deposition of calcium salts in muscle tissue. doelkens 2010-07-09T12:32:25Z SNOMEDCT_US:446993003 UMLS:C2960760 Skeletal muscle calcinosis human_phenotype HP:0100249 Calcification of muscles Deposition of calcium salts in muscle tissue. HPO:probinson Calcium deposition affecting the Meninges. doelkens 2010-07-14T03:41:34Z UMLS:C4022181 human_phenotype HP:0100250 In general, meningeal calcifications are plaque-like and bilateral as seen on CT-scans. Meningeal calcification Calcium deposition affecting the Meninges. HPO:sdoelken The presence of dysplastic regions in metaphyseal regions. doelkens 2010-07-14T05:15:56Z HP:0000948 HP:0005002 HP:0005636 HP:0005704 HP:0006427 MSH:C536252 SNOMEDCT_US:27837003 UMLS:C0265294 human_phenotype HP:0100255 Metaphyseal dysplasia The presence of dysplastic regions in metaphyseal regions. HPO:sdoelken A form of polydactyly in which the extra digit or digits are localized on the side of the thumb or great toe. doelkens 2010-07-20T11:00:32Z SNOMEDCT_US:205135003 UMLS:C0345354 Polydactyly, preaxial human_phenotype HP:0100258 Preaxial polydactyly A form of polydactyly in which the extra digit or digits are localized on the side of the thumb or great toe. HPO:probinson Polydactyly, preaxial HPO:skoehler A form of polydactyly in which the extra digit or digits are localized on the side of the fifth finger or fifth toe. doelkens 2010-07-20T11:00:32Z HP:0005808 MSH:C562429 UMLS:C0220697 Polydactyly, postaxial Postaxial hexadactyly human_phenotype HP:0100259 Postaxial polydactyly A form of polydactyly in which the extra digit or digits are localized on the side of the fifth finger or fifth toe. HPO:probinson An abnormality of the structure or form of the tendons, also often called sinews. doelkens 2010-07-20T01:20:19Z UMLS:C4021026 Abnormal shape of tendon Abnormality of the sinew human_phenotype HP:0100261 A tendon (or sinew) is a tough band of fibrous connective tissue that usually connects muscle to bone and is capable of withstanding tension. Tendons are similar to ligaments and fascia as they are all made of collagen except that ligaments join one bone to another bone, and fascia connect muscles to other muscles. Tendons and muscles work together and can only exert a pulling force. Abnormal tendon morphology An abnormality of the structure or form of the tendons, also often called sinews. HPO:sdoelken Abnormal shape of tendon ORCID:0000-0001-5208-3432 doelkens 2010-08-10T01:57:00Z SNOMEDCT_US:42091004 UMLS:C0333759 Muscle fibre hypertrophy human_phenotype HP:0100293 Muscle fiber hypertrophy doelkens 2010-11-11T03:44:27Z UMLS:C4022134 human_phenotype HP:0100346 Fibular deviation of the 5th toe The proximal interphalangeal joint of the fifth toe cannot be straightened actively or passively. UMLS:C4021016 Camptodactyly of the 5th toe Camptodactyly of the fifth toe human_phenotype HP:0100351 Contractures of the proximal interphalangeal joint of the 5th toe The proximal interphalangeal joint of the fifth toe cannot be straightened actively or passively. HPO:probinson The distal interphalangeal joint of the 5th toe cannot be straightened actively or passively. UMLS:C4022130 Contracture of the outermost hinge joint of the 5th toe human_phenotype HP:0100355 Contractures of the distal interphalangeal joint of the 5th toe The distal interphalangeal joint of the 5th toe cannot be straightened actively or passively. HPO:probinson Contracture of the outermost hinge joint of the 5th toe ORCID:0000-0001-6908-9849 The joint between the second metatarsal and the proximal phalanx of the 5th toe cannot be straightened actively or passively. UMLS:C4022126 human_phenotype HP:0100359 Contracture of the metatarsophalangeal joint of the 5th toe The joint between the second metatarsal and the proximal phalanx of the 5th toe cannot be straightened actively or passively. HPO:probinson doelkens 2010-11-11T04:18:29Z UMLS:C2750635 human_phenotype HP:0100360 Contractures of the joints of the upper limbs Developmental hypoplasia of one or more phalanx of little toe. UMLS:C4021012 Hypoplastic/small phalanges of the 5th toe Short little toe bone Short phalanx of the fifth toe Short pinkie toe bone Short pinky toe bone human_phenotype HP:0100368 Short phalanx of the 5th toe Developmental hypoplasia of one or more phalanx of little toe. HPO:probinson Short little toe bone ORCID:0000-0001-5208-3432 Short pinkie toe bone ORCID:0000-0001-5208-3432 Short pinky toe bone ORCID:0000-0001-5208-3432 UMLS:C4022120 Absent/small outermost little toe bone Absent/small outermost pinkie toe bone Absent/small outermost pinky toe bone Absent/underdeveloped outermost pinky toe bone human_phenotype HP:0100371 Aplasia/Hypoplasia of the distal phalanx of the 5th toe Absent/small outermost little toe bone ORCID:0000-0001-5208-3432 Absent/small outermost pinkie toe bone ORCID:0000-0001-5208-3432 Absent/small outermost pinky toe bone ORCID:0000-0001-5208-3432 Absent/underdeveloped outermost pinky toe bone ORCID:0000-0001-5208-3432 UMLS:C4022117 Absent/small middle 5th toe bone Absent/underdeveloped middle bone of little toe Absent/underdeveloped middle bone of pinkie toe Absent/underdeveloped middle bone of pinky toe human_phenotype HP:0100374 Aplasia/Hypoplasia of the middle phalanx of the 5th toe Absent/small middle 5th toe bone ORCID:0000-0001-5208-3432 Absent/underdeveloped middle bone of little toe ORCID:0000-0001-5208-3432 Absent/underdeveloped middle bone of pinkie toe ORCID:0000-0001-5208-3432 Absent/underdeveloped middle bone of pinky toe ORCID:0000-0001-5208-3432 Absence (agenesis) or underdevelopment of one or more of the proximal phalanges of the 5th toe. UMLS:C4022114 Absent/small innermost little toe bone Absent/small innermost pinkie toe bone Absent/small innermost pinky toe bone Absent/underdeveloped innermost 5th toe bone human_phenotype HP:0100377 Aplasia/hypoplasia of the proximal phalanx of the 5th toe Absence (agenesis) or underdevelopment of one or more of the proximal phalanges of the 5th toe. HPO:probinson Absent/small innermost little toe bone ORCID:0000-0001-5208-3432 Absent/small innermost pinkie toe bone ORCID:0000-0001-5208-3432 Absent/small innermost pinky toe bone ORCID:0000-0001-5208-3432 Absent/underdeveloped innermost 5th toe bone ORCID:0000-0001-5208-3432 Developmental hypoplasia of the distal phalanx of little toe. UMLS:C4021006 Hypoplastic/small distal phalanx of the 5th toe Short distal phalanx of the fifth toe Short outermost bone of the little toe Short outermost bone of the pinkie toe Short outermost bone of the pinky toe human_phenotype HP:0100391 Short distal phalanx of the 5th toe Developmental hypoplasia of the distal phalanx of little toe. HPO:sdoelken Short outermost bone of the little toe ORCID:0000-0001-5208-3432 Short outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Short outermost bone of the pinky toe ORCID:0000-0001-5208-3432 Developmental hypoplasia of the middle phalanx of the 5th toe. UMLS:C4021003 Hypoplastic/small middle phalanx of the 5th toe Short middle bone of little toe Short middle bone of pinkie toe Short middle bone of pinky toe Short middle phalanx of the fifth toe human_phenotype HP:0100394 Short middle phalanx of the 5th toe Developmental hypoplasia of the middle phalanx of the 5th toe. HPO:probinson Hypoplastic/small middle phalanx of the 5th toe Short middle bone of little toe ORCID:0000-0001-5208-3432 Short middle bone of pinkie toe ORCID:0000-0001-5208-3432 Short middle bone of pinky toe ORCID:0000-0001-5208-3432 Developmental hypoplasia of the proximal phalanx of fifth toe. UMLS:C4021000 Hypoplastic/small proximal phalanx of the 5th toe Short innermost bone of little toe Short innermost bone of pinkie toe Short innermost bone of pinky toe Short proximal phalanx of the fifth toe human_phenotype HP:0100397 Short proximal phalanx of the 5th toe Developmental hypoplasia of the proximal phalanx of fifth toe. HPO:probinson Hypoplastic/small proximal phalanx of the 5th toe Short innermost bone of little toe ORCID:0000-0001-5208-3432 Short innermost bone of pinkie toe ORCID:0000-0001-5208-3432 Short innermost bone of pinky toe ORCID:0000-0001-5208-3432 Short proximal phalanx of the fifth toe Partial or complete duplication of the distal phalanx of little toe. UMLS:C4020997 Duplication of the distal phalanx of the fifth toe Duplication of the outermost bone of the fifth toe Duplication of the outermost bone of the little toe Duplication of the outermost bone of the pinkie toe Duplication of the outermost bone of the pinky toe Partial/complete duplication of the distal phalanx of the 5th toe human_phenotype HP:0100400 Duplication of the distal phalanx of the 5th toe Partial or complete duplication of the distal phalanx of little toe. HPO:sdoelken Duplication of the outermost bone of the fifth toe ORCID:0000-0001-5208-3432 Duplication of the outermost bone of the little toe ORCID:0000-0001-5208-3432 Duplication of the outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Duplication of the outermost bone of the pinky toe ORCID:0000-0001-5208-3432 Partial or complete duplication of the proximal phalanx of fifth toe. UMLS:C4020991 Duplication of the innermost bone of the little toe Duplication of the innermost bone of the pinkie toe Duplication of the innermost bone of the pinky toe Duplication of the proximal phalanx of the fifth toe Partial/complete duplication of the proximal phalanx of the 5th toe human_phenotype HP:0100406 Duplication of the proximal phalanx of the 5th toe Partial or complete duplication of the proximal phalanx of fifth toe. HPO:probinson Duplication of the innermost bone of the little toe ORCID:0000-0001-5208-3432 Duplication of the innermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Duplication of the innermost bone of the pinky toe ORCID:0000-0001-5208-3432 Complete duplication of the distal phalanx of little toe. UMLS:C4020988 Complete duplication of the distal phalanx of the fifth toe Complete duplication of the outermost bone of the little toe Complete duplication of the outermost bone of the pinkie toe Complete duplication of the outermost bone of the pinky toe human_phenotype HP:0100409 Complete duplication of the distal phalanx of the 5th toe Complete duplication of the distal phalanx of little toe. HPO:sdoelken Complete duplication of the outermost bone of the little toe ORCID:0000-0001-5208-3432 Complete duplication of the outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Complete duplication of the outermost bone of the pinky toe ORCID:0000-0001-5208-3432 Complete duplication of the proximal phalanx of fifth toe. UMLS:C4020984 Complete duplication of the innermost bone of the little toe Complete duplication of the innermost bone of the pinkie toe Complete duplication of the innermost bone of the pinky toe Complete duplication of the proximal phalanx of the fifth toe human_phenotype HP:0100415 Complete duplication of the proximal phalanx of the 5th toe Complete duplication of the proximal phalanx of fifth toe. HPO:sdoelken Complete duplication of the innermost bone of the little toe ORCID:0000-0001-5208-3432 Complete duplication of the innermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Complete duplication of the innermost bone of the pinky toe ORCID:0000-0001-5208-3432 The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers cannot be extended to 180 degrees by either active or passive extension. doelkens 2010-12-14T10:46:57Z HP:0005651 HP:0005662 HP:0005713 HP:0005801 HP:0005821 HP:0006195 HP:0006218 HP:0006240 HP:0009698 SNOMEDCT_US:202281000 UMLS:C0409348 Camptodactyly of hands Camptodactyly of proximal interphalangeal joint Contractures of the proximal interphalangeal joints of the fingers Flexion contractures of proximal interphalangeal joints Permanent flexion of the finger Proximal interphalangeal finger joint contractures human_phenotype HP:0100490 Note that some restrict the use of the term to inability to extend the proximal interphalangeal joint of the fifth finger. We do not restrict the term in this way. This term should not be used if the patient has Clenched hand. A similar effect can be created by radial angulation within the distal phalanx with thickening of the epiphysis, which is called Kirner deformity or dystelephalangy. The affected digits should be specified. Camptodactyly of finger The distal interphalangeal joint and/or the proximal interphalangeal joint of the fingers cannot be extended to 180 degrees by either active or passive extension. HPO:sdoelken PMID:19125433 Permanent flexion of the finger orcid.org/0000-0002-6548-5200 doelkens 2010-12-14T10:58:11Z HP:0100239 UMLS:C4020971 Abnormality of lower limb joint Abnormality of the joints of the lower limbs human_phenotype HP:0100491 Abnormality of lower limb joint Abnormality of lower limb joint Abnormality of the joints of the lower limbs Contractures of one ore more joints of the feet meaning chronic loss of joint motion due to structural changes in non-bony tissue. doelkens 2010-12-14T11:03:38Z UMLS:C4022042 human_phenotype HP:0100492 Joint contractures involving the joints of the feet Contractures of one ore more joints of the feet meaning chronic loss of joint motion due to structural changes in non-bony tissue. HPO:sdoelken A decreased concentration of ammonia in the blood. doelkens 2010-12-17T03:54:51Z UMLS:C4022041 human_phenotype HP:0100493 Hypoammonemia A decreased concentration of ammonia in the blood. HPO:gcarletti doelkens 2010-12-17T04:25:31Z UMLS:C4022039 human_phenotype HP:0100498 Deviation of toes doelkens 2010-12-17T04:26:14Z UMLS:C4020970 Lateral deviation of toes human_phenotype HP:0100500 Fibular deviation of toes A reduced circulating concentration of folic acid, which is also known as vitamin B9. doelkens 2010-12-17T06:13:04Z MSH:D005494 SNOMEDCT_US:190633005 UMLS:C0016412 Folate deficiency Vitamin B9 deficiency human_phenotype HP:0100507 Reduced blood folate concentration A reduced circulating concentration of folic acid, which is also known as vitamin B9. HPO:probinson Folate deficiency An anomaly in the metabolism of a vitamin. doelkens 2010-12-17T06:17:22Z UMLS:C4022036 Abnormality of vitamin metabolism human_phenotype HP:0100508 Vitamins are organic substances that are essential in minute quantities and not produced within the body, instead being present in natural foodstuffs. Vitamins act as coenzymes or precursors of coenzymes in the regulation of metabolic processes. Abnormality of vitamin metabolism An anomaly in the metabolism of a vitamin. HPO:probinson Abnormality of vitamin metabolism doelkens 2010-12-17T06:19:15Z UMLS:C4022035 Abnormality of vitamin D metabolism human_phenotype HP:0100511 Abnormality of vitamin D metabolism Abnormality of vitamin D metabolism A reduced concentration of Vitamin D. doelkens 2010-12-17T06:19:35Z MSH:D014808 SNOMEDCT_US:34713006 UMLS:C0042870 Deficient in vitamin D Vitamin D deficiency human_phenotype HP:0100512 Low levels of vitamin D Deficient in vitamin D Vitamin D deficiency The presence of an abscess of the liver. doelkens 2010-12-20T11:13:14Z HP:0001400 MSH:D008100 SNOMEDCT_US:27916005 UMLS:C0023885 Hepatic abscess Liver abscess human_phenotype HP:0100523 Liver abscess The presence of an abscess of the liver. HPO:probinson Liver abscess Congenital duplication of all or part of a limb. doelkens 2010-12-20T11:32:41Z SNOMEDCT_US:34488005 UMLS:C0265551 Dimelia Limb duplication human_phenotype HP:0100524 Limb duplication Limb duplication An abnormality of phosphate homeostasis or concentration in the body. doelkens 2010-12-20T11:58:32Z UMLS:C4022032 Abnormality of phosphate homeostasis human_phenotype HP:0100529 Abnormal blood phosphate concentration An abnormality of phosphate homeostasis or concentration in the body. HPO:probinson Inflammation of the eye, parts of the eye or the periorbital region. doelkens 2010-12-20T03:53:42Z HP:0007891 UMLS:C4020969 Inflammatory abnormality of the eye Ocular inflammation human_phenotype HP:0100533 Inflammatory abnormality of the eye Inflammation of the eye, parts of the eye or the periorbital region. HPO:sdoelken Inflammatory abnormality of the eye An abnormal site of the kidney. doelkens 2010-12-20T06:43:50Z UMLS:C4020968 Abnormal localisation of kidneys human_phenotype HP:0100542 Abnormal localization of kidney An abnormal site of the kidney. HPO:probinson Abnormal localisation of kidneys An abnormality of the forebrain, which has as its parts the telencephalon, diencephalon, lateral ventricles and third ventricle. doelkens 2010-12-21T02:12:53Z UMLS:C4020967 Abnormal shape of forebrain Abnormality of the forebrain human_phenotype HP:0100547 Abnormality of forebrain morphology An abnormality of the forebrain, which has as its parts the telencephalon, diencephalon, lateral ventricles and third ventricle. HPO:probinson Abnormal shape of forebrain ORCID:0000-0001-5208-3432 An abnormality of the formation and mineralization of one or more vertebrae. doelkens 2010-12-21T04:50:43Z UMLS:C4020966 Abnormal bone maturation of vertebra Abnormal vertebral ossification Abnormality of ossification/mineralisation of vertebrae human_phenotype HP:0100569 Abnormally ossified vertebrae An abnormality of the formation and mineralization of one or more vertebrae. HPO:probinson Abnormal bone maturation of vertebra ORCID:0000-0001-5208-3432 A cardiac diverticulum is a rare congenital malformation which is either fibrous or muscular. doelkens 2010-12-21T05:11:26Z UMLS:C4020965 Ventricular diverticulum human_phenotype HP:0100571 Cardiac diverticulum A cardiac diverticulum is a rare congenital malformation which is either fibrous or muscular. HPO:sdoelken A fibrous cardiac diverticulum refers to an aneurysm and usually appears as an isolated congenital anomaly. doelkens 2010-12-21T05:14:00Z UMLS:C4020964 Congenital ventricular aneurysm human_phenotype HP:0100572 Fibrous cardiac diverticulum A fibrous cardiac diverticulum refers to an aneurysm and usually appears as an isolated congenital anomaly. HPO:sdoelken doelkens 2010-12-21T05:14:00Z UMLS:C4022021 human_phenotype HP:0100573 Muscular cardiac diverticulum Inflammation of the urinary bladder. doelkens 2010-12-27T12:49:16Z MSH:D003556 SNOMEDCT_US:38822007 UMLS:C0010692 Cystitis of the urinary bladder Urinary bladder inflammation human_phenotype HP:0100577 Urinary bladder inflammation Inflammation of the urinary bladder. HPO:probinson Urinary bladder inflammation An inflammation of the endocardium, the inner layer of the heart, which usually involves the heart valves. doelkens 2010-12-27T02:57:48Z MSH:D004696 SNOMEDCT_US:56819008 UMLS:C0014118 human_phenotype HP:0100584 Endocarditis An inflammation of the endocardium, the inner layer of the heart, which usually involves the heart valves. HPO:sdoelken doelkens 2010-12-27T03:13:07Z UMLS:C4022016 human_phenotype HP:0100587 Abnormality of the preputium The presence of an abscess of the peritoneum. doelkens 2010-12-27T04:30:53Z SNOMEDCT_US:73962000 UMLS:C0267756 human_phenotype HP:0100592 Peritoneal abscess The presence of an abscess of the peritoneum. HPO:probinson doelkens 2010-12-27T04:35:28Z UMLS:C4022015 human_phenotype HP:0100593 Calcification of cartilage The nostrils (the paired channels of the nose) are not present. doelkens 2010-12-27T05:07:16Z HP:0100597 UMLS:C4020707 UMLS:C4020963 Abouphalia Aplasia of the nares Missing nostrils human_phenotype Aplasia/Hypoplasia of the nares HP:0100596 Absent nares The nostrils (the paired channels of the nose) are not present. HPO:probinson Missing nostrils ORCID:0000-0001-5889-4463 A general term for inflammation of the muscles without respect to the underlying cause. doelkens 2010-12-28T11:14:59Z MSH:D009220 SNOMEDCT_US:128496001 SNOMEDCT_US:26889001 UMLS:C0027121 Muscle inflammation human_phenotype HP:0100614 Many such conditions are considered likely to be caused by autoimmune conditions, rather than directly due to infection, although autoimmune conditions can be activated or exacerbated by infections. It is also a documented side effect of the lipid-lowering drugs such as statins and fibrates. Elevation of creatine kinase in blood is indicative of myositis. Myositis A general term for inflammation of the muscles without respect to the underlying cause. HPO:sdoelken Muscle inflammation ORCID:0000-0001-5208-3432 doelkens 2010-12-28T04:14:55Z UMLS:C4020962 Wide rib cage Wide thorax human_phenotype HP:0100625 Enlarged thorax Wide rib cage The presence of a diverticulum of the esophagus. doelkens 2010-12-29T02:22:08Z MSH:D004936 SNOMEDCT_US:204667006 SNOMEDCT_US:414133009 UMLS:C0014854 Esophageal pouch human_phenotype HP:0100628 A diverticulum is a blind ended outpouching through the wall of a tubular organ or bounded cavity. Esophageal diverticulum The presence of a diverticulum of the esophagus. HPO:probinson Presence of a cyst (sac-like structure) located in the larynx. doelkens 2010-12-29T05:48:37Z SNOMEDCT_US:195867000 UMLS:C0339880 human_phenotype HP:0100640 Laryngeal cyst Presence of a cyst (sac-like structure) located in the larynx. HPO:probinson PMID:24040590 Inflammation of the thyroid gland. doelkens 2010-12-29T06:08:32Z MSH:D013966 SNOMEDCT_US:82119001 UMLS:C0040147 Thyroid gland inflammation human_phenotype HP:0100646 Thyroiditis Inflammation of the thyroid gland. HPO:probinson Thyroid gland inflammation ORCID:0000-0001-5208-3432 doelkens 2010-12-30T11:39:15Z UMLS:C4022001 Abnormality of the cerebral blood vessels human_phenotype HP:0100659 Abnormality of the cerebral vasculature Abnormality of the cerebral blood vessels ORCID:0000-0001-5208-3432 Inflammation of cartilage. doelkens 2010-12-30T12:57:50Z SNOMEDCT_US:46176001 UMLS:C0008439 Cartilage inflammation human_phenotype HP:0100662 Chondritis Inflammation of cartilage. HPO:sdoelken Cartilage inflammation A developmental disorder in which there is a duplication the entire intestine or of a portion of the intestine. doelkens 2010-12-30T01:23:50Z SNOMEDCT_US:3845008 UMLS:C0266166 UMLS:C4020702 Bowel duplication human_phenotype Gut duplication HP:0100668 Intestinal duplication A developmental disorder in which there is a duplication the entire intestine or of a portion of the intestine. HPO:probinson Bowel duplication Gut duplication An abnormality of the pigmentation of the mucosa of the mouth. doelkens 2010-12-30T01:25:45Z Abnormal color of the oral mucosa UMLS:C4020959 Abnormal pigmentation of oral cavity Abnormal pigmentation of oral mucous membrane Abnormal pigmentation of the oral mucosa/gingivae human_phenotype HP:0100669 Abnormal pigmentation of the oral mucosa An abnormality of the pigmentation of the mucosa of the mouth. HPO:probinson Abnormal color of the oral mucosa ORCID:0000-0001-5889-4463 Abnormal pigmentation of oral mucous membrane ORCID:0000-0001-5889-4463 A developmental disorder in which there is a duplication of a portion of the muscle and submucosa of the esophagus without epithelial duplication. doelkens 2010-12-30T02:08:38Z SNOMEDCT_US:66865009 UMLS:C0266135 human_phenotype HP:0100681 Esophageal duplication is a rare cause of mediastinal mass. An esophageal duplication may be a simple epithelial cyst or duplication that contains muscle and submucosa but not epithelium. In most cases, the duplication is located in the lower thrid of the esophagus, and the most common associated symptom is difficulty in swallowing. Esophageal duplication occurs because of maldevelopment of the posterior division of embryonic foregut. Esophageal duplication A developmental disorder in which there is a duplication of a portion of the muscle and submucosa of the esophagus without epithelial duplication. HPO:probinson PMID:10464795 An abnormality of the Arachnoid mater. doelkens 2011-03-31T12:43:27Z UMLS:C4020955 Abnormality of the arachnoid mater Abnormality of the arachnoidea human_phenotype HP:0100700 Abnormal arachnoid mater morphology An abnormality of the Arachnoid mater. HPO:sdoelken An abnormality of the pia mater. doelkens 2011-03-31T12:44:41Z UMLS:C4021994 Abnormality of the pia mater human_phenotype HP:0100701 Abnormal pia mater An abnormality of the pia mater. HPO:sdoelken An abnormality of the thoracic vertebral column. doelkens 2011-05-05T09:37:17Z UMLS:C4021989 Abnormality of the thoracic spine HP:0100711 Abnormal thoracic spine morphology An abnormality of the thoracic vertebral column. HPO:probinson Any structural abnormality of the lumbar vertebral column. doelkens 2011-05-05T09:37:33Z UMLS:C4021988 Abnormality of the lumbar spine HP:0100712 Abnormal lumbar spine morphology Any structural abnormality of the lumbar vertebral column. HPO:probinson A sectoral indentation of the crystalline lens, usually due to zonular weakness or absence. doelkens 2011-06-06T02:16:53Z SNOMEDCT_US:204134008 UMLS:C0344516 human_phenotype HP:0100719 Lens coloboma A sectoral indentation of the crystalline lens, usually due to zonular weakness or absence. HPO:probinson doelkens 2011-06-06T04:50:47Z UMLS:C2748652 Big face Large face Large facies human_phenotype HP:0100729 Large face Big face ORCID:0000-0001-5889-4463 Large face Large facies ORCID:0000-0001-5889-4463 An anomaly of one or more epiphyses of one or more vertebrae. doelkens 2011-06-06T05:13:08Z UMLS:C4020953 Abnormal shape of the end part of the vertebra bone Abnormality of the vertebral epiphyses human_phenotype HP:0100734 Abnormality of vertebral epiphysis morphology Abnormal shape of the end part of the vertebra bone ORCID:0000-0001-5208-3432 An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively. doelkens 2011-06-07T10:40:36Z HP:0003012 MSH:D008206 SNOMEDCT_US:111590001 SNOMEDCT_US:234087005 SNOMEDCT_US:3305006 SNOMEDCT_US:362971004 UMLS:C0024228 UMLS:C4021976 human_phenotype Lymphatic disease HP:0100763 Abnormality of the lymphatic system An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively. HPO:probinson An abnormality of the tonsils. doelkens 2011-06-07T10:43:35Z UMLS:C4021975 human_phenotype HP:0100765 Abnormality of the tonsils An abnormality of the tonsils. HPO:probinson A structural anomaly of the vessel that contains or conveys lymph fluid. doelkens 2011-06-07T10:44:54Z UMLS:C4021974 Abnormality of the lymphatic vessels HP:0100766 Abnormal lymphatic vessel morphology A structural anomaly of the vessel that contains or conveys lymph fluid. https://en.wikipedia.org/wiki/Lymphatic_vessel An abnormality of the placenta, the organ that connects the developing fetus to the uterine wall to enable nutrient uptake, waste elimination, and gas exchange. doelkens 2011-06-07T11:03:03Z SNOMEDCT_US:169957005 SNOMEDCT_US:33552005 UMLS:C1306893 Abnormality of the placenta Placental issue HP:0100767 The placenta is a fetomaternal organ. The fetal portion of the placenta is the villous chorion and the maternal portion is the decidua basalis. The two portions are connected by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. Abnormal placenta morphology An abnormality of the placenta, the organ that connects the developing fetus to the uterine wall to enable nutrient uptake, waste elimination, and gas exchange. HPO:probinson Placental issue Excessive growth or abnormal thickening of bone tissue. doelkens 2011-06-07T05:17:19Z MSH:D015576 SNOMEDCT_US:13814009 SNOMEDCT_US:203514008 UMLS:C0020492 Bone Hypertrophy Bone overgrowth human_phenotype HP:0100774 Hyperostosis refers to a localized bone overgrowth process (as opposed to sclerosis, which refers to a generalized disturbance with increased bone density). Hyperostosis Excessive growth or abnormal thickening of bone tissue. HPO:probinson Bone overgrowth ORCID:0000-0001-5208-3432 A congenital underdevelopment (aplasia or hypoplasia) of the pancreas. doelkens 2011-06-09T11:45:58Z UMLS:C4021968 Absent/small pancreas Absent/underdeveloped pancreas human_phenotype HP:0100800 Aplasia/Hypoplasia of the pancreas A congenital underdevelopment (aplasia or hypoplasia) of the pancreas. HPO:sdoelken Absent/small pancreas ORCID:0000-0001-5208-3432 Absent/underdeveloped pancreas ORCID:0000-0001-5208-3432 The middle finger is more than 2 SD above the mean for newborns 27 to 41 weeks EGA or above the 97th centile for children from birth to 16 years of age AND the five digits retain their normal length proportions relative to each other (i.e., it is not the case that the middle finger is the only lengthened digit), or, Fingers that appear disproportionately long compared to the palm of the hand. doelkens 2011-06-09T01:13:15Z HP:0006010 UMLS:C1858091 Long fingers human_phenotype HP:0100807 Long fingers The middle finger is more than 2 SD above the mean for newborns 27 to 41 weeks EGA or above the 97th centile for children from birth to 16 years of age AND the five digits retain their normal length proportions relative to each other (i.e., it is not the case that the middle finger is the only lengthened digit), or, Fingers that appear disproportionately long compared to the palm of the hand. PMID:19125433 Long fingers An outpouching of the gastric wall. doelkens 2011-06-09T01:43:31Z MSH:D013273 SNOMEDCT_US:75198005 UMLS:C0038355 Stomach diverticulum human_phenotype HP:0100808 Gastric diverticulum may be asymptomatic or may present with a vague sensation of fullness or discomfort in the upper abdomen, or with acute upper gastrointestinal bleed or perforation. Gastric diverticulum An outpouching of the gastric wall. HPO:probinson PMID:22257431 Congenital absence or underdevelopment of the colon. doelkens 2011-06-09T01:54:57Z UMLS:C4021964 Absent/small colon Absent/underdeveloped colon human_phenotype HP:0100811 Aplasia/Hypoplasia of the colon Congenital absence or underdevelopment of the colon. HPO:probinson Absent/small colon ORCID:0000-0001-5208-3432 Absent/underdeveloped colon ORCID:0000-0001-5208-3432 doelkens 2011-06-09T02:18:39Z UMLS:C4021963 Darkening of skin of the lips Hyperpigmentation of lip vermillion Increased pigmentation on the lips human_phenotype HP:0100816 Lip hyperpigmentation Darkening of skin of the lips ORCID:0000-0001-5889-4463 Hyperpigmentation of lip vermillion ORCID:0000-0001-5889-4463 Increased pigmentation on the lips ORCID:0000-0001-5889-4463 An abnormality of emotional behaviour. doelkens 2011-06-23T11:07:13Z UMLS:C4020949 Abnormal emotion/affect behaviour human_phenotype HP:0100851 Abnormal emotion/affect behavior An abnormality of emotional behaviour. HPO:sdoelken An abnormality of fear/anxiety-related behavior, which may relate to either abnormally reduced fear/anxiety-related response or increased fear/anxiety-related response. doelkens 2011-06-23T11:13:16Z HP:0001296 UMLS:C4018849 Abnormal fear/anxiety-related behaviour human_phenotype HP:0100852 Abnormal fear/anxiety-related behavior An abnormality of fear/anxiety-related behavior, which may relate to either abnormally reduced fear/anxiety-related response or increased fear/anxiety-related response. HPO:sdoelken Abnormal fear/anxiety-related behaviour Decreased ossification of the vertebral bodies. doelkens 2011-11-30T09:59:32Z UMLS:C4021953 human_phenotype HP:0100856 Poorly ossified vertebrae Decreased ossification of the vertebral bodies. HPO:sdoelken Increase in bone density of the vertebral body. doelkens 2011-11-30T10:12:34Z HP:0004578 UMLS:C4021951 Vertebral body sclerosis human_phenotype HP:0100861 Sclerotic vertebral body Increase in bone density of the vertebral body. HPO:probinson doelkens 2011-11-30T10:47:46Z UMLS:C4021950 Absent femoral head human_phenotype HP:0100862 Aplasia of the femoral head Absent femoral head ORCID:0000-0001-5208-3432 doelkens 2011-11-30T10:48:08Z UMLS:C4021949 Absent neck of thighbone human_phenotype HP:0100863 Aplasia of the femoral neck Absent neck of thighbone ORCID:0000-0001-5208-3432 An abnormally short femoral neck (which is the process of bone, connecting the femoral head with the femoral shaft). doelkens 2011-11-30T10:48:34Z HP:0003032 HP:0008779 HP:0008793 UMLS:C1836184 Hypoplasia of the femoral neck Hypoplastic femoral neck Short femoral necks Short neck of thighbone human_phenotype HP:0100864 Short femoral neck An abnormally short femoral neck (which is the process of bone, connecting the femoral head with the femoral shaft). HPO:probinson Short neck of thighbone ORCID:0000-0001-5208-3432 Underdevelopment of the iliac bones. doelkens 2011-11-30T11:11:24Z UMLS:C1849063 Short pelvis bones human_phenotype HP:0100866 Short iliac bones Underdevelopment of the iliac bones. PMID:29019756 Short pelvis bones ORCID:0000-0001-5208-3432 Cystic, urine-containing intrarenal cavities lined with transitional cell epithelium that communicate through a narrow channel with the collecting system. doelkens 2011-12-01T02:29:09Z SNOMEDCT_US:433036004 UMLS:C2315541 Caliceal diverticulum Pelvic diverticulum Renal pelvic diverticulum human_phenotype HP:0100877 Renal diverticulum Cystic, urine-containing intrarenal cavities lined with transitional cell epithelium that communicate through a narrow channel with the collecting system. HPO:sdoelken doelkens 2011-12-01T02:32:26Z SNOMEDCT_US:198319004 UMLS:C0151994 Enlarged uterus human_phenotype HP:0100878 Enlarged uterus Enlarged uterus doelkens 2011-12-01T02:33:12Z SNOMEDCT_US:66998000 UMLS:C0392039 Enlarged ovaries human_phenotype HP:0100879 Enlarged ovaries Enlarged ovaries An abnormality in the placement of the ocular globe (eyeball). doelkens 2011-12-13T04:25:29Z UMLS:C4021946 Abnormality of eyeball location Abnormality of eyeball position Abnormality of globe position human_phenotype HP:0100886 Abnormality of globe location An abnormality in the placement of the ocular globe (eyeball). HPO:sdoelken Abnormality of eyeball location ORCID:0000-0001-5889-4463 Abnormality of eyeball position ORCID:0000-0001-5889-4463 Abnormality of globe position ORCID:0000-0001-5889-4463 An abnormality in the size of the ocular globe (eyeball). doelkens 2011-12-13T04:25:29Z HP:0010725 UMLS:C4021945 Abnormality of eyeball size Eye size difference human_phenotype HP:0100887 Abnormality of globe size An abnormality in the size of the ocular globe (eyeball). HPO:sdoelken Abnormality of eyeball size ORCID:0000-0001-5889-4463 Eye size difference An abnormality of the Common bile duct, a tube-like anatomic structure in the human gastrointestinal tract, formed by the union of the Common hepatic duct and the Cystic duct from the gall bladder. doelkens 2011-12-01T04:52:13Z UMLS:C4020944 Abnormality of the common bile duct human_phenotype HP:0100889 Abnormality of the ductus choledochus An abnormality of the Common bile duct, a tube-like anatomic structure in the human gastrointestinal tract, formed by the union of the Common hepatic duct and the Cystic duct from the gall bladder. HPO:sdoelken An elevation in bone density in one or more phalanges of the fingers. Sclerosis is normally detected on a radiograph as an area of increased opacity. doelkens 2011-12-02T09:34:05Z UMLS:C4020941 Increased bone density in the finger bone Sclerosis of the phalanges of the hand human_phenotype HP:0100899 Sclerosis of finger phalanx An elevation in bone density in one or more phalanges of the fingers. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in the finger bone ORCID:0000-0001-5208-3432 UMLS:C4021939 Increased bone density in the outermost little finger bone Increased bone density in the outermost pinkie finger bone Increased bone density in the outermost pinky finger bone human_phenotype HP:0100903 Sclerosis of the distal phalanx of the 5th finger Increased bone density in the outermost little finger bone ORCID:0000-0001-5208-3432 Increased bone density in the outermost pinkie finger bone ORCID:0000-0001-5208-3432 Increased bone density in the outermost pinky finger bone ORCID:0000-0001-5208-3432 UMLS:C4021935 Increased bone density in the middle bone of the little finger Increased bone density in the middle bone of the pinkie finger Increased bone density in the middle bone of the pinky finger human_phenotype HP:0100907 Sclerosis of the middle phalanx of the 5th finger Increased bone density in the middle bone of the little finger ORCID:0000-0001-5208-3432 Increased bone density in the middle bone of the pinkie finger ORCID:0000-0001-5208-3432 Increased bone density in the middle bone of the pinky finger ORCID:0000-0001-5208-3432 UMLS:C4021931 Increased bone density in innermost little finger bone Increased bone density in innermost pinkie finger bone Increased bone density in innermost pinky finger bone human_phenotype HP:0100911 Sclerosis of the proximal phalanx of the 5th finger Increased bone density in innermost little finger bone ORCID:0000-0001-5208-3432 Increased bone density in innermost pinkie finger bone ORCID:0000-0001-5208-3432 Increased bone density in innermost pinky finger bone ORCID:0000-0001-5208-3432 An elevation of bone density in the distal phalanx of the thumb. UMLS:C4021930 Increased bone density in the outermost bone of the thumb human_phenotype HP:0100912 Sclerosis can be identified on a radiograph as an area of increased opacity. Sclerosis of the distal phalanx of the thumb An elevation of bone density in the distal phalanx of the thumb. HPO:probinson Increased bone density in the outermost bone of the thumb ORCID:0000-0001-5208-3432 An elevation of bone density in the proximal phalanx of the thumb. UMLS:C4021929 Increased bone density in the innermost bone of the thumb human_phenotype HP:0100913 Sclerosis of the proximal phalanx of the thumb An elevation of bone density in the proximal phalanx of the thumb. HPO:probinson Increased bone density in the innermost bone of the thumb ORCID:0000-0001-5208-3432 UMLS:C4021928 Increased bone density in 1st long bone of hand human_phenotype HP:0100914 Sclerosis of the 1st metacarpal Increased bone density in 1st long bone of hand ORCID:0000-0001-5208-3432 An elevation in bone density in one or more distal phalanges of the fingers. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4020940 Increased bone density in outermost finger bone Sclerosis of the distal phalanges of the hand human_phenotype HP:0100915 Sclerosis of distal finger phalanx An elevation in bone density in one or more distal phalanges of the fingers. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in outermost finger bone ORCID:0000-0001-5208-3432 An elevation in bone density in one or more middle phalanges of the fingers. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4020939 Increased bone density in middle finger bone of hand Sclerosis of the middle phalanges of the hand human_phenotype HP:0100916 Sclerosis of middle finger phalanx An elevation in bone density in one or more middle phalanges of the fingers. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in middle finger bone of hand ORCID:0000-0001-5208-3432 An elevation in bone density in one or more proximal phalanges of the fingers. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4020938 Increased bone density in innermost finger bone Sclerosis of the proximal phalanges of the hand human_phenotype HP:0100917 Sclerosis of proximal finger phalanx An elevation in bone density in one or more proximal phalanges of the fingers. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in innermost finger bone ORCID:0000-0001-5208-3432 An elevation in bone density in one or more phalanges of the fifth finger. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4020934 Increased bone density in little finger bone Increased bone density in pinkie finger bone Increased bone density in pinky finger bone Sclerosis of the phalanges of the 5th finger human_phenotype HP:0100921 Sclerosis of 5th finger phalanx An elevation in bone density in one or more phalanges of the fifth finger. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in little finger bone ORCID:0000-0001-5208-3432 Increased bone density in pinkie finger bone ORCID:0000-0001-5208-3432 Increased bone density in pinky finger bone ORCID:0000-0001-5208-3432 UMLS:C4020933 Increased bone density in thumb bone Sclerosis of the phalanges of the thumb human_phenotype HP:0100922 Sclerosis of thumb phalanx Increased bone density in thumb bone ORCID:0000-0001-5208-3432 An elevation in bone density in one or more phalanges of the toes. Sclerosis is normally detected on a radiograph as an area of increased opacity. doelkens 2011-12-02T11:08:43Z UMLS:C4020932 Increased bone density in the toe bone Sclerosis of the phalanges of the toes human_phenotype HP:0100924 Sclerosis of toe phalanx An elevation in bone density in one or more phalanges of the toes. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in the toe bone ORCID:0000-0001-5208-3432 An elevation in bone density in one or more foot bones. Sclerosis is normally detected on a radiograph as an area of increased opacity. doelkens 2011-12-02T11:12:32Z UMLS:C4020931 Increased bone density in foot bone Sclerosis of bones of the feet human_phenotype HP:0100925 Sclerosis of foot bone An elevation in bone density in one or more foot bones. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in foot bone ORCID:0000-0001-5208-3432 An elevation in bone density in one or more phalanges of the fifth toe. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4020927 Increased bone density in little toe bone Increased bone density in pinkie toe bone Increased bone density in pinky toe bone Sclerosis of the phalanges of the 5th toe human_phenotype HP:0100929 Sclerosis of 5th toe phalanx An elevation in bone density in one or more phalanges of the fifth toe. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in little toe bone ORCID:0000-0001-5208-3432 Increased bone density in pinkie toe bone ORCID:0000-0001-5208-3432 Increased bone density in pinky toe bone ORCID:0000-0001-5208-3432 An elevation in bone density in one or more phalanges of the big toe. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4020926 Increased bone density in big toe bone Sclerosis of the phalanges of the hallux human_phenotype HP:0100930 Sclerosis of hallux phalanx An elevation in bone density in one or more phalanges of the big toe. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in big toe bone ORCID:0000-0001-5208-3432 UMLS:C4021924 Increased bone density in the innermost bone of the little toe Increased bone density in the innermost bone of the pinkie toe Increased bone density in the innermost bone of the pinky toe human_phenotype HP:0100934 Sclerosis of the proximal phalanx of the 5th toe Increased bone density in the innermost bone of the little toe ORCID:0000-0001-5208-3432 Increased bone density in the innermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Increased bone density in the innermost bone of the pinky toe ORCID:0000-0001-5208-3432 UMLS:C4021920 Increased bone density in the middle bone of the little toe Increased bone density in the middle bone of the pinkie toe Increased bone density in the middle bone of the pinky toe human_phenotype HP:0100938 Sclerosis of the middle phalanx of the 5th toe Increased bone density in the middle bone of the little toe ORCID:0000-0001-5208-3432 Increased bone density in the middle bone of the pinkie toe ORCID:0000-0001-5208-3432 Increased bone density in the middle bone of the pinky toe ORCID:0000-0001-5208-3432 UMLS:C4021916 Increased bone density in the outermost bone of the little toe Increased bone density in the outermost bone of the pinkie toe Increased bone density in the outermost bone of the pinky toe human_phenotype HP:0100942 Sclerosis of the distal phalanx of the 5th toe Increased bone density in the outermost bone of the little toe ORCID:0000-0001-5208-3432 Increased bone density in the outermost bone of the pinkie toe ORCID:0000-0001-5208-3432 Increased bone density in the outermost bone of the pinky toe ORCID:0000-0001-5208-3432 UMLS:C4021915 Increased bone density in the innermost bone of the big toe human_phenotype HP:0100943 Sclerosis of the proximal phalanx of the hallux Increased bone density in the innermost bone of the big toe ORCID:0000-0001-5208-3432 UMLS:C4021914 Increased bone density in the outermost bone of the big toe human_phenotype HP:0100944 Sclerosis of the distal phalanx of the hallux Increased bone density in the outermost bone of the big toe ORCID:0000-0001-5208-3432 UMLS:C4021913 Increased bone density in the 1st long bone of foot human_phenotype HP:0100945 Sclerosis of the 1st metatarsal Increased bone density in the 1st long bone of foot ORCID:0000-0001-5208-3432 An elevation in bone density in one or more proximal phalanges of the toes. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4020925 Increased bone density in innermost toe bone Sclerosis of the proximal phalanges of the toes human_phenotype HP:0100946 Sclerosis of proximal toe phalanx An elevation in bone density in one or more proximal phalanges of the toes. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in innermost toe bone ORCID:0000-0001-5208-3432 An elevation in bone density in one or more middle phalanges of the toes. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4020924 Increased bone density in middle toe bone Sclerosis of the middle phalanges of the toes human_phenotype HP:0100947 Sclerosis of middle toe phalanx An elevation in bone density in one or more middle phalanges of the toes. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in middle toe bone ORCID:0000-0001-5208-3432 An elevation in bone density in one or more distal phalanges of the toes. Sclerosis is normally detected on a radiograph as an area of increased opacity. UMLS:C4020923 Increased bone density in the outermost bone of the toes Sclerosis of the distal phalanges of the toes human_phenotype HP:0100948 Sclerosis of distal toe phalanx An elevation in bone density in one or more distal phalanges of the toes. Sclerosis is normally detected on a radiograph as an area of increased opacity. HPO:probinson Increased bone density in the outermost bone of the toes ORCID:0000-0001-5208-3432 Any structural abnormality of the medulla of the kidney. doelkens 2011-12-12T10:02:15Z HP:0005582 UMLS:C4021911 Abnormality of the renal medulla human_phenotype HP:0100957 The renal pyramids of the adult kidney resemble a cone with a broad base adjacent to the renal cortex and the narrow apex that is termed papilla. The adult renal medulla is made up of 10-18 pyramids. A pyramid consists of the medullary collecting ducts, loops of Henle, vasa recta (straight capillaries) and the interstitium. The main function of the medulla is to regulate concentration of the urine. The urine flows from the collecting ducts into the renal calyces and pelvis. Abnormal renal medulla morphology Any structural abnormality of the medulla of the kidney. HPO:probinson PMID:22343825 Nontender, round and firm, but slightly compressible, intradermal or subcutaneous cyst measuring 0.5-5 cm in diameter. Epidermal cysts are intradermal or subcutaneous tumors, grow slowly and occur on the face, neck, back and scrotum. They usually appear at or around puberty, and as a rule an affected individual has one solitary or a few cysts. sebastiankohler 2010-06-18T02:08:02Z MSH:D004814 SNOMEDCT_US:399999000 SNOMEDCT_US:417992006 SNOMEDCT_US:418323001 SNOMEDCT_US:418630001 SNOMEDCT_US:419603000 SNOMEDCT_US:419670003 SNOMEDCT_US:419893006 UMLS:C0014511 Epidermal cyst Epidermal inclusion cyst Infundibular cyst Keratin cyst Skin cyst human_phenotype Epidermoid cysts Sebaceous cyst HP:0200040 A cyst is a cavity containing liquid, semisolid, or solid material. An epidermoid cyst is a benign cyst that develops out of ectodermal tissue and consists of a thin layer of squamous epithelium. An epidermal cyst may or may not be painful or release pus, and are usually noticed as a bump on the skin. Epidermal cysts and trichilemmal cysts are clinically indistinguishable. The wall of the epidermal cyst conserves the epidermal layers, but the wall of the trichilemmal cysts, which arise from the external root sheath, shows palisading of unlayered epithelial cells. Homogeneous horny material that is further degraded to fat and cholesterol forms within both types of cysts. Epidermoid cyst Nontender, round and firm, but slightly compressible, intradermal or subcutaneous cyst measuring 0.5-5 cm in diameter. Epidermal cysts are intradermal or subcutaneous tumors, grow slowly and occur on the face, neck, back and scrotum. They usually appear at or around puberty, and as a rule an affected individual has one solitary or a few cysts. HPO:skoehler Skin cyst Epidermoid cysts HPO:skoehler Disproportionately small hand. sebastiankohler SNOMEDCT_US:299032009 UMLS:C0575802 Disproportionately small hands Small hand human_phenotype Small hands HP:0200055 Small hand Disproportionately small hand. HPO:probinson Disproportionately small hands Small hand Small hands HPO:skoehler Lack of skin pigmentation (coloring). sebastiankohler 2013-06-05T10:22:18Z UMLS:C2673954 Absent skin pigmentation Lack of skin coloration human_phenotype HP:0200098 Absent skin pigmentation Lack of skin pigmentation (coloring). HPO:probinson Absent skin pigmentation Lack of skin coloration ORCID:0000-0001-5208-3432 Median longitudinal ear length greater than two SD above the mean determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. UMLS:C1848657 Long ear Long ears The commonly used term Macrotia is a bundled term comprising increased length and width (surface area). Long ear Median longitudinal ear length greater than two SD above the mean determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. PMID:19152421 eom:2028381d5c61842a Long ear Long ears HPO:skoehler Median longitudinal ear length less than two SD above the mean determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. UMLS:C3551041 Short ear Short ears The commonly used term Microtia is a bundled term comprising decreased length and width (surface area). Short ear Median longitudinal ear length less than two SD above the mean determined by the maximal distance from the superior aspect to the inferior aspect of the external ear. PMID:19152421 eom:2cff5ac9b681fc73 Short ear Short ears HPO:skoehler Abnormality of the first branch of the internal carotid artery. UMLS:C4073185 Ophthalmic artery anomaly The ophthalmic artery (OA) is the first branch of the internal carotid artery distal to the cavernous sinus. Branches of the OA supply all the structures in the orbit as well as some structures in the nose, face and meninges. Abnormality of ophthalmic artery Abnormality of the first branch of the internal carotid artery. ORCID:0000-0001-5889-4463 Ophthalmic artery anomaly ORCID:0000-0001-5889-4463 Any abnormality of the part of the nervous system that consists of the nerves and ganglia outside of the brain and spinal cord. UMLS:C4073187 Abnormality of the peripheral nervous system Abnormality of the peripheral nervous system Any abnormality of the part of the nervous system that consists of the nerves and ganglia outside of the brain and spinal cord. ORCID:0000-0001-5889-4463 Abnormality of the peripheral nervous system Any abnormality of the part of the peripheral nervous system associated with sensation and skeletal muscle voluntary control of body movements. UMLS:C4073188 The SoNS consists of afferent and efferent nerves. Afferent nerves are responsible for relaying sensation to the central nervous system; efferent nerves are responsible for stimulating muscle contraction, including all the non-sensory neurons connected with skeletal muscles and skin. Abnormality of the somatic nervous system Any abnormality of the part of the peripheral nervous system associated with sensation and skeletal muscle voluntary control of body movements. ORCID:0000-0001-5889-4463 An abnormality of nerve cell cluster or a group of nerve cell bodies located in the autonomic nervous system. UMLS:C4073193 Abnormality of ganglion An abnormality of nerve cell cluster or a group of nerve cell bodies located in the autonomic nervous system. ORCID:0000-0001-5889-4463 https://en.wikipedia.org/wiki/Ganglion An abnormality of nerve cell cluster or a group of nerve cell bodies located in the peripheral autonomic nervous system. UMLS:C4073194 Abnormality of ganglion of peripheral nervous system An abnormality of nerve cell cluster or a group of nerve cell bodies located in the peripheral autonomic nervous system. ORCID:0000-0001-5889-4463 https://en.wikipedia.org/wiki/Ganglion An abnormality of nerve cell cluster or a group of nerve cell bodies located in the autonomic nervous system of the cranium. UMLS:C4073195 Abnormality of cranial ganglion An abnormality of nerve cell cluster or a group of nerve cell bodies located in the autonomic nervous system of the cranium. ORCID:0000-0001-5889-4463 https://en.wikipedia.org/wiki/Ganglion A gap in the lip or lips. 2017-06-20T22:17:35Z ORCID:0000-0001-5208-3432 Cleft lip Cleft of the lip Cleft lip Cleft lip Any structural anomaly of the bile-secreting organ that is important for detoxification, for fat, carbohydrate, and protein metabolism, and for glycogen storage. 2017-09-20T00:22:53Z ORCID:0000-0001-5208-3432 Fyler:4447 Abnormal liver morphology Any structural anomaly of the bile-secreting organ that is important for detoxification, for fat, carbohydrate, and protein metabolism, and for glycogen storage. MP:0000598 Any structural anomaly of the hollow epithelial tube found on the dorsal side of the vertebrate embryo that develops into the central nervous system (i.e. brain and spinal cord). 2017-09-20T00:25:37Z ORCID:0000-0001-5208-3432 Fyler:4339 Abnormal neural tube morphology Any structural anomaly of the hollow epithelial tube found on the dorsal side of the vertebrate embryo that develops into the central nervous system (i.e. brain and spinal cord). MP:0002151 An increase in the level of L-glutamic acid in the blood. 2018-01-29T22:56:49Z ORCID:0000-0001-5208-3432 Increased level of L-glutamic acid in blood An increase in the level of L-glutamic acid in the blood. PMID:7623444 An increase in the level of ribose in the urine. 2018-01-30T00:47:12Z ORCID:0000-0001-5208-3432 Ribose is a pentose monosaccharide. Increased level of ribose in urine An increase in the level of ribose in the urine. PMID:14988808 An increase in the level of ribose in the cerebrospinal fluid. 2018-01-30T00:47:46Z ORCID:0000-0001-5208-3432 Increased level of ribose in cerebrospinal fluid Increased level of ribose in CSF An increase in the level of ribose in the cerebrospinal fluid. PMID:14988808 Any abnormality of the chest muscles. 2018-05-01T17:37:03Z Muscle issues in the chest Abnormality of the chest musculature Abnormal morphology of the chest musculature Muscle issues in the chest Any abnormality of the back muscles. 2018-05-01T17:38:59Z Muscle issues in the back Abnormality of the back musculature Muscle issues in the back Any abnormality of the shoulder muscles. 2018-05-01T17:39:54Z Abnormality of the shoulder musculature Muscle issues in the shoulder Abnormal morphology of the shoulder musculature Muscle issues in the shoulder A reduced concentration of folic acid, which is also known as vitamin B9 in the cerebrospinal fluid. 2018-09-12T00:12:26Z Folate deficiency in cerebrospinal fluid Cerebral folate deficiency is usually measured as low levels of folate in the CSF, in the presence of normal folate metabolism outside the nervous system. Folate deficiency in CSF A reduced concentration of folic acid, which is also known as vitamin B9 in the cerebrospinal fluid. PMID:15581159 An abnormality in any umbilical cord measurement performed after birth, such as the blood gas level. 2018-09-12T00:35:41Z Abnormal cord blood measurement An abnormality in any umbilical cord measurement performed after birth, such as the blood gas level. PMID:7926229 2018-09-12T00:44:12Z Abnormal blood gas level in cord blood Absence of the sebaceous gland, the holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts. Absence of sebaceous glands Absent sebaceous glands Absence of the sebaceous gland, the holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts. MP:0000647 An abnormality of the muscles of the structure of the nose. UMLS:C4073200 Abnormality of muscle of nose Abnormality of musculature of the nose Abnormality of nasal musculature Abnormality of nasal musculature An abnormality of the muscles of the structure of the nose. ORCID:0000-0001-5889-4463 Abnormality of muscle of nose Abnormality of musculature of the nose Abnormality of nasal musculature Inflammation of the urethra. Urethritis is characterized by discharge, dysuria and/or urethral discomfort but may be asymptomatic. Common etiologies include gonococcal urethritis as well as infection by chlamydia trachomatis, mycoplasma genitalium, ureaplasma urealyticum, trichomonas vaginalis, anaerobes, herpes simplex virus, and adenovirus. Urethritis Inflammation of the urethra. PMID:26220178 Underdevelopment of the musculature of the pelvis. 2017-05-25T16:53:10Z ORCID:0000-0001-7941-2961 Hypoplasia of the musculature of the pelvis An elevation in bone density in one or more carpal bones of the hand. ORCID:0000-0003-0169-8159 2017-06-01T16:54:00Z ORCID:0000-0001-7941-2961 Sclerosis of the carpal bones An elevation in bone density in one or more carpal bones of the hand. PMID:21120491 A decreased amount of valine in the blood. 2018-10-01T14:47:05Z Low blood valine concentration Hypovalinemia A decreased amount of valine in the blood. https://orcid.org/0000-0001-7941-2961 Low blood valine concentration https://orcid.org/0000-0001-7941-2961 An decreased concentration of tyrosine in the blood. 2018-10-01T15:01:56Z Decreased tyrosine in blood Low blood tyrosine concentration Hypotyrosinemia An decreased concentration of tyrosine in the blood. https://orcid.org/0000-0001-7941-2961 Decreased tyrosine in blood https://orcid.org/0000-0001-7941-2961 Low blood tyrosine concentration https://orcid.org/0000-0001-7941-2961 An increased amount of serine in the blood. 2018-10-01T16:54:02Z Elevated circulating serine levels High blood serine levels Increased serine blood concentration Hyperserinemia High blood serine levels https://orcid.org/0000-0001-7941-2961 Increased serine blood concentration https://orcid.org/0000-0001-7941-2961 A decreased amount of phenylalanine in the blood. 2018-10-03T19:58:21Z Decreased blood phenylalanine Low blood phenylalanine Hypophenylalaninemia A decreased amount of phenylalanine in the blood. http://orcid.org/0000-0001-7941-2961 Decreased blood phenylalanine http://orcid.org/0000-0001-7941-2961 Low blood phenylalanine http://orcid.org/0000-0001-7941-2961 A decreased amount of lysine in the blood. 2018-10-03T20:04:58Z Decreased blood lysine Low blood lysine levels Hypolysinemia A decreased amount of lysine in the blood. http://orcid.org/0000-0001-7941-2961 Decreased blood lysine http://orcid.org/0000-0001-7941-2961 Low blood lysine levels http://orcid.org/0000-0001-7941-2961 Decreased amount of leucine in the blood. 2018-10-04T13:17:00Z Decreased blood concentration of leucine Low blood leucine levels Hypoleucinemia Decreased amount of leucine in the blood. http://orcid.org/0000-0001-7941-2961 Decreased blood concentration of leucine http://orcid.org/0000-0001-7941-2961 Low blood leucine levels http://orcid.org/0000-0001-7941-2961 A decreased amount of isoleucine in the blood. 2018-10-04T13:22:24Z Decreased blood isoleucine concentration Low blood isoleucine levels Hypoisoleucinemia A decreased amount of isoleucine in the blood. http://orcid.org/0000-0001-7941-2961 Decreased blood isoleucine concentration http://orcid.org/0000-0001-7941-2961 Low blood isoleucine levels http://orcid.org/0000-0001-7941-2961 Any deviation from the normal concentration of glutamate in the blood circulation. 2018-10-04T14:22:57Z Abnormality of glutamate metabolism Abnormal circulating glutamate concentration An increased amount of arginine levels in the blood. 2018-10-05T14:45:02Z High blood arginine levels Increased blood arginine concentration Hyperargininemia An increased amount of arginine levels in the blood. http://orcid.org/0000-0001-7941-2961 High blood arginine levels http://orcid.org/0000-0001-7941-2961 Increased blood arginine concentration http://orcid.org/0000-0001-7941-2961 An abnormal decrease in ornithine in the blood. 2018-10-12T13:25:49Z Decreased blood ornithine concentrations Low blood ornithine levels Hypoornithinemia An abnormal decrease in ornithine in the blood. http://orcid.org/0000-0001-7941-2961 Decreased blood ornithine concentrations http://orcid.org/0000-0001-7941-2961 Low blood ornithine levels http://orcid.org/0000-0001-7941-2961 An abnormality of the partial pressure of oxygen in the arterial blood. 2018-10-17T15:14:35Z Abnormal blood O2 level Abnormal blood oxygen levels Abnromal O2 blood concentration Abnormal blood oxygen level An abnormality of the partial pressure of oxygen in the arterial blood. HPO:probinson Abnormal blood O2 level Abnormal blood oxygen levels http://orcid.org/0000-0001-7941-2961 Abnromal O2 blood concentration http://orcid.org/0000-0001-7941-2961 Any deviation from the normal concentration of a carboxylic acid in the cerebrospinal fluid. 2019-02-25T15:15:53Z Abnormal CSF carboxylic acid concentration Any deviation from the normal concentration of amino acids in the cerebrospinal fluid. 2019-02-25T15:20:22Z HP:0032364 Abnormal CSF amino acid level Abnormal amino acid levels in cerebrospinal fluid Abnormal cerebrospinal fluid amino acid level Abnormal CSF amino acid concentration Any deviation from the normal concentration of amino acids in the cerebrospinal fluid. PMID:715764 Abnormal amino acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of branched-chain amino acids in the cerebrospinal fluid. 2019-02-25T15:24:13Z Abnormal branched-chain amino acid levels in cerbrospinal fluid Abnormal CSF branched chain amino acid concentration Any deviation from the normal concentration of branched-chain amino acids in the cerebrospinal fluid. PMID:715764 Abnormal branched-chain amino acid levels in cerbrospinal fluid PMID:715764 Any deviation from the normal concentration of valine in the cerebrospinal fluid. 2019-02-25T15:28:13Z Abnormal valine levels in cerebrospinal fluid Abnormal CSF valine concentration Any deviation from the normal concentration of valine in the cerebrospinal fluid. PMID:715764 Abnormal valine levels in cerebrospinal fluid PMID:715764 Any increased amount from normal of valine in the cerebrospinal fluid. 2019-02-25T15:37:57Z High valine levels in cerebrospinal fluid Increased CSF valine concentration Any increased amount from normal of valine in the cerebrospinal fluid. PMID:715764 High valine levels in cerebrospinal fluid PMID:715764 Any decreased amount from normal of valine in the cerebrospinal fluid. 2019-02-25T15:40:23Z Low valine levels in cerebrospinal fluid Decreased CSF valine concentration Any decreased amount from normal of valine in the cerebrospinal fluid. PMID:715764 Low valine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of leucine in the cerebrospinal fluid. 2019-02-25T15:52:19Z Abnormal leucine levels in cerebrospinal fluid Abnormal CSF leucine concentration Any deviation from the normal concentration of leucine in the cerebrospinal fluid. PMID:715764 Abnormal leucine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of leucine in the cerebrospinal fluid. 2019-02-25T15:52:49Z Low leucine levels in cerebrospinal fluid Decreased CSF leucine concentration Abnormally decreased levels of leucine in the cerebrospinal fluid. PMID:715764 Low leucine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of leucine in cerebrospinal fluid. 2019-02-25T15:53:12Z High leucine levels in cerebrospinal fluid Increased CSF leucine concentration Abnormally increased levels of leucine in cerebrospinal fluid. PMID:715764 High leucine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of isoleucine in the cerebrospinal fluid. 2019-02-25T16:24:44Z Abnormal isoleucine levels in cerebrospinal fluid Abnormal CSF isoleucine concentration Any deviation from the normal concentration of isoleucine in the cerebrospinal fluid. PMID:715764 Abnormal isoleucine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of isoleucine in cerebrospinal fluid. 2019-02-25T16:25:11Z High levels of isoleucine in cerebrospinal fluid Increased CSF isoleucine concentration Abnormally increased levels of isoleucine in cerebrospinal fluid. PMID:715764 High levels of isoleucine in cerebrospinal fluid PMID:715764 Abnormally decreased levels of isoleucine in cerebrospinal fluid. 2019-02-25T16:25:36Z Low levels of isoleucine in cerebrospinal fluid Decreased CSF isoleucine concentration Abnormally decreased levels of isoleucine in cerebrospinal fluid. PMID:715764 Low levels of isoleucine in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of glutamine-family amino acids in the cerebrospinal fluid. 2019-02-25T16:41:53Z Abnormal glutamine family amino acid levels in cerebrospinal fluid Abnormal CSF glutamine family amino acid concentration Any deviation from the normal concentration of glutamine-family amino acids in the cerebrospinal fluid. PMID:715764 Abnormal glutamine family amino acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of glutamic acid in the cerebrospinal fluid. 2019-02-25T16:56:56Z Abnormal glutamic acid levels in cerebrospinal fluid Abnormal CSF glutamate concentration Any deviation from the normal concentration of glutamic acid in the cerebrospinal fluid. PMID:715764 Abnormal glutamic acid levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of glutamic acid in cerebrospinal fluid. 2019-02-25T16:57:13Z High glutamic acid levels in cerebrospinal fluid Increased CSF glutamate concentration Abnormally increased levels of glutamic acid in cerebrospinal fluid. PMID:715764 High glutamic acid levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of glutamic acid in cerebrospinal fluid. 2019-02-25T16:57:30Z Low glutamic acid levels in cerebrospinal fluid Decreased CSF glutamate concentration Abnormally decreased levels of glutamic acid in cerebrospinal fluid. PMID:715764 Low glutamic acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of arginine in the cerebrospinal fluid. 2019-02-25T17:12:23Z Abnormal arginine levels in cerebrospinal fluid Abnormal CSF arginine concentration Any deviation from the normal concentration of arginine in the cerebrospinal fluid. PMID:715764 Abnormal arginine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of arginine in cerebrospinal fluid. 2019-02-25T17:12:38Z High arginine levels in cerebrospinal fluid Increased CSF arginine concentration Abnormally increased levels of arginine in cerebrospinal fluid. PMID:715764 High arginine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of arginine in cerebrospinal fluid. 2019-02-25T17:12:54Z Low arginine levels in cerebrospinal fluid Decreased CSF arginine concentration Abnormally decreased levels of arginine in cerebrospinal fluid. PMID:715764 Low arginine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of aspartate-family amino acids in the cerebrospinal fluid. 2019-02-25T18:30:37Z Abnormal aspartate-family amino acid levels in cerebrospinal fluid Abnormal CSF aspartate family amino acid concentration Any deviation from the normal concentration of aspartate-family amino acids in the cerebrospinal fluid. PMID:715764 Any deviation from the normal concentration of lysine in the cerebrospinal fluid. 2019-02-25T18:31:42Z Abnormal lysine levels in cerebrospinal fluid Abnormal CSF lysine concentration Any deviation from the normal concentration of lysine in the cerebrospinal fluid. PMID:715764 Abnormal lysine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of lysine in cerebrospinal fluid. 2019-02-25T18:31:54Z Low lysine levels in cerebrospinal fluid Decreased CSF lysine concentration Abnormally decreased levels of lysine in cerebrospinal fluid. PMID:715764 Low lysine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of lysine in cerebrospinal fluid. 2019-02-25T18:32:16Z High lysine levels in cerebrospinal fluid Increased CSF lysine concentration Any deviation from the normal concentration of methionine in the cerebrospinal fluid. 2019-02-25T18:58:00Z Abnormal methionine levels in cerebrospinal fluid Abnormal CSF methionine concentration Any deviation from the normal concentration of methionine in the cerebrospinal fluid. PMID:715764 Abnormal methionine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of methionine in cerebrospinal fluid. 2019-02-25T18:58:44Z High methionine levels in cerebrospinal fluid Increased CSF methionine concentration Abnormally increased levels of methionine in cerebrospinal fluid. PMID:715764 High methionine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of aromatic amino acids in the cerebrospinal fluid. 2019-02-25T19:28:05Z Abnormal aromatic amino acid levels in cerebrospinal fluid Abnormal CSF aromatic amino acid concentration Any deviation from the normal concentration of aromatic amino acids in the cerebrospinal fluid. PMID:715764 Abnormal aromatic amino acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of phenylalanine in the cerebrospinal fluid. 2019-02-25T19:28:51Z Abnormal phenylalanine levels in cerebrospinal fluid Abnormal CSF phenylalanine concentration Any deviation from the normal concentration of phenylalanine in the cerebrospinal fluid. PMID:715764 Abnormal phenylalanine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of tyrosine in the cerebrospinal fluid. 2019-02-25T19:48:03Z Abnormal tyrosine levels in cerebrospinal fluid Abnormal CSF tyrosine concentration Any deviation from the normal concentration of tyrosine in the cerebrospinal fluid. PMID:715764 Abnormal tyrosine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of tyrosine in cerebrospinal fluid. 2019-02-25T19:53:00Z High tyrosine levels in cerebrospinal fluid Increased CSF tyrosine concentration Abnormally increased levels of tyrosine in cerebrospinal fluid. PMID:715764 High tyrosine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of tyrosine in cerebrospinal fluid. 2019-02-25T19:53:22Z Low tyrosine levels in the cerebrospinal fluid Decreased CSF tyrosine concentration Abnormally decreased levels of tyrosine in cerebrospinal fluid. PMID:715764 Low tyrosine levels in the cerebrospinal fluid PMID:715764 Abnormally increased levels of phenylalanine in cerebrospinal fluid. 2019-02-25T20:13:37Z High phenylalanine levels in cerebrospinal fluid Increased CSF phenylalanine concentration Abnormally increased levels of phenylalanine in cerebrospinal fluid. PMID:715764 High phenylalanine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of phenylalanine in cerebrospinal fluid. 2019-02-25T20:13:51Z Low phenylalanine levels in cerebrospinal fluid Decreased CSF phenylalanine concentration Abnormally decreased levels of phenylalanine in cerebrospinal fluid. PMID:715764 Low phenylalanine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of serine-family amino acids in the cerebrospinal fluid. 2019-02-25T20:27:34Z Abnormal serine-family amino acid levels in cerebrospinal fluid Abnormal CSF serine family amino acid concentration Any deviation from the normal concentration of serine-family amino acids in the cerebrospinal fluid. PMID:715764 Abnormal serine-family amino acid levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of serine in the cerebrospinal fluid. 2019-02-25T20:30:42Z Abnormal serine levels in cerebrospinal fluid Abnormal CSF serine concentration Any deviation from the normal concentration of serine in the cerebrospinal fluid. PMID:715764 Abnormal serine levels in cerebrospinal fluid PMID:715764 Abnormally increased levels of serine in cerebrospinal fluid. 2019-02-25T20:32:30Z High serine levels in cerebrospinal fluid Increased CSF serine concentration Abnormally increased levels of serine in cerebrospinal fluid. PMID:715764 High serine levels in cerebrospinal fluid PMID:715764 Abnormally decreased levels of serine in cerebrospinal fluid. 2019-02-25T20:32:46Z Low serine levels in cerebrospinal fluid Decreased CSF serine concentration Abnormally decreased levels of serine in cerebrospinal fluid. PMID:715764 Low serine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of glycine in the cerebrospinal fluid. 2019-02-25T20:40:09Z Abnormal glycine levels in cerebrospinal fluid. Abnormal CSF glycine concentration Any deviation from the normal concentration of glycine in the cerebrospinal fluid. PMID:715764 Abnormal glycine levels in cerebrospinal fluid. PMID:715764 Abnormally increased levels of glycine in cerebrospinal fluid. 2019-02-25T20:40:30Z High glycine levels in cerebrospinal fluid Increased CSF glycine concentration Abnormally increased levels of glycine in cerebrospinal fluid. PMID:715764 High glycine levels in cerebrospinal fluid PMID:715764 Any deviation from the normal concentration of ornithine in the cerebrospinal fluid. 2019-02-26T15:36:15Z Abnormal ornithine levels in cerebrospinal fluid Abnormal CSF ornithine concentration Any deviation from the normal concentration of ornithine in the cerebrospinal fluid. PMID:20551690 Abnormal ornithine levels in cerebrospinal fluid PMID:20551690 Abnormally increased levels of ornithine in cerebrospinal fluid. 2019-02-26T15:36:36Z High ornithine levels in cerebrospinal fluid Increased CSF ornithine concentration Abnormally increased levels of ornithine in cerebrospinal fluid. PMID:20551690 High ornithine levels in cerebrospinal fluid PMID:20551690 Any deviation from the normal concentration of citrulline in the cerebrospinal fluid. 2019-02-26T15:48:42Z Abnormal citrulline levels in cerebrospinal fluid Abnormal CSF citrulline concentration Any deviation from the normal concentration of citrulline in the cerebrospinal fluid. PMID:16793028 Abnormal citrulline levels in cerebrospinal fluid PMID:16793028 Abnormally increased levels of citrulline in cerebrospinal fluid. 2019-02-26T15:49:01Z High citrulline levels in cerebrospinal fluid Increased CSF citrulline concentration Abnormally increased levels of citrulline in cerebrospinal fluid. PMID:16793028 High citrulline levels in cerebrospinal fluid PMID:16793028 The most dramatic and severe form of hair loss characterized by an absence of hair follicles. 2019-08-21T15:12:23Z Atrichia The most dramatic and severe form of hair loss characterized by an absence of hair follicles. PMID:14676077 Any structural anomaly of an inner ear epithelium. haendel 2014-07-15T23:41:38Z UMLS:C4073211 human_phenotype HP:3000002 Abnormal inner ear epithelium morphology Any structural anomaly of an inner ear epithelium. GOC:TermGenie An abnormality of a buccal mucosa. vasilevs 2015-08-07T00:13:17Z UMLS:C4073228 Abnormality of cheek mucosa Abnormality of inside lining of cheek human_phenotype HP:3000019 Abnormality of buccal mucosa An abnormality of a buccal mucosa. GOC:TermGenie Abnormality of cheek mucosa ORCID:0000-0001-5889-4463 Abnormality of inside lining of cheek ORCID:0000-0001-5889-4463 An abnormality of a cartilage of external ear. vasilevs 2015-08-07T00:15:54Z UMLS:C4073231 human_phenotype HP:3000022 Abnormality of cartilage of external ear An abnormality of a cartilage of external ear. GOC:TermGenie Any structural abnormality of a facial artery, one of the branches of the external carotid artery. vasilevs 2015-08-07T00:16:03Z UMLS:C4073233 Abnormality of facial artery human_phenotype HP:3000024 Abnormal facial artery morphology Any structural abnormality of a facial artery, one of the branches of the external carotid artery. GOC:TermGenie ORCID:0000-0001-5889-4463 Any abnormality of nasopharyngeal adenoids. vasilevs 2015-08-07T00:27:21Z UMLS:C4073241 Abnormality of adenoids Abnormality of nasopharyngeal adenoids Abnormality of nasopharyngeal tonsil Abnormality of pharyngeal tonsil human_phenotype HP:3000033 The adenoid, a mass of lymphatic tissue situated posterior to the nasal cavity, in the roof of the nasopharynx, where the nose blends into the throat. Abnormal nasopharyngeal adenoid morphology Abnormality of adenoids ORCID:0000-0001-5889-4463 Abnormality of nasopharyngeal tonsil ORCID:0000-0001-5889-4463 Abnormality of pharyngeal tonsil ORCID:0000-0001-5889-4463 The adenoid, a mass of lymphatic tissue situated posterior to the nasal cavity, in the roof of the nasopharynx, where the nose blends into the throat. GOC:TermGenie ORCID:0000-0001-5889-4463 An abnormality of a blood vessel of the head, including branches of the arterial and venous systems of the head. vasilevs 2015-08-07T00:36:02Z UMLS:C4073244 Abnormality of blood vessel of head Abnormality of head blood vessel Abnormality of vasculature of head human_phenotype HP:3000036 Abnormality of head blood vessel An abnormality of a blood vessel of the head, including branches of the arterial and venous systems of the head. GOC:TermGenie ORCID:0000-0001-5889-4463 Abnormality of blood vessel of head Abnormality of head blood vessel An abnormality of a blood vessel of the neck, including branches of the arterial and venous systems of the neck. vasilevs 2015-08-07T00:36:06Z UMLS:C4073245 Abnormality of blood vessel of neck Abnormality of neck blood vessel Abnormality of the cervical blood vessels Abnormality of the cervical vasculature Abnormality of the vasculature of the neck human_phenotype HP:3000037 Abnormality of neck blood vessel An abnormality of a blood vessel of the neck, including branches of the arterial and venous systems of the neck. GOC:TermGenie ORCID:0000-0001-5889-4463 Abnormality of blood vessel of neck Abnormality of neck blood vessel An abnormality of an external carotid artery. vasilevs 2015-08-07T00:36:24Z Abnormality of carotid artery Disorder of carotid artery UMLS:C4073249 human_phenotype HP:3000041 Abnormality of external carotid artery An abnormality of an external carotid artery. GOC:TermGenie Abnormality of carotid artery https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0001-5889-4463 Disorder of carotid artery https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0001-5889-4463 Any structural abnormality of a jugular vein. vasilevs 2015-08-07T01:04:39Z UMLS:C4073250 Abnormality of jugular vein human_phenotype HP:3000042 Abnormal jugular vein morphology Any structural abnormality of a jugular vein. GOC:TermGenie Abnormality of jugular vein An abnormality of a facial vein. vasilevs 2015-08-07T01:04:44Z UMLS:C4073251 Abnormal vein of face Abnormality of facial vein human_phenotype HP:3000043 Abnormal facial vein morphology An abnormality of a facial vein. GOC:TermGenie Abnormal vein of face ORCID:0000-0001-5208-3432 Abnormality of facial vein An abnormality of a genioglossus muscle. vasilevs 2015-08-07T01:04:53Z UMLS:C4073253 human_phenotype HP:3000045 Abnormality of genioglossus muscle An abnormality of a genioglossus muscle. GOC:TermGenie Any structural anomaly of the glossopharyngeal nerve, the ninth paired cranial nerve (CN IX). vasilevs 2015-08-07T01:08:41Z UMLS:C4073255 Abnormality of glossopharyngeal nerve human_phenotype HP:3000047 The glossopharyngeal nerve originates in the medulla oblongata. It Innervates the oropharynx, carotid body and sinus, as well as the posterior third of the tongue (where it mediates taste sensation), the middle ear cavity and the Eustachian tube. Additionally, it innervates the stylopharyngeus muscle of the pharynx. Abnormal glossopharyngeal nerve morphology Any structural anomaly of the glossopharyngeal nerve, the ninth paired cranial nerve (CN IX). GOC:TermGenie An abnormality of an odontoid tissue. vasilevs 2015-08-07T01:08:54Z UMLS:C4073258 Abnormality of hard tissues of teeth Abnormality of tooth hard tissue human_phenotype HP:3000050 Abnormality of odontoid tissue An abnormality of an odontoid tissue. GOC:TermGenie An abnormality of a hyoglossus muscle. vasilevs 2015-08-07T01:08:58Z UMLS:C4073259 Abnormality of hyoglossus muscle human_phenotype HP:3000051 Abnormal hyoglossus muscle morphology An abnormality of a hyoglossus muscle. GOC:TermGenie An abnormality of a hyoid bone. vasilevs 2015-08-07T01:09:03Z UMLS:C4073260 human_phenotype HP:3000052 Abnormality of hyoid bone An abnormality of a hyoid bone. GOC:TermGenie A structural anomaly of the hypopharyx, which is the most inferior portion of the pharynx. The hypopharynx continues from the oropharynx at the pharyngoepiglottic fold superiorly and extends inferiorly to the level of the inferior aspect of the cricoid cartilage, which marks the beginning of the cervical esophagus. vasilevs 2015-08-07T01:09:07Z UMLS:C4073261 Abnormality of hypopharynx Abnormality of lower pharynx HP:3000053 Abnormal hypopharynx morphology A structural anomaly of the hypopharyx, which is the most inferior portion of the pharynx. The hypopharynx continues from the oropharynx at the pharyngoepiglottic fold superiorly and extends inferiorly to the level of the inferior aspect of the cricoid cartilage, which marks the beginning of the cervical esophagus. GOC:TermGenie HPO:probinson Abnormality of hypopharynx Abnormality of lower pharynx ORCID:0000-0001-5889-4463 An abnormality of an artery of lower lip. vasilevs 2015-08-07T03:18:34Z UMLS:C4073264 Abnormality of the inferior labial artery human_phenotype HP:3000056 Abnormality of artery of lower lip An abnormality of an artery of lower lip. GOC:TermGenie An abnormality of an internal carotid artery. vasilevs 2015-08-07T03:19:02Z UMLS:C1860488 Abnormality of internal carotid artery human_phenotype HP:3000062 Abnormal internal carotid artery morphology An abnormality of an internal carotid artery. GOC:TermGenie An abnormality of an internal jugular vein. vasilevs 2015-08-07T03:19:06Z UMLS:C4073270 human_phenotype HP:3000063 Abnormality of internal jugular vein An abnormality of an internal jugular vein. GOC:TermGenie An abnormality of an intrinsic muscle of tongue. vasilevs 2015-08-07T03:19:10Z UMLS:C4073271 Abnormality of intrinsic lingual muscle human_phenotype HP:3000064 Abnormality of intrinsic muscle of tongue An abnormality of an intrinsic muscle of tongue. GOC:TermGenie Abnormality of intrinsic lingual muscle ORCID:0000-0001-5889-4463 An abnormality of a lacrimal artery. vasilevs 2015-08-07T03:38:25Z UMLS:C4073272 Abnormality of lacrimal artery human_phenotype HP:3000065 Abnormal lacrimal artery morphology An abnormality of a lacrimal artery. GOC:TermGenie An abnormality of a lacrimal sac. vasilevs 2015-08-07T03:38:31Z UMLS:C4073273 Abnormality of lacrimal sac human_phenotype HP:3000066 Abnormal lacrimal sac morphology An abnormality of a lacrimal sac. GOC:TermGenie Any structural abnormality of a lingual artery. vasilevs 2015-08-07T03:39:06Z UMLS:C4073281 Abnormality of lingual artery human_phenotype HP:3000074 Abnormal lingual artery morphology Any structural abnormality of a lingual artery. GOC:TermGenie Any structural anomaly of a lingual nerve. vasilevs 2015-08-07T03:39:10Z UMLS:C4073282 Abnormality of lingual nerve human_phenotype HP:3000075 The lingual nerve (LN) is one of the two terminal branches of the posterior division of the mandibular nerve. It supplies the general sensation to the mucosa of the anterior two-thirds of the tongue, the sublingual mucosa, the mandibular lingual gingiva and the floor of the mouth.The chorda tympani nerve, a branch of the facial nerve joins this nerve carrying taste fibers from the anterior two third of the tongue and parasympathetic fibers to the submandibular ganglion. Abnormal lingual nerve morphology Any structural anomaly of a lingual nerve. GOC:TermGenie PMID:27662622 A structural abnormality of a mandibular symphysis. vasilevs 2015-08-07T03:39:28Z UMLS:C4073286 Abnormality of mandible symphysis human_phenotype HP:3000079 Abnormality of mandibular symphysis A structural abnormality of a mandibular symphysis. GOC:TermGenie measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software information carrier In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. A quality of an information bearer that imparts the information content 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity dot plot Dot plot of SSC-H and FSC-H. A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification source code module The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. A source code module is a directive information entity that specifies, using a programming language, some algorithm. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000039 group:OBI source code module data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI histogram heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram scatter plot Comparison of gene expression values in two samples can be displayed in a scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry identifier An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. identifier A clinically prescribed procedure, therapy, intervention, or recommendation. 2018-11-16T20:07:28Z OGMS:0000096 health care process medical action health care process OGMS:0000096 All manners of treatment, be they pharmaceuticals, invasive procedures, etc. to relieve illness and injury in attempts to bring the body back to its normal state. 2018-11-16T20:08:29Z medical procedure NCIT:C25218 NCIT:C49236 OAE:0000094 OGMS:0000112 SIO:001024 clinical procedure treatment An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process. therapeutic procedure All manners of treatment, be they pharmaceuticals, invasive procedures, etc. to relieve illness and injury in attempts to bring the body back to its normal state. ISBN-10:0124105165 An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process. NCIT:C49236 Any procedure or test to diagnose a disease or disorder. 2018-11-16T20:10:20Z NCIT:C18020 OGMS:0000104 diagnostic technique procedure diagnostic testing diagnostic procedure Any procedure or test to diagnose a disease or disorder. NCIT:C18020 A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. 2018-11-16T20:10:35Z ERO:0000378 NCIT:C15329 NCIT:C17173 NCRO:0000228 OAE:0000067 SCDO:1000017 operation surgery surgical intervention surgical operation surgical procedure A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. NCIT:C15329 Any technology or method that aids in the visualization of any biological process, cell, tissue or organ for use in screening, diagnosis, surgical procedures or therapy. 2018-11-16T20:10:50Z NCIT:C17369 imaging procedure imaging technique medical imaging therapeutic imaging procedure therapeutic imaging technique clinical imaging procedure Any technology or method that aids in the visualization of any biological process, cell, tissue or organ for use in screening, diagnosis, surgical procedures or therapy. NCIT:C17369 Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting for diagnosis, treatment, or therapy. 2018-11-16T20:11:26Z NCIT:C25294 clinical lab testing clinical laboratory testing clinical testing lab testing clinical laboratory procedure Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting for diagnosis, treatment, or therapy. NCIT_C25294 http://orcid.org/0000-0001-7941-2961 obsolete therapeutic intervention false Behavioral or regulatory nutritional interventions aim at modifying nutritional intake which have an impact on health outcomes. 2018-11-16T20:12:00Z nutritional intervention nutrition intervention Behavioral or regulatory nutritional interventions aim at modifying nutritional intake which have an impact on health outcomes. http://orcid.org/0000-0001-7941-2961 Cognitive and behavioral interventions are therapies that are designed to decrease symptoms and foster the belief that one has control over thoughts, beliefs, attitudes, and skills to facilitate coping. 2018-11-16T20:12:16Z NCIT:C116519 NCIT:C15184 NCIT:C64345 cognitive and behavioral therapies cognitive and behavioral therapy cognitive and behavioural intervention cognitive behavior therapy cognitive behavioral therapy cognitive behaviour therapy cognitive behavioural therapy cognitive and behavioral intervention Cognitive and behavioral interventions are therapies that are designed to decrease symptoms and foster the belief that one has control over thoughts, beliefs, attitudes, and skills to facilitate coping. PMID:22796302 https://orcid.org/0000-0002-7463-6306 The treatment of deformity or disease through mechanical force and movement, including both active and passive exercises, intended to ameliorate injury, increase mobility, and improve overall function. 2018-11-16T20:12:31Z NCIT:C15302 OGMS:0000115 PT physiatric procedure physical medicine procedure physical therapeutics physical therapy procedure physiotherapy physiotherapy procedure physical therapy The treatment of deformity or disease through mechanical force and movement, including both active and passive exercises, intended to ameliorate injury, increase mobility, and improve overall function. NCIT:C15302 PT Complementary and alternative medicine (CAM) or “complementary health approaches” are a group of diverse medical and health care practices and products that are not presently considered to be part of conventional medicine. 2019-01-07T19:24:28Z NCIT:C51976 SCDO:0000271 CAM therapy complementary or alternative medical procedure complementary medicine complementary therapy complementary and alternative medical therapy Complementary and alternative medicine (CAM) or “complementary health approaches” are a group of diverse medical and health care practices and products that are not presently considered to be part of conventional medicine. NCCIH Treatment of a disease by means of exposure of the target or the whole body to radiation. Radiation therapy is often used as part of curative therapy and occasionally as a component of palliative treatment for cancer. Other uses include total body irradiation prior to transplantation. 2018-11-16T20:20:38Z NCIT:C15313 OGMS:0000116 RT radiation radiation therapy procedure radiotherapeutics radiotherapy radiation therapy Treatment of a disease by means of exposure of the target or the whole body to radiation. Radiation therapy is often used as part of curative therapy and occasionally as a component of palliative treatment for cancer. Other uses include total body irradiation prior to transplantation. NCIT:C15313 RT A type of treatment that uses substances derived from or made by living organisms to treat disease; this includes both naturally occurring and synthetic products. 2018-11-16T20:20:54Z NCIT:C15187 BRM therapy biologic therapies biological response modifier therapy biological therapy biotheraphy biologic therapy A type of treatment that uses substances derived from or made by living organisms to treat disease; this includes both naturally occurring and synthetic products. NCIT:C15187 BRM therapy Cell therapy is therapy in which cellular material is injected into a patient. 2018-11-16T20:21:19Z NCIT:C70601 cell therapy cellular therapies cellular therapy Cell therapy is therapy in which cellular material is injected into a patient. PMID:24471045 A therapy or action designed to prevent disease or ailment. 2018-11-16T20:21:49Z preventative clinical measures preventative medical actions preventative medical measures preventative therapies preventative therapy preventive medical actions preventive medical measures preventive therapeutics preventative therapeutics A broad subcategory of medical signs or objective indications of medical state which can be measured accurately and reproducibly. 2018-11-16T20:22:04Z NCIT:C63333 biomarker analysis A broad subcategory of medical signs or objective indications of medical state which can be measured accurately and reproducibly. PMID:20978388 A behavioral modification or implementation of a behavior designed to prevent disease or ailment. 2018-11-16T20:22:48Z behavioral preventative therapeutics behavioral preventive care behavioral preventive therapy preventative behavior therapy preventative behavioral therapy behavioral preventative care An approach that improves the quality of life of patients and their families facing the problems associated with life-threatening illness, through the prevention and relief of suffering by means of early identification and impeccable assessment and treatment of pain and other problems, physical, psychosocial, and spiritual’. 2018-11-16T20:23:01Z NCIT:C101516 NCIT:C15747 comfort care symptom management supportive care palliative therapeutics An approach that improves the quality of life of patients and their families facing the problems associated with life-threatening illness, through the prevention and relief of suffering by means of early identification and impeccable assessment and treatment of pain and other problems, physical, psychosocial, and spiritual’. PMID:27162584 A service delivery system that provides palliative care/medicine when life expectancy is 6 months or less and when curative or life-prolonging therapy is no longer indicated. 2018-11-16T20:23:10Z NCIT:C15252 hospice care A service delivery system that provides palliative care/medicine when life expectancy is 6 months or less and when curative or life-prolonging therapy is no longer indicated. PMID:22190887 Care for patients with a progressive life-limiting disease with a prognosis of months or less. 2019-01-09T20:15:05Z NCIT:C67359 end-of-life treatment management end-of life care Care for patients with a progressive life-limiting disease with a prognosis of months or less. PMID:23796586 Any medical procedure used to sustain the life of a patient in critical condition. 2019-01-09T20:25:04Z NCIT:C95171 OMIT:0009105 life support care Any medical procedure used to sustain the life of a patient in critical condition. NCIT:C95171 obsolete therapeutic avoidance of behavior false obsolete therapeutic mental or psychological behavior avoidance false obsolete stress avoidance false obsolete smoking avoidance false A clinical recommendation to avoid preventable diseases by vaccination or otherwise lowering risk for certain diseases. 2019-01-11T19:39:19Z disease avoidance preventable disease avoidance recommendation Avoidance of an illness or infection that can be spread from person to person, animal to person, animal to animal or person to animal by taking precautionary measures, such as good hygiene practices or vaccines. 2019-01-11T19:39:37Z avoid communicable disease communicable disease prevention communicable disease avoidance 2019-01-11T19:59:24Z physiologic state avoidance A medical requirement or recommendation to avoid dehydration. 2019-01-11T19:59:44Z avoid dehydration dehydration avoidance A medical requirement or recommendation to avoid hypertension. 2019-01-11T19:59:54Z avoid hypertension hypertension avoidance A medical recommendation to avoid obesity. 2019-01-11T20:01:31Z avoid obesity obesity avoidance A medical requirement or recommendation to avoid skin inflammation. 2019-01-11T20:03:43Z avoid skin abrasion avoid skin inflammation skin inflammation avoidance 2019-01-11T20:11:57Z therapeutic avoidance of physical activity 2019-01-11T20:12:16Z impact sports avoidance therapeutic impact activities avoidance 2019-01-11T20:13:10Z therapeutic isometric exercise avoidance A clinical recommendation to avoid or refrain from certain environmental exposures in order to maintain health or ameliorate symptoms. 2019-01-11T20:50:37Z therapeutic avoidance of environmental exposure 2019-01-11T20:50:51Z radiation exposure avoidance 2019-01-11T20:56:19Z sunlight avoidance 2019-01-11T20:56:39Z food consumption avoidance nutrition intake avoidance Any substance introduced into a living organism with therapeutic or diagnostic purpose. 2019-01-15T18:20:06Z CHEBI:52217 drug therapy drug treatment medication therapy pharmaceutical drug pharmaceutical treatment pharmacological treatment treatment with drug Medical treatment by means of drugs. pharmacotherapy Any substance introduced into a living organism with therapeutic or diagnostic purpose. CHEBI:52217  Medical treatment by means of drugs. http://orcid.org/0000-0001-7941-2961 Use of a drug to treat or prevent bacterial infections. 2019-01-15T18:59:44Z CHEBI:36047 antibacterial drug therapy antibacterial treatment antibiotic agent therapy treatment with an anti-bacterial drug treatment with an anti-bacterial medication treatment with an anti-bacterial therapy treatment with an antibacterial agent treatment with an antibacterial drug treatment with an antibacterial medication treatment with an antibacterial therapy treatment with antibacterial drug antibacterial agent therapy Use of a substance that inhibits or prevents the proliferation of neoplasms. 2019-01-15T19:01:01Z anticancer agent therapy CHEBI:35610 NCIT:C274 anti-neoplastic agent therapy antineoplastic agent therapy antineoplastic drug therapy cytostatic agent therapy cytostatic drug therapy treatment with anti-cancer drug treatment with anti-cancer medication treatment with anti-neoplastic drug treatment with anti-neoplastic medication treatment with antineoplastic agent treatment with antineoplastic drug treatment with antineoplastic medication antineoplastic agent therapy A medical recommendation of sustained exercise that places an increased oxygen demand on the cardiovascular system and promotes an increased efficiency of the body's use of oxygen. 2019-01-15T19:02:35Z NCIT:C39774 aerobic activity aerobic exercise aerobic exercise therapy A medical recommendation of sustained exercise that places an increased oxygen demand on the cardiovascular system and promotes an increased efficiency of the body's use of oxygen. NCIT:C39774 http://orcid.org/0000-0001-7941-2961 The administration of oxygen to an individual, usually to aid in respiration. 2019-01-15T19:14:17Z MeSH:D010102 NCIT:C94624 oxygen inhalation therapy oxygen support therapy Inhalation of oxygen aimed at restoring toward normal any pathophysiologic alterations of gas exchange in the cardiopulmonary system, as by the use of a respirator, nasal catheter, tent, chamber, or mask. (From Dorland, 27th ed & Stedman, 25th ed) supplemental oxygen therapy The administration of oxygen to an individual, usually to aid in respiration. NCIT:C94624 Inhalation of oxygen aimed at restoring toward normal any pathophysiologic alterations of gas exchange in the cardiopulmonary system, as by the use of a respirator, nasal catheter, tent, chamber, or mask. (From Dorland, 27th ed & Stedman, 25th ed) MeSH:D010102 2019-01-15T19:14:42Z lung volume reduction surgery Transference of a tissue or organ within an individual, between individuals of the same species, or between individuals of different species. 2019-01-15T19:15:04Z NCIT:C15342 NCIT:C15431 OBI:0000105 transplant procedure transplantation transplantation surgery transplantation surgical procedure grafting procedure transplantation procedure Transference of a tissue or organ within an individual, between individuals of the same species, or between individuals of different species. NCIT:C15342 obsolete lung transplantation surgical procedure false The surgical transfer of a healthy liver to a patient. 2020-06-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C15271 hepatic transplantation liver grafting liver transplantation liver transplantation surgical procedure surgical transplantation of the liver transplantation of liver liver transplantation liver transplantation surgical procedure 2019-01-15T19:31:56Z chemical exposure avoidance The use of ultrasound to produce images of structures in the human body. 2019-01-15T19:32:35Z ERO:0001325 NCIT:C17230 diagnostic ultrasound medical sonography sonography ultrasound procedure 2D ultrasounds produce a flat image of the organs. 3D images show three-dimensional external images of organs or fetus. 4D ultrasounds generates an image that is continuously updated, like amoving image. A procedure that uses high-energy sound waves to look at tissues and organs inside the body. The sound waves make echoes that form pictures of the tissues and organs on a computer screen (sonogram). Ultrasound may be used to help diagnose diseases, such as cancer. It may also be used during pregnancy to check the fetus (unborn baby) and during medical procedures, such as biopsies. Also called ultrasonography. ultrasonography procedure obsolete liver ultrasound procedure false A procedure to measure pancreatic secretion to discriminate between pancreatic and nonpancreatic causes of malabsorption. 2019-01-15T19:35:19Z NCIT:C97101 pancreatic function assessment pancreatic function testing 2019-01-15T19:35:36Z digestive system testing The act of receiving professional guidance in resolving personal conflicts and emotional problems. 2019-01-19T19:44:32Z NCIT:C15308 NCIT:C61547 NCIT:C63474 behaviour therapy behavioural counseling counseling intervention psychotherapy behavioral counseling The act of receiving professional guidance in resolving personal conflicts and emotional problems. NCIT:C61547 counseling intervention NCIT:C61547 Counseling designed to guide and support an individual to overcome alcohol dependence. 2019-01-19T19:46:47Z NCIT:C150658 alcoholism counseling Counseling designed to guide and support an individual to overcome alcohol dependence. NCIT:C150658 The process whereby an expert in hereditary disorders provides information about risk and clinical burden of a disorder or disorders to patients or relatives in families with genetic disorders as an aid to making informed and responsible decisions about marriage, children, early diagnosis, and handling disability. 2019-01-19T19:48:00Z NCIT:C15240 SCDO:0000443 genetic counseling The process whereby an expert in hereditary disorders provides information about risk and clinical burden of a disorder or disorders to patients or relatives in families with genetic disorders as an aid to making informed and responsible decisions about marriage, children, early diagnosis, and handling disability. NCIT:C15240 A wide range of techniques and psychotherapies aimed at controlling a person's level of stress. 2019-01-19T19:49:24Z NCIT:C67032 therapy for stress therapy to relieve stress stress management stress therapy stress management therapy A process by which a health professional provides education, recommendations, or interventions to help clients stop using tobacco products. 2019-01-19T19:51:07Z NCIT:C101244 smoking cessation counseling smoking cessation tobacco cessation counseling A process by which a health professional provides education, recommendations, or interventions to help clients stop using tobacco products. NCIT:C101244 smoking cessation http://orcid.org/0000-0001-7941-2961 The practice of piercing specific points on the body with very thin sterile needles in order to relieve pain or induce regional anesthesia. 2019-01-19T20:30:57Z NCIT:C15176 acupuncture therapy The practice of piercing specific points on the body with very thin sterile needles in order to relieve pain or induce regional anesthesia. NCIT:C15176 Continuous and profound contemplation or musing on a subject or series of subjects of a deep or abstruse nature; contemplation of spiritual matters. 2019-01-19T20:32:30Z NCIT:C51975 SCDO:0000741 meditation therapy Continuous and profound contemplation or musing on a subject or series of subjects of a deep or abstruse nature; contemplation of spiritual matters. NCIT:C51975 An ancient system of practices used to balance the mind and body through exercise, meditation (focusing thoughts), and control of breathing and emotions. Yoga is being studied as a way to relieve stress and treat sleep problems. 2019-01-19T20:34:15Z NCIT:C64897 yoga therapy An ancient system of practices used to balance the mind and body through exercise, meditation (focusing thoughts), and control of breathing and emotions. Yoga is being studied as a way to relieve stress and treat sleep problems. NCIT:C64897 An alternative medical system that focuses on the relationship between bodily structure (primarily that of the spine) and function, and how that relationship affects the preservation and restoration of health. Chiropractors use manipulative therapy as an integral treatment tool. 2019-01-19T20:35:28Z NCIT:C15204 chiropractic therapies chiropractic treatment chiropratic medicine chiropractic therapy An alternative medical system that focuses on the relationship between bodily structure (primarily that of the spine) and function, and how that relationship affects the preservation and restoration of health. Chiropractors use manipulative therapy as an integral treatment tool. NCIT:C15204 A therapeutic method of manipulation, methodical pressure, friction, and kneading of the body. 2019-01-19T20:36:55Z NCIT:C15276 massage massage and body work massage therapy A therapeutic method of manipulation, methodical pressure, friction, and kneading of the body. NCIT:C15276 Any alteration or treatment in an individual's diet with a planned goal, usually designed to improve the individual's overall health. 2019-01-19T20:39:14Z NCIT:C15447 diet behavioral nutritional intervention dietary intervention Any alteration or treatment in an individual's diet with a planned goal, usually designed to improve the individual's overall health. NCIT:C15447 The restriction of energy (calorie) intake below the amount required for weight maintenance. 2019-01-19T20:39:29Z LCD intake calorie restricted food intake carorie restriction in food intake low calorie diet intake primarily food‐based low‐calorie diet intake calorie restrictive diet intake The restriction of energy (calorie) intake below the amount required for weight maintenance. PMID:23748374 LCD intake Delivery of enteral nutrition via a tube placed into the stomach, duodenum, or jejunum. 2019-01-19T20:40:39Z NCIT:C93322 EN intake enteral nutrition support intake enteral tube feeding nutrition intake tube feeding nutrition intake enteral nutrition intake Delivery of enteral nutrition via a tube placed into the stomach, duodenum, or jejunum. NCIT:C93322 EN intake obsolete alcohol intake avoidance false 2019-01-19T20:54:50Z excessive alcohol avoidance 2019-01-19T20:55:05Z Some processed foods and soy contain large amounts of estrogen. estrogen-containing food avoidance 2019-01-19T20:59:49Z Some foods, particularly red meat, have high amounts of iron. excessive iron consumption avoidance 2019-01-19T21:00:36Z excessive protein consumption avoidance 2019-01-19T21:01:13Z fasting avoidance Abstinence from all or some kinds of food or drink, particularly for religious observance, medical nutrition therapy, or prior to a medical procedure. 2019-01-19T21:01:21Z NCIT:C63663 NPO fasting nil per os therapeutic fasting intermittant fasting fasting intervention Abstinence from all or some kinds of food or drink, particularly for religious observance, medical nutrition therapy, or prior to a medical procedure. PMID:16630428 PMID:27499591 https://orcid.org/0000-0002-7463-6306 NPO obsolete food consumption avoidance false obsolete meat consumption avoidance false obsolete nut consumption avoidance false obsolete seafood consumption avoidance false obsolete mussel consumption avoidance false 2019-01-19T21:05:54Z dietary iron supplementation avoidance obsolete saffron consumption avoidance false The addition of one or more elements and/or chemical compounds that are either absent or deficient in an individual's daily diet. 2019-01-19T21:07:25Z NCIT:C15425 nutritional supplementation The addition of one or more elements and/or chemical compounds that are either absent or deficient in an individual's daily diet. NCIT:C15425 Addition of multivitamin preparation to the diet for adequate and complete nutrition. 2019-01-19T21:08:59Z NCIT:C1654 dietary supplementation of multivitamin preparation multivitamin preparation supplemental intake supplementation of multivitamin preparation supplementation with multivitamin A dietary supplement containing all or most of the vitamins that may not be readily available in the diet. Vitamins may be classified according to their solubility either in lipids (vitamins A, D, E, K, F) or in water (vitamins C, B-complex). Present in minute amounts in various foods, vitamins are essential to maintaining normal metabolism and biochemical functions. multivitamin preparation multivitamin supplementation A dietary supplement containing all or most of the vitamins that may not be readily available in the diet. Vitamins may be classified according to their solubility either in lipids (vitamins A, D, E, K, F) or in water (vitamins C, B-complex). Present in minute amounts in various foods, vitamins are essential to maintaining normal metabolism and biochemical functions. NCIT:C1654 Addition of iron atom to a the diet for complete nutrition support. 2019-01-19T21:09:25Z dietary supplementation of iron atom iron atom supplemental intake oral iron supplementation supplementation of iron atom iron replacement therapy Oral iron supplementation is an effective and well‐studied option to replenish iron stores. iron supplementation Oral iron supplementation is an effective and well‐studied option to replenish iron stores. PMID:28328083 Addition of vitamin C to the diet for adequate and complete nutrition. 2019-01-19T21:09:48Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of vitamin C supplementation of vitamin C vitamin C supplemental intake vitamin C vitamin C supplementation Addition of vitamin D to a the diet for complete nutrition support. 2019-01-19T21:09:59Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of vitamin D supplementation of vitamin D vitamin D supplemental intake vitamin D supplementation obsolete amino acid supplementation false Addition of food antioxidant to a the diet for complete nutrition support. 2019-01-19T21:12:19Z NCIT:C67025 antioxidant therapy dietary supplementation of food antioxidant food antioxidant supplemental intake supplementation of food antioxidant Treatment with antioxidants in order to protect cells against damage caused by oxygen-free radicals. food antioxidant supplementation Treatment with antioxidants in order to protect cells against damage caused by oxygen-free radicals. NCIT:C67025 Administration of nutritional support by means of a tube passed into the stomach. 2019-01-19T21:13:59Z NCIT:C73430 gastrogavage nutrition intake gavage nutrition intake Administration of nutritional support by means of a tube passed into the stomach. NCIT:C73430 Total parenteral nutrition formulated for intravenous administration in patients who cannot eat or cannot get enough nutrients from the foods they eat. It is a liquid mixture of proteins, carbohydrates, fats, vitamins, minerals and other nutrients. 2019-01-19T21:16:22Z NCIT:C29484 TNA intake TPN intake total nutrient admixture intake hyperalimentation total parenteral nutrition intake Total parenteral nutrition formulated for intravenous administration in patients who cannot eat or cannot get enough nutrients from the foods they eat. It is a liquid mixture of proteins, carbohydrates, fats, vitamins, minerals and other nutrients. NCIT:C29484 TPN intake Any action taken for the purpose of improving or maintaining an individual's memory. 2019-01-19T21:26:54Z NCIT:C116526 working memory interventions memory aids memory intervention A behavioral modification or implementation of a behavior designed to prevent smoking. 2019-01-19T21:33:17Z NCIT:C16114 prevent smoking smoking prevention A behavioral modification or implementation of a behavior designed to prevent smoking. https://orcid.org/0000-0002-7463-6306 The prevention of conception or impregnation by the use of devices or drugs or surgery. 2019-01-19T21:34:14Z NCIT:C37932 birth control conception prevention contraceptive management pregnancy prevention contraceptive pregnancy prevention The prevention of conception or impregnation by the use of devices or drugs or surgery. NCIT:C37932 birth control NCIT:C37932 Immunization is the process whereby a person is made immune or resistant to an infectious disease, typically by the administration of a vaccine. 2019-01-19T21:36:12Z NCIT:C15258 OBI:1110094 immunization preventive immunization preventative immunization Immunization is the process whereby a person is made immune or resistant to an infectious disease, typically by the administration of a vaccine. WHO immunization NCIT:C15258 OBI:1110094 Active immunity refers to the process of exposing the body to an antigen to generate an adaptive immune response: the response takes days/weeks to develop but may be long lasting—even lifelong. 2019-01-20T00:31:42Z IDO:0000498 NCIT:C15416 VO:0000491 active immunization Active immunity refers to the process of exposing the body to an antigen to generate an adaptive immune response: the response takes days/weeks to develop but may be long lasting—even lifelong. PMID:18045976 Passive immunity refers to the process of providing IgG antibodies to protect against infection; it gives immediate, but short-lived protection. 2019-01-20T00:31:52Z NCIT:C15259 OBI:0001174 VO:0000492 passive immunization Passive immunity refers to the process of providing IgG antibodies to protect against infection; it gives immediate, but short-lived protection. PMID:18045976 2019-01-20T00:36:49Z disease exposure immunization The use of any device, marker, or other means for the purpose of detecting the presence of disease, usually in asymptomatic individuals. 2019-01-20T00:39:19Z NCIT:C15419 disease screening The use of any device, marker, or other means for the purpose of detecting the presence of disease, usually in asymptomatic individuals. NCIT:C15419 Testing conducted utilizing a manual or microprocessor audiometer to test for hearing loss. 2019-01-20T00:42:26Z NCIT:C38036 hearing exam procedure hearing testing procedure audiometric testing Testing conducted utilizing a manual or microprocessor audiometer to test for hearing loss. NCIT:C38036 The use of any device, marker, or other means for the purpose of detecting the presence of a tumor, usually before there are any symptoms. 2019-01-20T00:45:24Z NCIT:C15406 cancer screening The use of any device, marker, or other means for the purpose of detecting the presence of a tumor, usually before there are any symptoms. NCIT:C15406 The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder. 2019-01-20T00:46:22Z NCIT:C15709 genetic analysis genetic testing The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder. NCIT:C15709 Any test performed during pregnancy to assess fetal health and to detect for genetic abnormalities and various disorders. 2019-01-20T00:51:25Z pregnancy related screening prenatal screening Any test performed during pregnancy to assess fetal health and to detect for genetic abnormalities and various disorders. NCIT:C92721 An examination of tissue removed from the body to assess the presence, cause, or extent of a disease. 2019-01-20T00:52:34Z NCIT:C15189 OPMI:0000274 biopsy biopsy procedure A diagnostic or therapeutic procedure in which an endoscope is inserted in a tubular organ to examine the structural architecture and/or remove abnormal tissues. 2019-01-20T01:01:22Z NCIT:C16546 endoscopic exam endoscopy endoscopic procedure A diagnostic or therapeutic procedure in which an endoscope is inserted in a tubular organ to examine the structural architecture and/or remove abnormal tissues. NCIT:C16546 endoscopy NCIT:C16546 2019-01-20T01:03:18Z endoscopy by site location specific endoscopy 2019-01-20T01:03:28Z endoscopy by type specific type endoscopy specific technique endoscopy An endoscopic technique that allows deep intubation of the small intestine while using a standard endoscope. An inflatable balloon attached to the endoscope's tip acts as a stabilizer and a second balloon that is advanced ahead of the endoscope acts as a pulling device. 2019-01-20T18:48:29Z NCIT:C64865 balloon-guided endoscopy balloon-guided endoscopic procedure An endoscopic technique that allows deep intubation of the small intestine while using a standard endoscope. An inflatable balloon attached to the endoscope's tip acts as a stabilizer and a second balloon that is advanced ahead of the endoscope acts as a pulling device. NCIT:C64865 Endoscopy that employs the use of tissue stains to increase tissue contrast, and enhance the ability to identify various tissue dysplasia and other abnormalities. 2019-01-20T18:51:12Z NCIT:C116476 chromoendoscopy Endoscopy that employs the use of tissue stains to increase tissue contrast, and enhance the ability to identify various tissue dysplasia and other abnormalities. NCIT:C116476 A low-cost, high-resolution imaging tool consisting of a 1-mm diameter fiber-optic bundle that produces subcellular imaging at 1,000x magnification and 4 micrometer resolution, allowing for minimally invasive bioimaging. 2019-01-20T19:03:17Z NCIT:C116480 HRME high-resolution microendoscopy A low-cost, high-resolution imaging tool consisting of a 1-mm diameter fiber-optic bundle that produces subcellular imaging at 1,000x magnification and 4 micrometer resolution, allowing for minimally invasive bioimaging. NCIT:C116480 HRME A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered. 2019-01-20T19:19:15Z NCIT:C17007 PET scan positron emission tomography procedure A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered. NCIT:C17007 PET scan NCIT:C17007 Ultrasound imaging following the administration of a microbubble contrast agent. 2019-01-21T20:17:52Z NCIT:C148281 CEUS contrast-enhanced ultrasound procedure Ultrasound imaging following the administration of a microbubble contrast agent. NCIT:C148281 CEUS A postmortem examination of the body that includes an examination of the internal organs and structures after dissection to determine the cause of death and the nature of pathological changes. 2019-01-21T20:33:46Z NCIT:C25153 autopsy autopsy procedure A postmortem examination of the body that includes an examination of the internal organs and structures after dissection to determine the cause of death and the nature of pathological changes. NCIT:C25153 A procedure to examine and define cellular anatomy or function. The test results are often used by a clinician to diagnose disease or disordered function. 2019-01-21T20:36:01Z NCIT:C49132 clinical cytological procedure diagnostic cytological procedure clinical cytological testing The collecting of secretions and superficial cells of the body of uterus, cervix, and ovaries; examined with a microscope to detect any abnormal cells. 2019-01-21T20:38:23Z Papanicolaou smear procedure cervical smear procedure pap testing pap smear examination The collecting of secretions and superficial cells of the body of uterus, cervix, and ovaries; examined with a microscope to detect any abnormal cells. NCIT:C17348 Papanicolaou smear procedure NCIT:C17348 cervical smear procedure NCIT:C17348 pap testing NCIT:C17348 Examination under a microscope of cells found in sputum (mucus and other matter brought up from the lungs by coughing). The test checks for abnormal cells, such as lung cancer cells. 2019-01-21T20:45:16Z NCIT:C16192 sputum cytology testing sputum smear examination sputum smear testing sputum cytology examination Examination under a microscope of cells found in sputum (mucus and other matter brought up from the lungs by coughing). The test checks for abnormal cells, such as lung cancer cells. NCIT:C16192 Examination of the cells in urine. 2019-01-21T20:47:27Z urine cytology testing urine cytology examination Examination of the cells in urine. NCIT:C94473 Technique or procedure used for the study of the microanatomy of tissues and their cellular structure for the diagnosis or treatment of a disease. 2019-01-21T21:04:01Z NCIT:C16680 histological testing histological procedure Technique or procedure used for the study of the microanatomy of tissues and their cellular structure for the diagnosis or treatment of a disease. NCIT:C16680 http://orcid.org/0000-0001-7941-2961 obsolete clinical pathology procedure false A procedure to determine the number of cells in a clinical sample. 2019-01-21T21:16:16Z NCIT:C48938 cell count clinical pathology cell count clinical cell count A procedure to determine the number of cells in a clinical sample. NCIT:C48938 http://orcid.org/0000-0001-7941-2961 A lprocedure to measure hematopoietic components and investigate hematologic disorders in a blood sample. 2019-01-21T21:22:45Z NCIT:C49286 hematology procedure hematology testing The determination of the maximum amount of oxygen that can be combined chemically with hemoglobin in a volume of blood. 2019-01-21T21:29:03Z NCIT:C96614 OXYCAP testing oxygen capacity measurement oxygen capacity testing oxygen capacity assessment The determination of the maximum amount of oxygen that can be combined chemically with hemoglobin in a volume of blood. NCIT:C96614 OXYCAP testing A measure of the volume of red blood cells expressed as a percentage of the total blood volume. Normal in males is 43-49%, in females 37-43%. 2019-01-21T21:32:32Z NCIT:C64796 EVF testing HCT PCV measurement erythrocyte volume fraction testing hematocrit measurement hematocrit testing packed cell volume measurement hematocrit assessment A measure of the volume of red blood cells expressed as a percentage of the total blood volume. Normal in males is 43-49%, in females 37-43%. NCIT:C64796 EVF testing HCT PCV measurement packed cell volume measurement NCIT:C64796 A medical recommendation to avoid a particular therapy, intervention, medication, or procedure. 2019-01-07T19:23:10Z avoid procedure avoid therapy avoid activity avoid drug avoid medication therapeutic avoidance intervention A medical recommendation to avoid a particular therapy, intervention, medication, or procedure. http://orcid.org/0000-0001-7941-2961 Administration of intravenous infusions of alpha-1 proteinase inhibitor at regular schedules is a specific therapy for individuals with alpha-1 antitrypsin deficiency (AATD) with pulmonary involvement. 2019-01-22T17:27:25Z augmentation therapy Administration of intravenous infusions of alpha-1 proteinase inhibitor at regular schedules is a specific therapy for individuals with alpha-1 antitrypsin deficiency (AATD) with pulmonary involvement. PMID:28752465 obsolete antispastic agents false Treatment with a drug used in the treatment of Parkinson's disease. 2019-01-22T17:52:48Z CHEBI:48407 NCIT:C38149 anti-Parkinson agent therapy antiparkinson agent treatment antiparkinson drug therapy antiparkinson drug treatment antiparkinsonian agent therapy antiparkisonian agent treatment antiparkisonian drug treatment treatment with anti-Parkinson drug treatment with antiparkinson drug antiparkinson agent therapy Use of a substance used to treat or prevent parasitic infections. 2019-01-22T17:53:06Z CHEBI:35442 NCIT:C276 antiparasitic agent therapy antiparasitic drug therapy antiparasitics therapy antiparisitics drug treatment treatment with anti-parasitic agent treatment with anti-parasitic medication treatment with antiparasitic agent treatment with antiparasitic drug treatment with antiparasitic medication antiparasitic agent therapy A therapy capable of relieving pain without the loss of consciousness or without producing anaesthesia. In addition, analgesic is a role played by a compound which is exhibited by a capability to cause a reduction of pain symptoms. 2019-01-22T17:53:16Z CHEBI:35480 NCIT:C241 Analgesics therapy analgesic drug therapy analgesic medication therapy analgesic therapy treatment with analgesic analgesic pharmacotherapeutic agent therapy Treatment with a mood-stimulating drug used primarily in the treatment of affective disorders and related conditions. 2019-01-22T17:53:33Z CHEBI:35469 antidepressant drug therapy antidepressant therapy antidepressants treatment thymoanaleptics treatment thymoleptic agent therapy thymoleptic drug treatment therapy thymoleptics drug therapy treatment with antidepressant antidepressant agent therapy Use of a substance that attaches to and blocks cell receptors. 2019-01-22T17:54:06Z CHEBI:48706 NCIT:C69308 antagonist therapy treatment with antagonist receptor antagonist therapy 2019-01-22T17:54:15Z treatment with adrenal modifier treatment with adrenal modifying agent treatment with adrenal modifying drug treatment with adrenal modifying medication adrenal-modifying, hormonal agent therapy Treatment with a drug that alleviates anxiety, tension, and anxiety disorders, promote sedation, and have a calming effect without affecting the clarity of consciousness or neurologic conditions. 2019-01-22T17:54:43Z CHEBI:35474 anti-anxiety agent therapy anti-anxiety drug treatment anxiolytic agent drug treatment anxiolytic drug therapy anxiolytics drug therapies minor tranquiliser therapy minor tranquilizer treatment minor tranquilizing agent treatment minor tranquilizing drug therapy treatment with anxiolytic treatment with anxiolytic drug anxiolytic agent therapy Substance that may reduce inflammation, stimulate elimination of uric acid, or increase production of uric acid. 2019-01-22T17:55:18Z CHEBI:35841 CHEBI:35845 NCIT:C29733 anti-gout agent therapy anti-gout combination medicine therapy anti-gout drug therapy anti-gout preparation therapy antigout agent therapy antigout combination medicine therapy antigout drug therapy antigout medication therapy antigout preparation therapy antigout therapy gout suppressant agent treatment treatment with anti-gout drug treatment with anti-gout medication treatment with antigout agent treatment with antigout drug treatment with antigout medication treatment with gout suppressant agent treatment with gout suppressant drug treatment with gout suppressant medication treatment with uricosuric drug uricosuric drug therapy uricosuric agent therapy Substance that may reduce inflammation, stimulate elimination of uric acid, or increase production of uric acid. NCIT:C29733 Therapy using an agent that promotes the excretion of urine through its effects on kidney function 2019-01-22T17:55:27Z CHEBI:35498 NCIT:C448 diuretic agent drug treatment therapy diuretic drug therapy diuretic drugs therapy diuretic therapy diuretics therapy treatment with diuretic treatment with diuretic agent treatment with diuretic drug treatment with diuretic medication diuretic agent therapy Treatment with an agent that control agitated psychotic behavior, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect. 2019-01-22T17:57:29Z CHEBI:35476 antipsychotic agent therapy antipsychotic drug treatment antipsychotic therapy major tranquilizer drug treatment neuroleptic agent treatment neuroleptic therapies treatment with antipsychotic agent treatment with antipsychotic drug treatment with antipsychotic medication antipsychotic agent therapy Treatment with a drug used to prevent seizures or reduce their severity. 2019-01-22T17:57:37Z CHEBI:35623 NCIT:C264 anti-convulsant therapy anti-convulsive agent therapy anticonvulsant drug therapy anticonvulsant therapy anticonvulsive agent therapy antiepileptic therapy treatment with anticonvulsant treatment with anticonvulsant medication anticonvulsant agent therapy Treatment with a substance used in the prophylaxis or therapy of virus diseases. 2019-01-22T17:57:52Z CHEBI:36044 anti-viral drug therapy anti-virus drug treatment antiviral drug therapy treatment with an anti-virus agent treatment with an anti-virus drug treatment with an anti-virus medication treatment with an antiviral agent treatment with an antiviral drug treatment with an antiviral medication treatment with antiviral drug antiviral agent therapy Use of a compound that has anti-inflammatory effects. 2019-01-22T17:58:04Z CHEBI:67079 anti-inflammatory agent treatment therapy anti-inflammatory drug therapy anti-inflammatory medication therapy antiinflammatory agent therapy antiinflammatory drug therapy treatment with an anti-inflammatory drug treatment with an anti-inflammatory medication treatment with anti-inflammatory drug anti-inflammatory agent therapy A therapy utilizing a substance which produces loss of feeling or sensation. 2019-01-22T17:59:57Z CHEBI:38867 NCIT:C245 anaesthesia therapy anaesthetic medication therapy anaesthetic therapy anaesthetics therapy anesthesia therapy anesthetic drug therapy anesthetic medication therapy treatment with anaesthetic anesthetic agent therapy Treatment with medications to improve cognition and function for patients with dementia. 2019-01-22T18:00:43Z antidementia drug therapy antidementia medication treatment antidementia agent therapy Treatment with medications to improve cognition and function for patients with dementia. PMID:31517030 2019-01-22T18:01:36Z therapeutic antidotes, deterrents, and toxicologic agent therapy Treatment with a drug used to prevent nausea or vomiting. 2019-01-22T18:01:53Z CHEBI:50919 NCIT:C267 Treatment with antiemetics agent Treatment with antiemetics drug Treatment with antiemetics medication Treatment with antiemetics therapy anti-emetic agent therapy anti-emetic drug therapy anti-emetics therapy antiemetic drug therapy antiemetic therapy antiemetics medication treatment medication for nausea treatment medication for treatment of nausea treatment with antiemetic antiemetics agent therapy Use of a drug to prevent or treat fungal infections in humans or animals. 2019-01-22T18:02:00Z CHEBI:86327 anti-fungal drug therapy anti-fungal medication therapy antifungal drug therapy antifungal treatment antifungals therapy treatment with an anti-fungal drug treatment with an anti-fungal medication treatment with an antifungal drug treatment with an antifungal medication treatment with an antifungal therapy treatment with antifungal drug pharmaceutical fungicide therapy antifungal agent therapy 2019-01-22T18:11:18Z blood glucose regulator drug treatment blood glucose regulator therapy Use of a drug that acts on blood and blood-forming organs and those that affect the hemostatic system. 2019-01-22T18:11:44Z CHEBI:50248 https://www.drugbank.ca/categories/DBCAT000008 blood modifier treatment therapy blood modifying agent treatment hematologic agent therapy hematologic agent treatment therapy treatment with hematologic agent treatment with hematologic drug treatment with hematologic medication hematologic agent therapy Treatment with a drug that promotes coagulation. 2019-01-22T18:11:58Z coagulant treatment therapy promotion of coagulation treatment with coagulant coagulant agent therapy Use of an agent that prevents blood clotting. 2019-01-22T18:12:06Z CHEBI:50249 anticoagulant agent treatment anticoagulant drug treatment anticoagulant therapy treatment with anticoagulant anticoagulant agent therapy 2019-01-22T18:12:20Z blood formation agent therapy Use of a drug which antagonizes or impairs any mechanism leading to blood platelet aggregation, whether during the phases of activation and shape change or following the dense-granule release reaction and stimulation of the prostaglandin-thromboxane system. 2019-01-22T18:12:39Z CHEBI:50427 platelet aggregation inhibitor agent treatment platelet aggregation inhibitor therapy treatment with platelet aggregation antagonist treatment with platelet aggregation blocker treatment with platelet aggregation inhibitor platelet aggregation inhibitor agent therapy Use of a drug that affects the rate or intensity of cardiac contraction, blood vessel diameter or blood volume. 2019-01-22T18:13:06Z CHEBI:35554 NCIT:C78274 agent affecting cardiovascular system therapy cardiovascular agent drug treatment cardiovascular drug therapy cardiovascular drug treatment therapy cardiovascular system agent therapy cardiovascular system drug therapy treatment with cardiovascular agent treatment with cardiovascular drug treatment with cardiovascular medication treatment with cardiovascular therapy treatment with heart agent treatment with heart drug treatment with heart medication cardiovascular agent therapy Treatment with a drug that acts on an alpha-adrenergic receptor. 2019-01-22T18:14:42Z CHEBI:48539 a-adrenergic agent therapy a-adrenergic drug therapy a-adrenergic receptor agent therapy a-adrenergic receptor drug therapy alpha adrenergic drug therapy alpha adrenergic receptor agent therapy alpha adrenergic receptor drug treatment alpha adrenergics drug therapy alpha-adrenergic agent treatment alpha-adrenergic drug therapy alpha-adrenergic drug treatment therapy alpha-adrenergic modifier therapy alpha-adrenergic modifying agent therapy alpha-adrenergic receptor agent therapy alpha-adrenergic receptor drug therapy alpha-adrenergic receptor drug treatment treatment with alpha adrenergic agent treatment with alpha adrenergic drug treatment with alpha adrenergic medication treatment with alpha-adrenergic agent treatment with alpha-adrenergic drug treatment with alpha-adrenergic medication treatment with alpha-adrenergic receptor agent treatment with alpha-adrenergic receptor drug treatment with alpha-adrenergic receptor medication alpha-adrenergic agent therapy Treatment with an agent that selectively binds to and activates alpha-adrenergic receptors. 2019-01-22T18:15:26Z CHEBI:48539 a-adrenergic agonist drug treatment a-adrenergic agonist therapy a-adrenergic receptor agonist therapy alpha adrenergic agonist agent drug treatment alpha adrenergic agonist drug therapy alpha adrenergic agonist treatment alpha adrenergic receptor agonist therapy alpha adrentergic receptor agonist agent therapy alpha-adrenergic agonist therapy alpha-adrenergic drug therapy alpha-adrenergic receptor agonist drug therapy alpha-adrenergic receptor agonist treatment alpha-adrenoceptor agonist agent therapy alpha-adrenoceptor agonist drug therapy alpha-adrenoceptor agonist therapy treatment with alpha-adrenergic drug alpha-adrenergic agonist agent therapy Treatment with an agent that binds to but does not activate alpha-adrenergic receptors thereby blocking the actions of endogenous or exogenous alpha-adrenergic agonists. 2019-01-22T18:15:59Z CHEBI:37890 a-adrenergic antagonist agent therapy a-adrenergic antagonist therapy a-adrenergic receptor antagonist drug treatment alpha adrenergic antagonist drug therapy alpha blocker therapy alpha-adrenergic antagonist agent treatment alpha-adrenergic antagonist drug therapy alpha-adrenergic antagonist drug treatment alpha-adrenergic antagonist medication therapy alpha-adrenergic antagonist therapy alpha-adrenergic blockader therapy alpha-adrenergic blocker therapy alpha-adrenergic blocking agent therapy alpha-adrenergic receptor antagonist agent therapy alpha-adrenergic receptor antagonist drug therapy alpha-adrenergic receptor blockader therapy alpha-adrenergic receptor blocker therapy alpha-adrenoceptor antagonist therapy treatment with alpha-adrenergic antagonist treatment with alpha-adrenergic antagonist drug treatment with alpha-adrenergic antagonist medication alpha-adrenergic antagonist agent therapy Treatment with a drug for prevention of cardiac arrhythmias. Anti-arrhythmia drugs may affect the polarisation-repolarisation phase of the action potential, its excitability or refractoriness, or impulse conduction or membrane responsiveness within cardiac fibres. 2019-01-22T18:17:04Z CHEBI:38070 NCIT:C47793 anti-arrhythmia agent therapy anti-arrhythmia drug therapy anti-arrhythmic agent therapy anti-arrhythmic drug treatment therapy anti-arrythmic agent therapy antiarrhythmic agent therapy antiarrhythmic drug therapy antiarrhythmic drug treatment treatment with anti-arrhythmia agent treatment with anti-arrhythmia drug treatment with anti-arrhythmia medication treatment with anti-arrhythmic agent treatment with anti-arrhythmic drug treatment with anti-arrhythmic medication treatment with anti-arrythmic drug treatment with antiarrhythmic agent treatment with antiarrhythmic drug treatment with antiarrhythmic medication antiarrhythmic agent therapy Treatment with a drug that acts on beta-adrenergic receptors. 2019-01-22T18:17:27Z CHEBI:48540 b-adrenergic drug treatment beta adrenergic receptor agent treatment beta adrenergic receptor drug therapy beta-adrenergic agent treatment beta-adrenergic drug therapy beta-adrenergic drug treatment beta-adrenergic modifier therapy beta-adrenergic modifying agent therapy beta-adrenergic modifying drug treatment beta-adrenergics therapy treatment with beta-adrenergic agent treatment with beta-adrenergic drug treatment with beta-adrenergic medication beta-adrenergic agent therapy An agent that binds to but does not activate beta-adrenergic receptors thereby blocking the actions of endogenous or exogenous beta-adrenergic agonists. 2019-01-22T18:17:55Z CHEBI:35530 Beta blocker therapy Beta-adrenergic blocking agent therapy b-adrenergic antagonist therapy b-adrenergic receptor antagonist therapy beta adrenergic antagonist agent treatment beta adrenergic antagonist drug treatment beta adrenergic receptor antagonist therapy beta-adrenergic antagonist agent treatment beta-adrenergic antagonist therapy beta-adrenergic receptor antagonist agents beta-adrenergic receptor antagonist drug treatment beta-adrenergic receptor antagonist therapy beta-adrenergic receptor blockader therapy beta-adrenoceptor antagonist therapy treatment with beta blocker agent treatment with beta blocker drug treatment with beta blocker medication treatment with beta-adrenergic antagonist treatment with beta-adrenergic antagonist agent treatment with beta-adrenergic antagonist drug treatment with beta-adrenergic antagonist medication beta-adrenergic antagonist agent therapy An agent that binds to but does not activate beta-adrenergic receptors thereby blocking the actions of endogenous or exogenous beta-adrenergic agonists. CHEBI:35530 obsolete calcium channel blocker agent therapy false Therapy using an agent that reduces plasma lipids, such as cholesterol or low density lipoproteins (LDL), acting systemically or locally (intestines) to decrease fat digestion, absorption, production, and accumulation in the plasma and reducing pathogenic atherosclerosis and thrombosis. 2019-01-22T18:19:20Z NCIT:C29703 anti-lipemic therapy anti-lipidemic agent therapy antihyperlipemic agent therapy antihyperlipidaemic agent therapy antihyperlipidemic agent therapy antihyperlipidemic drug therapy antilipemic drug therapy antilipemic therapy antilipidemic agent therapy antilipidemic drug treatment therapy dyslipidemia agent therapy dyslipidemia drug treatment therapy dyslipidemic agent drug treatment dyslipidemic drug therapy dyslipidemic drugs therapy hypolipidemic agent therapy lipid-lowering agent therapy treatment with anti-lipidemic agent treatment with anti-lipidemic drug treatment with anti-lipidemic medication treatment with antilipemic drug treatment with antilipidemic agent treatment with antilipidemic drug treatment with antilipidemic medication treatment with dyslipidemic agent treatment with dyslipidemic drug treatment with dyslipidemic medication dyslipidemic agent therapy Treatment with Renin-angiotensin-aldosterone system (RAAS) inhibitors, a group of drugs that act by inhibiting the renin-angiotensin-aldosterone system and include angiotensin-converting enzyme (ACE) inhibitors, angiotensin-receptor blockers (ARBs), and direct renin inhibitors 2019-01-22T18:19:47Z Treatment with RAAS inhibitor renin-angiotensin-aldosterone system inhibitor therapy treatment with renin-angiotensin-aldosterone system inhibitor RAAS inhibitor therapy A therapy using a drug to cause dilation of the blood vessels. 2019-01-22T18:20:06Z CHEBI:35620 NCIT:C29707 vasodilating agent therapy vasodilating drug treatment therapy vasodilator agent therapy vasodilator drug therapies vasodilator drug therapy vasodilator drug treatment therapy vasodilator therapies vasodilator agent therapy A therapy using a drug to cause dilation of the blood vessels. CHEBI:35620 obsolete other cardiovascular agent therapy false Use of a drug that has principally analgesic, antipyretic and anti-inflammatory actions. Non-narcotic analgesics do not bind to opioid receptors. 2019-01-22T18:22:25Z CHEBI:35481 non-narcotic analgesic agent therapy non-narcotic analgesic drug therapy non-narcotic analgesic medication treatement non-narcotic analgesic therapy non-opioid analgesic agent therapy non-opioid analgesics drug therapy non-opioid analgesics medication therapy non-opioid analgesics medication treatment non-opioid analgesics therapy treatment with non-narcotic analgesic non-opioid analgesics agent therapy Use of a narcotic or opioid substance, synthetic or semisynthetic agent producing profound analgesia, drowsiness, and changes in mood. 2019-01-22T18:22:42Z narcotic therapy CHEBI:35482 narcotic analgesic medication therapy narcotic analgesic medication treatment narcotic analgesic therapy opioid analgesic drug therapy opioid analgesic medication therapy opioid analgesic medication treatment opioid analgesic therapy opioid analgesics opioid therapy treatment with opioid analgesic opioid analgesics agent therapy Treatment with any member of a group of drugs that reversibly inhibit the propagation of signals along nerves. Wide variations in potency, stability, toxicity, water-solubility and duration of action determine the route used for administration, e.g. topical, intravenous, epidural or spinal block. 2019-01-22T18:24:45Z CHEBI:36333 local anaesthesia therapy local anaesthetic medication therapy local anaesthetic therapy local anaesthetics therapy local anesthesia therapy local anesthesia treatment local anesthetic agent therapy local anesthetics therapy treatment with local anaesthetic epidural therapy spinal block therapy topical anesthesia therapy topical anesthetic therapy local anesthetic agent therapy An antibacterial substance with aminoglycoside structure. 2019-01-22T18:25:15Z CHEBI:47779 aminoglycoside drug therapy aminoglycoside drug treatment aminoglycosides therapy aminoglycoside agent therapy An antibacterial substance with aminoglycoside structure. Use of a class of beta-lactam antibiotics differing from the penicillins in having a 6-membered, rather than a 5-membered, side ring. 2019-01-22T18:25:44Z CHEBI:23066 cephalosporin antibacterial agent therapy cephalosporin beta-lactam therapy cephalosporin drug therapy cephalosporin drug treatment cephalosporin therapies cephalosporin therapy cephalosporin treatment cephalosporins therapy treatment with cephalosporin treatment with cephalosporin agent treatment with cephalosporin antibacterial drug treatment with cephalosporin antibacterial medication treatment with cephalosporin antibiotic drug treatment with cephalosporin antibiotic medication Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. treatment with cephalosporin drug treatment with cephalosporin medication cephalosporin agent therapy Although cephalosporins are among the most commonly used antibiotics in the treatment of routine infections, and their use is increasing over time, they can cause a range of hypersensitivity reactions, from mild, delayed-onset cutaneous reactions to life-threatening anaphylaxis in patients with immunoglobulin E (IgE)-mediated allergy. CHEBI:23066 Use of an antibacterial substance with penicillin structure. 2019-01-22T18:26:03Z CHEBI:17334 penicillin antibacterial therapy penicillin antibacterial treatment penicillin beta-lactam therapy penicillin drug therapy penicillin drug treatment penicillin therapy penicillin treatment penicillins treatment with a penicillin agent treatment with a penicillin drug treatment with a penicillin medication treatment with a penicillin therapy treatment with penicillin treatment with penicillin antibacterial drug treatment with penicillin antibacterial medication treatment with penicillin antibiotic agent treatment with penicillin antibiotic drug treatment with penicillin antibiotic medication treatment with penicillin antibiotic therapy penicillin agent therapy Use of an antibacterial substance with penicillin structure. obsolete other beta-lactams false Use of a drug with a macrocyclic lactone with a ring of twelve or more members which exhibits antibiotic activity. 2019-01-22T18:26:31Z macrolides CHEBI:25105 Treatment with a macrolide antibacterial agent Treatment with a macrolide antibacterial drug Treatment with a macrolide antibacterial medication Treatment with a macrolide antibiotic agent Treatment with a macrolide antibiotic drug Treatment with a macrolide antibiotic medication macrolide antibacterial drug therapy macrolide antibacterial therapy macrolide antibiotic therapy macrolide drug therapy macrolide drug treatment treatment with macrolide antibiotic macrolide antibacterial agent therapy Use of an organonitrogen heterocyclic antibiotic whose structure contains a quinolone or quinolone-related skeleton. 2019-01-22T18:26:50Z quinolones CHEBI:86324 quinolone antibacterial therapy quinolone antibiotic agent treatment quinolone antibiotic therapy treatment with quinolone antibacterial agent treatment with quinolone antibacterial drug treatment with quinolone antibacterial medication treatment with quinolone antibiotic treatment with quinolone antibiotic agent treatment with quinolone antibiotic drug treatment with quinolone antibiotic medication quinolone antibacterial agent therapy Use of a class of sulfonamides whose members generally have bacteriostatic antibiotic properties. 2019-01-22T18:27:30Z sulfonamides therapy CHEBI:87228 sulfonamide antibacterial drug therapy sulfonamide antibacterial therapy sulfonamide antibiotic therapy sulfonamide drug therapy sulfonamide drug treatment treatment with a sulfonamide antibacterial drug treatment with a sulfonamide antibacterial medication treatment with a sulfonamide antibiotic agent treatment with a sulfonamide antibiotic drug treatment with a sulfonamide antibiotic medication treatment with a sulfonamide antibiotic therapy treatment with sulfonamide antibiotic sulfonamide antibacterial agent therapy Treatment with a broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. 2019-01-22T18:28:05Z CHEBI:27902 tetracycline antibiotic therapy tetracycline drug therapy tetracycline drug treatment tetracycline therapy treatment with a tetracycline antibacterial agent treatment with a tetracycline antibacterial drug treatment with a tetracycline antibacterial medication treatment with a tetracycline antibacterial therapy treatment with a tetracycline antibiotic agent treatment with a tetracycline antibiotic drug treatment with a tetracycline antibiotic medication treatment with a tetracycline antibiotic therapy treatment with tetracycline tetracycline therapy obsolete other antibacterial agents false Treatment with a drug that can regulate intracellular calcium levels. 2019-01-22T18:28:49Z CHEBI:38808 calcium channel modifier drug therapy calcium channel modulator therapy treatment with calcium channel modifying agent treatment with calcium channel modifying medication treatment with calcium channel modulator calcium channel modifying agent therapy Treatment with a substance, such as agonists, antagonists, degradation or uptake inhibitors, depleters, precursors, and modulators of receptor function, used for its pharmacological actions on GABAergic systems. 2019-01-22T18:29:21Z CHEBI:51374 GABA agent therapy GABA augmenting agent therapy GABA augmenting therapy gamma-aminobutyric acid drug therapy gamma-aminobutyric acid modulating agent therapy treatment with GABA agent treatment with GABA drug treatment with GABA medication treatment with gamma-aminobutyric acid augmenting agent treatment with gamma-aminobutyric acid augmenting drug treatment with gamma-aminobutyric acid augmenting medication gamma-aminobutyric acid augmenting agent therapy 2019-01-22T18:29:56Z glutamate reducing agent therapy Use of a drug that inhibits sodium influx through cell membranes. 2019-01-22T18:30:15Z CHEBI:38633 Na+ channel blocker therapy Na+ channel inhibitor drug therapy sodium channel blocker drug therapy sodium channel blocker therapy sodium channel inhibitor drug therapy treatment with Na+ channel inhibitor treatment with sodium channel antagonist treatment with sodium channel blocker treatment with sodium channel inhibitor sodium channel inhibitor therapy obsolete anticonvulsants, other false They are a group of drugs that block the normal breakdown of acetylcholine (ACh) into acetate and choline and thereby increase both the levels and duration of actions of acetylcholine found in the central and peripheral nervous system. 2019-01-22T18:32:56Z CHEBI:37733 EC 3.1.1.8 (cholinesterase) inhibitor therapy cholinesterase inhibitor drug treatment cholinesterase inhibitor medication therapy treatment with EC 3.1.1.8 (cholinesterase) inhibitor Neurogenerative diseases such as Alzheimer disease, Parkinson disease, and Lewy body dementia are indications for cholinesterase inhibitor therapy. cholinesterase inhibitor therapy They are a group of drugs that block the normal breakdown of acetylcholine (ACh) into acetate and choline and thereby increase both the levels and duration of actions of acetylcholine found in the central and peripheral nervous system. PMID:31335056 Neurogenerative diseases such as Alzheimer disease, Parkinson disease, and Lewy body dementia are indications for cholinesterase inhibitor therapy. PMID:31335056 2019-01-22T18:33:33Z glutamate modulator therapy glutamate pathway modifying drug treatment glutamatergic drug therapy glutamatergic drug treatment glutamatergic pathway modifying agent therapy obsolete antidementia agents, other false A drug that acts as an inhibitor that interferes with the action of monoamine oxidase (EC 1.4.3.4). 2019-01-22T18:36:08Z CHEBI:38623 NCIT:C667 EC 1.4.3.4 (monoamine oxidase) inhibitor therapy MAO drug therapy MAO drug treatment MAO inhibitor therapy MAOI therapy inhibitors of MAO therapy inhibitors of monoamine oxidase therapy treatment with EC 1.4.3.4 (monoamine oxidase) inhibitor Any substance that inhibits monoamine oxidase (MAO), an enzyme that catalyzes the oxidative deamination of monoamines and plays a role in the inactivation of neurotransmitters. monoamine oxidase inhibitor agent therapy MAO inhibitor therapy MAOI therapy Any substance that inhibits monoamine oxidase (MAO), an enzyme that catalyzes the oxidative deamination of monoamines and plays a role in the inactivation of neurotransmitters. NCIT:C667 Treatment with a medication that increases the extracellular level of the neurotransmitter serotonin (5-HT) and norepinephrine by inhibiting their reuptake into the presynaptic cell. 2019-01-22T18:40:17Z OMIT:0001323 SNRI agent therapy SNRI drug therapy SNRI drug treatment serotonin and noradrenaline reuptake inhibitor agent therapy serotonin and noradrenaline reuptake inhibitor drug therapy serotonin and noradrenaline reuptake inhibitor drug treatment serotonin and norepinephrine reuptake inhibitor therapy serotonin-noradrenaline reuptake inhibitor agent therapy serotonin-noradrenaline reuptake inhibitor drug treatment serotonin-norepinephrine reuptake inhibitor drug treatment serotonin-norepinephrine reuptake inhibitor agent therapy Treatment with mood-stimulating agents which contain a tricyclic structure and are used primarily in the treatment of affective disorders and related conditions. 2019-01-22T18:41:18Z NCIT:C94727 tricyclic antidepressant drug therapy tricyclic antidepressant drug treatment tricyclic antidepressant agent therapy obsolete antidepressants, other false Treatment with a therapeutic substance used to counteract the toxic action(s) of a specified xenobiotic. 2019-01-22T18:41:49Z CHEBI:50247 antidote drug therapy antidote agent therapy Treatment with a therapeutic substance used to counteract the toxic action(s) of a specified xenobiotic. PMID:9079217 Medication given to prevent or deter a patient from using a substance. 2019-01-22T18:42:02Z abuse deterrent drug treatment abuse deterrent agent therapy 2019-01-22T18:42:18Z toxicologic drug therapy toxicologic agent therapy Treatment with a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. 2019-01-22T18:44:08Z CHEBI:24261 glucocorticoid therapy treatment with a glucocorticoid drug treatment with a glucocorticoid medication treatment with a glucocorticoid therapy treatment with glucocorticoid glucocorticoid agent therapy Treatment with a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood. CHEBI:24261 Treatment with an anti-inflammatory drug that is not a steroid. In addition to anti-inflammatory actions, non-steroidal anti-inflammatory drugs have analgesic, antipyretic, and platelet-inhibitory actions. They act by blocking the synthesis of prostaglandins by inhibiting cyclooxygenase, which converts arachidonic acid to cyclic endoperoxides, precursors of prostaglandins. 2019-01-22T18:44:26Z CHEBI:35475 NSAID therapy NSAIDs therapy anti-inflammatory drug therapy non-steroidal anti-inflammatory drug therapy non-steroidal anti-inflammatory medication treatment treatment with NSAID drug treatment with NSAID medication treatment with NSAID therapy treatment with anti-inflammatory drug treatment with non-steroidal anti-inflammatory drug treatment with non-steroidal anti-inflammatory medication nonsteroidal anti-inflammatory agent therapy NSAID therapy NSAIDs therapy Treatment with medications to alleviate symptoms and occurrence of migraine headaches. 2019-01-22T18:45:01Z anti migraine drug therapy anti-migraine drug therapy anti-migraine medication therapy migraine headache therapy migraine medication treatment migraine treatment standard migraine therapies treatment for migraine treatment of migraine treatment with antimigraine agent antimigraine agent therapy Treatment with medications to alleviate symptoms and occurrence of migraine headaches. http://orcid.org/0000-0001-7941-2961 Use of medication to treat migraine headache symptoms acutely. 2019-01-22T18:45:12Z abortive anti migraine medication therapy abortive anti-migraine drug therapy abortive migraine headache treatment abortive migraine medication therapy abortive migraine treatment abortive therapy for migraine headache abortive treatment of migraine standard migraine abortive therapies symptomatic treatment of migraine treatment with abortive antimigraine agent abortive antimigraine agent therapy Use of medication to treat migraine headache symptoms acutely. http://orcid.org/0000-0001-7941-2961 Use of medication to decrease the occurrence of migraine headaches. 2019-01-22T18:45:30Z prophylactic migraine headache treatment prophylactic migraine therapy prophylactic migraine treatment prophylactic treament of migraine headache prophylactic treatment of migraine treatment with prophylactic antimigraine agent prophylactic antimigraine agent therapy Use of medication to decrease the occurrence of migraine headaches. http://orcid.org/0000-0001-7941-2961 Medication given by mouth or by injection to treat myasthenia gravis. 2019-01-22T18:47:33Z anti-myasthenic drug therapy antimyasthenic drug therapy antimyasthenic medication therapy antimyasthenic agent therapy Treatment with a drug to activate the parasympathetic nervous system (PSNS). They can act as direct agonists of acetylcholine receptors (ACh) or indirect agonists of ACh. While direct agonists act by binding directly to muscarinic or nicotinic ACh receptors, indirect agonists prolong the action of endogenous acetylcholine by inhibiting acetylcholinesterase. 2019-01-22T18:47:49Z cholinomimetic agents therapy cholinomimetic drug therapy cholinomimetic medication therapy parasympathomimetic agent therapy parasympathomimetic drug therapy parasympathomimetic drug treatment parasympathomimetic medication therapy treatment with cholinomimetic agent treatment with cholinomimetic drug treatment with cholinomimetic medication treatment with parasympathomimetic agent treatment with parasympathomimetic drug treatment with parasympathomimetic medication Direct agonists of ACh are used topically in ophthalmology to induce miosis, while indirect agonists are used to treat, e.g., postoperative ileus or urinary retention and myasthenia gravis. parasympathomimetic therapy Use of a treat or prevent infections caused by Mycobacteria, a genus of actinobacteria. 2019-01-22T18:48:12Z CHEBI:64912 antimycobacterial drug therapy antimycobacterial drug treatment antimycobacterials therapy antimycobacterium therapy treatment with an anti-mycobacterial agent treatment with an anti-mycobacterial drug treatment with an anti-mycobacterial medication treatment with an anti-mycobacterial therapy treatment with an antimycobacterial agent treatment with an antimycobacterial drug treatment with an antimycobacterial medication treatment with antimycobacterial drug antimycobacterial agent therapy Use of a substance that kills or slows the growth of Mycobacterium tuberculosis and is used in the treatment of tuberculosis. 2019-01-22T18:49:27Z CHEBI:33231 antitubercular agent therapy antitubercular drug therapy antitubercular drug treatment antituberculosis agent therapy treatment with an anti-tubercular agent treatment with an anti-tubercular drug treatment with an anti-tubercular medication treatment with an anti-tubercular therapy treatment with an antitubercular agent treatment with an antitubercular drug treatment with an antitubercular medication treatment with antitubercular agent tuberculostatic agent therapy antitubercular agent therapy Use of a substance that suppresses Mycobacterium leprae, ameliorates the clinical manifestations of leprosy, and/or reduces the incidence and severity of leprous reactions. 2019-01-22T18:49:45Z CHEBI:35816 leprostatic drug therapy leprostatic drug treatment treatment with a leprostatic agent treatment with a leprostatic drug treatment with a leprostatic medication treatment with a leprostatic therapy treatment with leprostatic drug leprostatic agent therapy An antineoplastic agent that replaces hydrogen atom(s) in nucleophilic moieties with alky radical(s), hindering proper function. Alkylating agents exhibit cytotoxic effects through the alkylation of DNA, resulting in strand cross-linking, ultimately inhibiting DNA replication and cancer cell growth. 2019-01-22T18:50:33Z CHEBI:22333 NCIT:C1590 NCIT:C223 alkylating agent therapy alkylating drug therapy anti-neoplastic alkylating agent therapy antineoplastic alkylating agent therapy treatment with alkylating agent treatment with alkylating drug treatment with alkylating medication Highly reactive chemical that introduces alkyl radicals into biologically active molecules and thereby prevents their proper functioning. It could be used as an antineoplastic agent, but it might be very toxic, with carcinogenic, mutagenic, teratogenic, and immunosuppressant actions. It could also be used as a component of poison gases. alkylating agent therapy An antineoplastic agent that replaces hydrogen atom(s) in nucleophilic moieties with alky radical(s), hindering proper function. Alkylating agents exhibit cytotoxic effects through the alkylation of DNA, resulting in strand cross-linking, ultimately inhibiting DNA replication and cancer cell growth. NCIT:C1590 Highly reactive chemical that introduces alkyl radicals into biologically active molecules and thereby prevents their proper functioning. It could be used as an antineoplastic agent, but it might be very toxic, with carcinogenic, mutagenic, teratogenic, and immunosuppressant actions. It could also be used as a component of poison gases. CHEBI:22333 Use of an agent or endogenous substance that inhibits the formation of capillaries from existing blood vessels. 2019-01-22T18:50:46Z CHEBI:48422 NCIT:C1742 angiogenesis antagonist therapy angiogenesis blocker therapy angiogenesis inhibitor therapy anti-angiogenic agent therapy antiangiogenesis agent therapy antiangiogenic agent drug treatment treatment with angiogenesis antagonist agent treatment with angiogenesis antagonist drug treatment with angiogenesis antagonist medication treatment with angiogenesis blocker agent treatment with angiogenesis blocker drug treatment with angiogenesis blocker medication treatment with angiogenesis inhibitor treatment with angiogenesis inhibitor agent treatment with angiogenesis inhibitor drug treatment with angiogenesis inhibitor medication treatment with anti-angiogenic agent treatment with anti-angiogenic drug treatment with anti-angiogenic medication treatment with antiangiogenic agent treatment with antiangiogenic drug treatment with antiangiogenic medication angiostatic agent therapy antiangiogenic agent therapy obsolete antiestrogen agent therapy false Treatment of cancer that utilizes antimetabolite substances to disrupt DNA, RNA, or protein synthesis. 2019-01-22T18:51:33Z NCIT:C15183 anti-metabolite agent drug treatment antimetabolite agent drug treatment antimetabolite cancer drug antimetabolite cancer medication antimetabolites therapy cancer drug antimetabolite treatment with anti-metabolite agent treatment with anti-metabolite drug treatment with anti-metabolite medication treatment with antimetabolite agent treatment with antimetabolite drug treatment with antimetabolite medication antimetabolite agent therapy Treatment of cancer that utilizes antimetabolite substances to disrupt DNA, RNA, or protein synthesis. NCIT:C15183 Treatment with an EC 1.14.14.* (oxidoreductase acting on paired donors, incorporating of 1 atom of oxygen, with reduced flavin or flavoprotein as one donor) inhibitor which interferes with the action of aromatase (EC 1.14.14.14) and so reduces production of estrogenic steroid hormones. 2019-01-22T18:54:45Z CHEBI:50790 EC 1.14.14.14 (aromatase) inhibitor therapy aromatase inhibitor drug therapy aromatase inhibitor drug treatment treatment with EC 1.14.14.14 (aromatase) inhibitor treatment with aromatase inhibitor agent treatment with aromatase inhibitor drug treatment with aromatase inhibitor medication treatment with estrogen synthetase inhibitor agent treatment with estrogen synthetase inhibitor drug treatment with estrogen synthetase inhibitor medication treatment with estrogen synthetase inhibitor therapy treatment with oestrogen synthetase inhibitor agent treatment with oestrogen synthetase inhibitor drug treatment with oestrogen synthetase inhibitor medication aromatase inhibitor agent therapy 2019-01-22T18:55:15Z antineoplastic molecular target inhibitor drug treatment cancer targeted inhibitor drug treatment cancer targeted inhibitor therapy targeted cancer drug therapy targeted cancer therapy treatment with targeted cancer drug treatment with targeted cancer medication treatment with targeted cancer therapy antineoplastic molecular target inhibitor agent therapy 2019-01-22T18:55:45Z NCIT:C15490 antineoplastic monoclonal antibodies therapy antineoplastic monoclonal antibody drug treatment antineoplastic monoclonal antibody agent therapy Use of any of a group of agents that includes retinol (Vitamin A) and related compounds with potential antineoplastic and/or chemopreventive activities. 2019-01-22T18:56:30Z NCIT:C804 retinoic acid agent therapy retinoic acid drug therapy retinoid drug therapy retinoid drug treatment treatment with retinoic acid agent treatment with retinoic acid drug treatment with retinoic acid medication treatment with retinoic acid therapy treatment with retinoid agent treatment with retinoid drug treatment with retinoid medication treatment with retinoid therapy A retinoic acid agent binds to and/or activates specific nuclear retinoic acid receptors (RARs) and retinoid X receptors (RXRs), thereby modulating transcription of genes responsible for cell differentiation and proliferation. A retinoic acid agent may exhibit immunomodulatory and anti-inflammatory properties and may inhibit ornithine decarboxylase, resulting in a decrease in polyamine synthesis and keratinization. retinoid agent therapy Substance intended to kill parasitic worms (helminths). 2019-01-22T18:57:26Z CHEBI:35443 anthelminitic agent drug therapy anthelmintic drug therapy anthelmintic drug treatment antihelminthics vermifuge therapy vermicide therapy anthelmintic agent therapy Substance intended to kill parasitic worms (helminths). CHEBI:35443 Treatment with an antimicrobial drug which is used to treat or prevent protozoal infections. 2019-01-22T18:57:54Z CHEBI:35820 antiprotozoal drug therapy antiprotozoal drug treatment antiprotozoals therapy treatment with an antiprotozoal agent treatment with an antiprotozoal drug treatment with an antiprotozoal medication treatment with antiprotozoal drug protozoan drug treatment antiprotozoal agent therapy An agent used to as a treament of ectoparasitic infestations. 2019-01-22T18:58:53Z CHEBI:38956 ectoparasiticide therapy ectoparasiticide agent therapy An agent used to as a treament of ectoparasitic infestations. http://orcid.org/0000-0001-7941-2961 Treatment with an antiviral drug used for treatment of cytomegalovirus infection. 2019-01-22T18:59:18Z Anti-CMV agent therapy anti-CMV medication reatment anti-cmv drug therapy anti-cmv therapy anti-cytomegalovirus drug therapy anti-cytomegalovirus drug treatment anti-cytomegalovirus medication treatment antiviral treatment of cytomegalovirus therapy cytomegalovirus drug treatment therapy anti-cytomegalovirus agent therapy Treatment with an antiviral drug used for treatment of cytomegalovirus infection. PMID:21827432 Treatment with a drug which can have different modes of action but which tend to be less likely than first generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements. 2019-01-22T19:00:47Z CHEBI:65191 atypical antipsychotic agent treatment atypical antipsychotic drug therapies atypical antipsychotic drug treatment atypical antipsychotic therapies second generation antipsychotic agent therapy second generation antipsychotic drug treatment second generation antipsychotic therapy treatment with atypical antipsychotic treatment with second generation antipsychotic atypical antipsychotic agent therapy Treatment with a drug which can have different modes of action but which tend to be more likely than second generation antipsychotics to cause extrapyramidal motor control disabilities such as body rigidity or Parkinson's disease-type movements; such body movements can become permanent even after treatment has ceased. 2019-01-22T19:01:06Z CHEBI:65190 conventional antipsychotic drug treatment conventional antipsychotic therapies first generation antipsychotic agent treatment first generation antipsychotic drug treatment first generation antipsychotic therapy treatment with conventional antipsychotic treatment with first generation antipsychotic typical antipsychotic agent therapy typical antipsychotic drug treatment typical antipsychotic therapy conventional antipsychotic agent therapy 2019-01-22T19:02:05Z CHEBI:53784 anti-spasticity agent therapy antispasmodic agent therapy antispasmodic drug therapy antispastic agent therapy antispastic drug treatment antispasticity agent drug treatment antispasticity drug therapy treatmeant with antispasticity drug treatmeant with antispasticity medication treatment with a antispasmodic drug treatment with a antispasmodic medication treatment with a antispasmodic therapy treatment with antispasticity agent antispasticity agent therapy Use of a drug for the treatment and prophylaxis of infection with hepatitis virus(es). 2019-01-22T20:15:16Z anti-hepatitis agent therapy anti-hepatitis drug therapy anti-hepatitis drug treatment antihepatitis drug therapy antihepatitis drug treatment treatment with anti-hepatitis drug treatment with anti-hepatitis medication treatment with antihepatitis medication antihepatitis agent therapy Use of any drug that counters herpes. 2019-01-22T20:15:33Z anti-herpes agent therapy anti-herpes drug therapy anti-herpes medication therapy antiherpetic agent drug therapy antiherpetic agent drug treatment treatment with anti-herpes agent treatment with anti-herpes drug treatment with antiherpetic agent treatment with antiherpetic drug treatment with antiherpetic medication antiherpetic agent therapy Treatment with an antiviral agent that destroys or inhibits the replication of the human immunodeficiency virus. 2019-01-22T20:16:07Z CHEBI:64946 NCIT:C1660 anti-HIV agent therapy anti-HIV drug treatment antiviral agent therapy treatment with anti-HIV agent treatment with anti-HIV drug treatment with anti-human immunodeficiency virus agent treatment with anti-human immunodeficiency virus drug treatment with anti-human immunodeficiency virus medication treatment with antiviral agent anti-human immunodeficiency virus agent therapy Treatment with a drug which interferes with the binding, fusion and entry of an HIV virion to a human cell. By blocking this step in HIV's replication cycle, such agents slow the progression from HIV infection to AIDS. 2019-01-22T20:18:25Z CHEBI:59886 HIV fusion inhibitor therapy anti-HIV theraoym fusion inhibitor drug treatment anti-HIV therapy, fusion inhibitor drug treatment with HIV fusion inhibitor treatment with HIV fusion inhibitor agent treatment with HIV fusion inhibitor drug treatment with HIV fusion inhibitor medication treatment with HIV fusion inhibitor therapy HIV fusion inhibitor therapy Treatment with a substance structurally unlike a nucleoside molecule that is capable of inhibiting the function of a reverse transcriptase. These compounds do not bind to the active site of the polymerase but in a less conserved pocket near the active site, causing a distortion in the shape of the active site and resulting in inhibition of enzymatic function, chain termination, and inhibition of viral replication. 2019-01-22T20:18:58Z NCIT:C97453 anti-HIV non-nucleoside reverse transcriptase inhibitor drug therapy anti-HIV non-nucleoside reverse transcriptase inhibitor drug treatment treatment with anti-HIV therapy, non-nucleoside reverse transcriptase inhibitor agent treatment with anti-HIV therapy, non-nucleoside reverse transcriptase inhibitor drug treatment with anti-HIV therapy, non-nucleoside reverse transcriptase inhibitor medication non-nucleoside reverse transcriptase inhibitor therapy Nucleoside reverse transcriptase inhibitors (NRTIs) block reverse transcriptase (an HIV enzyme). 2019-01-22T20:20:58Z NRTI drug therapy anti-HIV nucleoside and nucleotide reverse transcriptase inhibitor drug treatment treatment with NRTI agent treatment with NRTI drug treatment with NRTI medication treatment with nucleoside and nucleotide reverse transcriptase inhibitor medication treatment with nucleoside-nucleotide reverse transcriptase inhibitor drug treatment with nucleoside-nucleotide reverse transcriptase inhibitor medication treatment with nucleoside/nucleotide reverse transcriptase inhibitor drug treatment with nucleoside/nucleotide reverse transcriptase inhibitor medication nucleoside and nucleotide reverse transcriptase inhibitor therapy Use of an inhibitor of HIV protease, an enzyme required for production of proteins needed for viral assembly. 2019-01-22T20:21:25Z CHEBI:35660 NCIT:C97366 HIV protease inhibitor drug therapy HIV protease inhibitor drug treatment HIV protease inhibitor therapy treatment with HIV protease inhibitor treatment with HIV protease inhibitor agent treatment with HIV protease inhibitor drug treatment with HIV protease inhibitor medication HIV protease inhibitor therapy Treatment with a drug used for the treatment and prophylaxis of infection with influenza viruses. 2019-01-22T20:21:48Z anti-flu medication therapy anti-influenza drug therapy anti-influenza drug treatment treatment with anti-influenza drug treatment with anti-influenza medication anti-influenza agent therapy obsolete anxiolytics, other false 2019-01-22T20:32:25Z antidepressant anxiolytics Treatment with used to treat bipolar disorders or mania associated with other affective disorders. 2019-01-22T20:33:05Z CHEBI:35477 antimanic agent drug treatment antimanic agent treatment therapy antimanic drug therapies antimanic drug therapy antimanics bipolar agent drug therapy bipolar agent drug treatment bipolar disorder agent therapy treatment with antimanic agent treatment with antimanic drug treatment with antimanic medication antimanic agent therapy 2019-01-22T20:33:31Z anti-diabetic therapy antidiabetic agent drug treatment antidiabetic therapy antidiabetic agent therapy 2019-01-22T20:33:43Z glycemic agent drug therapy glycemic regulation agent therapy glycemic regulation drug treatment glycemic regulator agent therapy glycemic agent therapy A synthetic or animal-derived form of insulin used in the treatment of diabetes mellitus. Therapeutic insulin is formulated to be short-, intermediate- and long-acting in order to individualize an insulin regimen according to individual differences in glucose and insulin metabolism. Therapeutic insulin may be derived from porcine, bovine or recombinant sources. Endogenous human insulin, a pancreatic hormone composed of two polypeptide chains, is important for the normal metabolism of carbohydrates, proteins and fats and has anabolic effects on many types of tissues. 2019-01-22T20:33:51Z NCIT:C581 insulin drug treatment insulin therapy therapeutic insulin preparations treatment therapeutic insulin treatment A synthetic or animal-derived form of insulin used in the treatment of diabetes mellitus. Therapeutic insulin is formulated to be short-, intermediate- and long-acting in order to individualize an insulin regimen according to individual differences in glucose and insulin metabolism. Therapeutic insulin may be derived from porcine, bovine or recombinant sources. Endogenous human insulin, a pancreatic hormone composed of two polypeptide chains, is important for the normal metabolism of carbohydrates, proteins and fats and has anabolic effects on many types of tissues. NCIT:C581 Treatment with drugs producing both physiological and psychological effects through a variety of mechanisms involving the central nervous system. 2019-01-22T20:34:31Z CHEBI:35470 CNS agent therapy CNS drug therapy central nervous system drug therapy treatment with central nervous system drug central nervous system agent therapy CNS agent therapy CNS drug therapy Treatment with a class of central nervous system stimulants based on the structure of the parent amphetamine 1-phenylpropan-2-amine. 2019-01-22T20:35:07Z CHEBI:35338 NCIT:C62006 amphetamine drug intake amphetamine drug therapy amphetamines therapy treatment with amphetamine agent treatment with amphetamine drug treatment with amphetamine medication treatment with amphetamines amphetamine agent therapy Use of non-stimulant (non-amphetamine) medication for treatment of Attention Deficit Hyperactivity Disorder (ADHD). 2019-01-22T20:35:24Z non-amphetamine ADHD agent therapy non-amphetamine ADHD drug therapy non-stimulant ADHD treatment non-stimulant Attention Deficient Hyperactivity Disorder agent therapy non-stimulant ADHD agent therapy Use of non-stimulant (non-amphetamine) medication for treatment of Attention Deficit Hyperactivity Disorder (ADHD). http://orcid.org/0000-0001-7941-2961 obsolete non-amphetamines, other false 2019-01-22T20:35:53Z dental and oral agent therapy Use of a drug to treat or prevent skin disorders or for the routine care of skin. 2019-01-22T20:36:09Z CHEBI:50177 dermatologic agent therapy dermatologic drug therapy dermatologic drug treatment treatment with dermatolic drug treatment with dermatolic medication treatment with dermatolical drug treatment with dermatolical medication treatment with dermatologic drug dermatological agent therapy obsolete enzyme replacements and modifier agent therapy false Use of a drug for its effects on the gastrointestinal system, e.g. controlling gastric acidity, regulating gastrointestinal motility and water flow, and improving digestion. 2019-01-22T20:36:38Z CHEBI:55324 gastrointestinal agent treatment gastrointestinal drug therapy gastrointestinal drug treatment gastrointestinal drug treatment therapy treatment with gastrointestinal drug treatment with gastrointestinal medication gastrointestinal agent therapy 2019-01-22T20:37:00Z gastrointestinal anti-spasmodic agent therapy gastrointestinal antispasmodic agent therapy gastrointestinal antispasmodic drug treatment gastrointestinal antispasmodic treatment therapy gastrointestinal antispasmodics agent therapy H2-receptor antagonists are the drugs that selectively bind to but do not activate histamine H2 receptors, thereby blocking the actions of endogenous histamine. 2019-01-22T20:37:14Z CHEBI:37961 H2 blocker treatment therapy H2 blocking agent treatment therapy H2 receptor antagonist treatment therapy H2 receptor blockader treatment H2-receptor blocker therapy Histamine2 antagonist therapy histamine H2 receptor antagonist therapy histamine H2 receptor antagonist treatment histamine2 blocking agent therapy H2-receptor antagonist agent therapy H2-receptor antagonists are the drugs that selectively bind to but do not activate histamine H2 receptors, thereby blocking the actions of endogenous histamine. CHEBI:37961 2019-01-22T20:37:54Z irritable bowel syndrome agent therapy 2019-01-22T20:38:16Z gastrointestinal protectant drug treatment gastrointestinal protectant treatment therapy gastrointestinal protectant agent therapy Any one of the substituted benzimidazole compounds with anti-ulcer activity. A proton pump inhibitor is orally administered in the neutrally charged, inactive form and, upon entering the acidic environment of the parietal cell, gets protonated and converted into its active form. The active form will covalently and irreversibly bind to the proton pump, the H+/K+-ATPase, located on the surface of parietal cells. This leads to an inhibition of the transport of hydrogen ions, in exchange for potassium ions, into the gastric lumen and results in an inhibition of gastric acid secretion. 2019-01-22T20:38:35Z NCIT:C29723 PPI agent therapy PPI drug therapy PPI treatment therapy proton pump inhibitor drug treatment proton pump inhibitor treatment therapy proton pump inhibitor agent therapy Any one of the substituted benzimidazole compounds with anti-ulcer activity. A proton pump inhibitor is orally administered in the neutrally charged, inactive form and, upon entering the acidic environment of the parietal cell, gets protonated and converted into its active form. The active form will covalently and irreversibly bind to the proton pump, the H+/K+-ATPase, located on the surface of parietal cells. This leads to an inhibition of the transport of hydrogen ions, in exchange for potassium ions, into the gastric lumen and results in an inhibition of gastric acid secretion. NCIT:C29723 PPI agent therapy PPI drug therapy PPI treatment therapy obsolete gastrointestinal agents, other false Use of a drug to treat conditions of the reproductive organs and excretory system or urinary tract. 2019-01-22T20:39:18Z treatment with genitourinary agent treatment with genitourinary drug treatment with genitourinary medication genitourinary agent therapy 2019-01-22T20:39:46Z urinary antispasmodic agent therapy 2019-01-22T20:40:09Z benign prostate hypertrophy agent therapy 2019-01-22T20:40:24Z phosphate binders agent therapy obsolete genitourinary agents, other false 2019-01-22T20:42:45Z Glucocorticoids/ Mineralocorticoids therapy 2019-01-22T20:44:06Z treatment with pituitary modifier treatment with pituitary modifying agent treatment with pituitary modifying drug treatment with pituitary modifying medication pituitary-modifying, hormonal agent therapy 2019-01-22T20:45:21Z treatment with prostaglandin modifier treatment with prostaglandin modifying agent treatment with prostaglandin modifying drug treatment with prostaglandin modifying medication prostaglandin-modifying, hormonal agent therapy 2019-01-22T20:46:02Z sex hormone modifying drug treatment sex hormone modifying agent therapy Use of any agent that can alter hormone levels or modulate hormone effects. 2019-01-22T20:49:54Z NCIT:C147908 hormone modifiers hormone modifying agent hormone modifying drug hormone modifying drugs hormone therapies hormone therapy hormone therapy agents hormone therapy drugs treatment with hormone modifiers hormone modifying therapy 2019-01-22T20:51:04Z treatment with thyroid modifier treatment with thyroid modifying agent treatment with thyroid modifying drug treatment with thyroid modifying medication thyroid-modifying hormonal agent therapy Use of a compound which stimulates anabolism and inhibits catabolism. Anabolic agents stimulate the development of muscle mass, strength, and power. 2019-01-22T20:51:34Z CHEBI:36413 anabolic agent therapy anabolic steroid modifying drug treatment treatment with anabolic steroid anabolic steroid modifying agent therapy 2019-01-22T20:51:44Z treatment with androgen agent treatment with androgen drug treatment with androgen medication treatment with androgen modifying agent treatment with androgen modifying drug androgen modifying agent therapy A drug which acts to modulates estrogenic activity in the body, either by modulating the amount of estrogen or by modulating the activity of whatever estrogen is present. 2019-01-22T20:52:07Z CHEBI:50739 estrogen modifying drug therapy estrogen modifying medication therapy estrogen receptor modulator therapy oestrogen modifying agent therapy oestrogen modifying drug therapy treatment with estrogen receptor modulator treatment with estrogent modifying medication treatment with oestrogen modifying medication estrogen modifying agent therapy 2019-01-22T20:52:15Z progestin modifying drug treatment treatment with progestin modifier treatment with progestin modifying agent treatment with progestin modifying drug treatment with progestin modifying medication progestin modifying agent therapy 2019-01-22T20:52:46Z selective-estrogen receptor modifying agent therapy Use of a drug to treat hyperparathyroidism by reducing the excessive production of parathyroid hormones. 2019-01-22T20:53:28Z CHEBI:50827 antiparathyroid agent therapy antiparathyroid drug therapy treatment with antiparathyroid drug treatment with antiparathyroid medication treatment with parathyroid-suppressant agent treatment with parathyroid-suppressant drug treatment with parathyroid-suppressant medication parathyroid-suppressant hormonal agent therapy 2019-01-22T20:54:46Z treatment with androgen agonist treatment with androgen stimulant androgen stimulant agent therapy Use of a compound which inhibits or antagonizes the biosynthesis or actions of androgens. 2019-01-22T20:55:10Z CHEBI:35497 androgen antagonist therapy treatment with androgen antagonist treatment with androgen blocker treatment with androgen suppressant agent androgen suppressant agent therapy 2019-01-22T20:59:15Z treatment with thyroid agonist treatment with thyroid stimulating agent treatment with thyroid stimulating drug treatment with thyroid stimulating medication treatment with thyroid-stimulating agent thyroid-stimulating hormonal agent therapy Use of a drug to treat hyperthyroidism by reducing the excessive production of thyroid hormones. 2019-01-22T20:59:33Z CHEBI:50671 anti-thyroid drug treatment treatment with anti-thyroid agent treatment with antithyroid agent treatment with antithyroid drug treatment with antithyroid medication antithyroid agent therapy Use of a drug that induces, enhances, restores or suppresses the host's immune system, or an agent that utilizes or is derived from a component of the immune system. 2019-01-22T21:00:01Z CHEBI:50846 NCIT:C308 immune factor therapy immune mediator treatment therapy immune modulator therapy immune regulator therapy immunological agent treatment therapy immunomodulating agent treatment therapy immunomodulator therapy immunomodulator treatment therapy immunomodulatory agent treatment therapy immunotherapeutic agent treatment therapy immunotherapy agent immunotherapy treatment treatment with immunological agent treatment with immunological drug treatment with immunological medication treatment with immunomodifying agent treatment with immunomodifying drug treatment with immunomodifying medication treatment with immunomodulator immunological agent therapy Use of a substance that augments, stimulates, activates, potentiates, or modulates the immune response at either the cellular or humoral level. 2019-01-22T21:00:13Z CHEBI:50847 immune stimulant agent therapy immunoactivator treatment therapy immunoadjuvant treatment therapy immunologic adjuvant treatment therapy immunological adjuvant therapy immunological adjuvant treatment therapy immunopotentiator treatment therapy immunostimulant treatment therapy treatment with immune stimulant treatment with immunoactivator treatment with immunoadjuvant treatment with immunological adjuvant A classical agent (Freund's adjuvant, BCG, Corynebacterium parvum, et al.) contains bacterial antigens. It could also be endogenous (e.g., histamine, interferon, transfer factor, tuftsin, interleukin-1). Its mode of action is either non-specific, resulting in increased immune responsiveness to a wide variety of antigens, or antigen-specific, i.e., affecting a restricted type of immune response to a narrow group of antigens. The therapeutic efficacy is related to its antigen-specific immunoadjuvanticity. immune stimulant agent therapy A classical agent (Freund's adjuvant, BCG, Corynebacterium parvum, et al.) contains bacterial antigens. It could also be endogenous (e.g., histamine, interferon, transfer factor, tuftsin, interleukin-1). Its mode of action is either non-specific, resulting in increased immune responsiveness to a wide variety of antigens, or antigen-specific, i.e., affecting a restricted type of immune response to a narrow group of antigens. The therapeutic efficacy is related to its antigen-specific immunoadjuvanticity. CHEBI:50847 Use of an agent that suppresses immune function by one of several mechanisms of action. 2019-01-22T21:00:25Z CHEBI:35705 NCIT:C574 immune suppressant agent treatment immunosuppressant agent therapy immunosuppressant treatment therapy immunosuppressive agent therapy immunosuppressive agent treatment therapy immunosuppressor agent therapy treatment immunosuppressant treatment with immune suppressant treatment with immunosuppressive treatment with immunosuppressive agent Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response. immune suppressant agent therapy Classical cytotoxic immunosuppressants act by inhibiting DNA synthesis. Others may act through activation of T-cells or by inhibiting the activation of helper cells. In addition, an immunosuppressive agent is a role played by a compound which is exhibited by a capability to diminish the extent and/or voracity of an immune response. CHEBI:35705 2019-01-22T21:00:40Z passive immunizing agent therapy The drug treatment of inflammatory bowel disease (IBD), which may include the use of anti-inflammatory agents and agents that reduce the symptoms associated with IBD. 2019-01-22T21:01:33Z PMID:21857074 anti-IBD drug treatment therapy anti-inflammatory bowel disease drug treatment anti-inflammatory bowel disease therapy inflammatory bowel disease agent therapy The drug treatment of inflammatory bowel disease (IBD), which may include the use of anti-inflammatory agents and agents that reduce the symptoms associated with IBD. PMID:21857074 The salts or esters of salicylic acids, or salicylate esters of an organic acid. Some of these have analgesic, antipyretic, and anti-inflammatory activities by inhibiting prostaglandin synthesis. 2019-01-22T21:02:35Z CHEBI:30762 https://www.drugbank.ca/categories/DBCAT000579 salicylate agent therapy The salts or esters of salicylic acids, or salicylate esters of an organic acid. Some of these have analgesic, antipyretic, and anti-inflammatory activities by inhibiting prostaglandin synthesis. https://www.drugbank.ca/categories/DBCAT000579 2019-01-22T21:04:21Z metabolic bone disease drug treatment metabolic bone disease agent therapy Use of a drug to treat eye conditions or eye diseases. 2019-01-22T21:04:40Z CHEBI:66981 ophthalmic agent therapy ophthalmic drug treatment ophthalmics drug treatment ophthalmological agent treatment ophthalmologicals therapy ophthalmology agent therapy ophthalmology agent treatment therapy ophthalmology drug therapy treatment with ophthalmic agent treatment with ophthalmic drug treatment with ophthalmic medication treatment with ophthalmology drug ophthalmic agent therapy 2019-01-22T21:04:55Z ophthalmic anti-allergy agent therapy Use of a drug which can be used to prevent or alleviate glaucoma, a disease in which the optic nerve is damaged, resulting in progressive, irreversible loss of vision. 2019-01-22T21:05:20Z CHEBI:39456 antiglaucoma drug therapy ophthalmic antiglaucoma agent therapy treatment with anti-glaucoma agent treatment with anti-glaucoma medication treatment with antiglaucoma agent treatment with antiglaucoma drug treatment with antiglaucoma medication antiglaucoma agent therapy 2019-01-22T21:05:47Z ophthalmic anti-inflammatory agent therapy 2019-01-22T21:06:19Z ophthalmic prostaglandin and prostamide agent therapy obsolete ophthalmic agents, other false Treatment with a substance intended for administration either on the outer ear or into the auditory canal. 2019-01-22T21:08:34Z NCIT:C69040 NCIT:C69040 treatment with otic medication otic agent therapy Use of an agent that exerts a physiologic effect on any anatomic entity that is part of the respiratory tract and airways. 2019-01-22T21:08:56Z NCIT:C78273 agent affecting respiratory system treatment respiratory tract agent treatment respiratory tract drug treatment therapy treatment with respiratory tract agent treatment with respiratory tract medication respiratory tract agent therapy Use of an agent that exerts a physiologic effect on any anatomic entity that is part of the respiratory tract and airways. NCIT:C78273 Use of drugs that bind to but do not activate histamine receptors, thereby blocking the actions of histamine or histamine agonists. 2019-01-22T21:09:06Z CHEBI:37956 antihistamine drug treatment antihistimine drug therapy histamine antagonist therapy histamine receptor blocker drug treatment histamine receptor blocker therapy treatment with antihistamine treatment with histamine antagonist treatment with histamine blocker antihistamine agent therapy 2019-01-22T21:09:38Z inhaled corticosteroid drug treatment inhaled corticosteroid agent therapy Use of a drug designed to prevent leukotriene synthesis or activity by blocking binding at the receptor level. 2019-01-22T21:09:53Z CHEBI:49159 antileukotriene drug treatment leukotriene antagonist therapy treatment with antileukotriene agent treatment with antileukotriene medication treatment with leukotriene antagonist treatment with leukotriene blocker antileukotriene agent therapy Use of an agent that causes an increase in the expansion of a bronchus or bronchial tubes. 2019-01-22T21:10:11Z CHEBI:35523 NCIT:C319 bronchodilator agent therapy bronchodilator agent treatment bronchodilator drug treatment broncholytic agent therapy treatment with bronchodilator treatment with bronchodilator agent bronchodilator agent therapy 2019-01-22T21:10:37Z anticholinergic bronchodilator drug treatment anticholinergic bronchodilator agent therapy 2019-01-22T21:11:08Z phosphodiesterase inhibitor bronchodilator drug treatment phosphodiesterase inhibitor bronchodilator agent therapy 2019-01-22T21:11:37Z sympathomimetic bronchodilator drug therapy sympathomimetic bronchodilator agent therapy 2019-01-22T21:12:02Z NCIT:C29714 mast cell stabiliser agent therapy mast cell stabiliser drug treatment mast cell stabilizer drug treatment mast cell stabilizer agent therapy 2019-01-22T21:12:15Z pulmonary antihypertensive drug treatment pulmonary antihypertensive agent therapy obsolete respiratory tract agents, other false Treatment with a central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. 2019-01-22T21:14:36Z CHEBI:35717 NCIT:C29756 hypnotic agent therapy hypnotic drug therapy hypnotics agent therapy sedative agent drug therapy sedative agent drug treatment sedative and hypnotic drug treatment sedative drug therapy sedative drug treatment sedative therapy sedative treatment therapy sedative-hypnotic drug treatment sedatives and hypnotic drug therapy sedatives/hypnotic drug treatment treatment with sedative sedatives and hypnotic agent therapy Treatment with a central nervous system depressant used to induce drowsiness or sleep or to reduce psychological excitement or anxiety. CHEBI:35717 Use of a drug used to produce muscle relaxation (excepting neuromuscular blocking agents). Its primary clinical and therapeutic use is the treatment of muscle spasm and immobility associated with strains, sprains, and injuries of the back and, to a lesser degree, injuries to the neck. Also used for the treatment of a variety of clinical conditions that have in common only the presence of skeletal muscle hyperactivity, for example, the muscle spasms that can occur in multiple sclerosis. 2019-01-22T21:14:48Z CHEBI:51371 NCIT:C29696 muscle relaxant agent therapy muscle relaxant therapy skeletal muscle relaxant drug treatment treatment with muscle relaxant skeletal muscle relaxant agent therapy Use of a substance for the prophylaxis or therapy of infectious diseases. 2019-04-10T19:56:29Z CHEBI:35441 anti-infective drug therapy anti-infectives antiinfective agent therapy antiinfective agents antiinfective drug treatment with anti-infective agent treatment with anti-infective drug treatment with anti-infective medication treatment with antiinfective agent treatment with antiinfective drug treatment with antiinfective medication anti-infective agent therapy Removal of tissue from the head. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 head biopsy biopsy of head Removal of tissue from the abdomen. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 abdomen biopsy biopsy of abdomen Removal of tissue from the adipose tissue. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 adipose tissue biopsy biopsy of adipose tissue Removal of tissue from the adrenal cortex. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 adrenal cortex biopsy biopsy of adrenal cortex Removal of tissue from the adrenal gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 adrenal gland biopsy biopsy of adrenal gland Removal of tissue from the anal canal. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 anal canal biopsy biopsy of anal canal Removal of tissue from the anus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C51586 anus biopsy biopsy of anus Removal of tissue from the aorta. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 aorta biopsy biopsy of aorta Removal of tissue from the body of uterus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 body of uterus biopsy biopsy of body of uterus Removal of tissue from the bone element. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 bone element biopsy biopsy of bone element Removal of tissue from the bone marrow. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 bone marrow biopsy biopsy of bone marrow Removal of tissue from the bone tissue. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 bone tissue biopsy biopsy of bone tissue Removal of tissue from the brain. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 brain biopsy biopsy of brain Removal of tissue from the brainstem. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 brainstem biopsy biopsy of brainstem Removal of tissue from the breast. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 breast biopsy biopsy of breast Removal of tissue from the bronchus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 bronchus biopsy biopsy of bronchus Removal of tissue from the caecum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 caecum biopsy biopsy of caecum Removal of tissue from the cardiac ventricle. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 cardiac ventricle biopsy biopsy of cardiac ventricle Removal of tissue from the cerebellum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 cerebellum biopsy biopsy of cerebellum Removal of tissue from the cerebral cortex. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 cerebral cortex biopsy biopsy of cerebral cortex Removal of tissue from the chest wall. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 chest wall biopsy biopsy of chest wall Removal of tissue from the chordate pharynx. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 chordate pharynx biopsy biopsy of chordate pharynx Removal of tissue from the choroid plexus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 choroid plexus biopsy biopsy of choroid plexus Removal of tissue from the cochlea. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 cochlea biopsy biopsy of cochlea Removal of tissue from the colon. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 colon biopsy biopsy of colon Removal of tissue from the colorectum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 colorectum biopsy biopsy of colorectum Removal of tissue from the dermis. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 dermis biopsy biopsy of dermis Removal of tissue from the diaphragm. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 diaphragm biopsy biopsy of diaphragm Removal of tissue from the dorsal plus ventral thalamus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 dorsal plus ventral thalamus biopsy biopsy of dorsal plus ventral thalamus Removal of tissue from the duodenum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 duodenum biopsy biopsy of duodenum Removal of tissue from the endocardium. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 endocardium biopsy biopsy of endocardium Removal of tissue from the endocrine pancreas. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 endocrine pancreas biopsy biopsy of endocrine pancreas Removal of tissue from the endometrium. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 endometrium biopsy biopsy of endometrium Removal of tissue from the esophagus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 esophagus biopsy biopsy of esophagus Removal of tissue from the eye. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 eye biopsy biopsy of eye Removal of tissue from the fallopian tube. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 fallopian tube biopsy biopsy of fallopian tube Removal of tissue from the frontal lobe. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 frontal lobe biopsy biopsy of frontal lobe Removal of tissue from the gall bladder. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 gall bladder biopsy biopsy of gall bladder Removal of tissue from the genitourinary system. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 genitourinary system biopsy biopsy of genitourinary system Removal of tissue from the gonad. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 gonad biopsy biopsy of gonad Removal of tissue from the heart. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 heart biopsy biopsy of heart Removal of tissue from the hypopharynx. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 hypopharynx biopsy biopsy of hypopharynx Removal of tissue from the hypothalamus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 hypothalamus biopsy biopsy of hypothalamus Removal of tissue from the intestine. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 intestine biopsy biopsy of intestine Removal of tissue from the jaw skeleton. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 jaw skeleton biopsy biopsy of jaw skeleton Removal of tissue from the lacrimal apparatus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 lacrimal apparatus biopsy biopsy of lacrimal apparatus Removal of tissue from the large intestine. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 large intestine biopsy biopsy of large intestine Removal of tissue from the larynx. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 larynx biopsy biopsy of larynx Removal of tissue from the limb. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 limb biopsy biopsy of limb Removal of tissue from the lip. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 lip biopsy biopsy of lip Removal of tissue from the liver. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 liver biopsy biopsy of liver Removal of tissue from the lower respiratory tract. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 lower respiratory tract biopsy biopsy of lower respiratory tract Removal of tissue from the lower urinary tract. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 lower urinary tract biopsy biopsy of lower urinary tract Removal of tissue from the lumbar region of vertebral column. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 lumbar region of vertebral column biopsy biopsy of lumbar region of vertebral column Removal of tissue from the lung. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 lung biopsy biopsy of lung Removal of tissue from the lymph node. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 lymph node biopsy biopsy of lymph node Removal of tissue from the lymphatic part of lymphoid system. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 lymphatic part of lymphoid system biopsy biopsy of lymphatic part of lymphoid system Removal of tissue from the mammalian vulva. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 mammalian vulva biopsy vulva biopsy vulval biopsy biopsy of vulva Removal of tissue from the medulla oblongata. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 medulla oblongata biopsy biopsy of medulla oblongata Removal of tissue from the mouth. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 mouth biopsy muscle biopsy biopsy of mouth Removal of tissue from the muscle organ. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 muscle organ biopsy biopsy of muscle Removal of tissue from the muscle tissue. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 muscle tissue biopsy biopsy of muscle tissue Removal of tissue from the nasolacrimal duct. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 nasolacrimal duct biopsy biopsy of nasolacrimal duct Removal of tissue from the nasopharynx. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 nasopharynx biopsy biopsy of nasopharynx Removal of tissue from the neck. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 neck biopsy biopsy of neck Removal of tissue from the ovary. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 ovary biopsy biopsy of ovary Removal of tissue from the pancreas. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 pancreas biopsy biopsy of pancreas Removal of tissue from the penis. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 penis biopsy biopsy of penis Removal of tissue from the perianal skin. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 perianal skin biopsy biopsy of perianal skin Removal of tissue from the peritoneum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 peritoneum biopsy biopsy of peritoneum Removal of tissue from the pituitary gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 pituitary gland biopsy biopsy of pituitary gland Removal of tissue from the pleura. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 pleura biopsy biopsy of pleura Removal of tissue from the rectum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 rectum biopsy biopsy of rectum Removal of tissue from the retina. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 retina biopsy biopsy of retina Removal of tissue from the saliva-secreting gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 saliva-secreting gland biopsy biopsy of saliva-secreting gland Removal of tissue from the scrotum. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 scrotum biopsy biopsy of scrotum Removal of tissue from the sebaceous gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 sebaceous gland biopsy biopsy of sebaceous gland Removal of tissue from the small intestine. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 small intestine biopsy biopsy of small intestine Removal of tissue from the spinal cord. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 spinal cord biopsy biopsy of spinal cord Removal of tissue from the spleen. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 spleen biopsy biopsy of spleen Removal of tissue from the stomach. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 stomach biopsy biopsy of stomach Removal of tissue from the subglottis. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 subglottis biopsy biopsy of subglottis Removal of tissue from the submandibular gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 submandibular gland biopsy biopsy of submandibular gland Removal of tissue from the testis. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 testis biopsy biopsy of testis Removal of tissue from the thymus. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 thymus biopsy biopsy of thymus Removal of tissue from the thyroid gland. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 thyroid gland biopsy biopsy of thyroid gland Removal of tissue from the tongue. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 tongue biopsy biopsy of tongue Removal of tissue from the tonsil. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 tonsil biopsy biopsy of tonsil Removal of tissue from the trachea. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 trachea biopsy biopsy of trachea Removal of tissue from the upper digestive tract. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 upper digestive tract biopsy biopsy of upper digestive tract Removal of tissue from the upper respiratory tract. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 upper respiratory tract biopsy biopsy of upper respiratory tract Removal of tissue from the ureter. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 ureter biopsy biopsy of ureter Removal of tissue from the urethra. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 urethra biopsy biopsy of urethra Removal of tissue from the urinary bladder. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 urinary bladder biopsy biopsy of urinary bladder Removal of tissue from the uterine cervix. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 uterine cervix biopsy biopsy of uterine cervix Removal of tissue from the vagina. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 vagina biopsy biopsy of vagina Removal of tissue from the vermiform appendix. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 vermiform appendix biopsy biopsy of vermiform appendix Removal of tissue from the zone of skin. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 skin biopsy zone of skin biopsy biopsy of skin Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. 2019-04-26T17:25:14Z NCIT:C16809 MRI scan for therapeutics NMRI nuclear magnetic resonance imaging for medical therapy therapeutic MRI medical magnetic resonance imaging procedure Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders. NCIT:C16809 MRI scan for therapeutics NMRI therapeutic MRI A medical examination performed using of magnetic resonance imaging to image the head. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the head head MRI head magnetic resonance imaging MRI of the head A medical examination performed using of magnetic resonance imaging to image the abdomen. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the abdomen abdomen MRI abdomen magnetic resonance imaging MRI of the abdomen A medical examination performed using of magnetic resonance imaging to image the brain. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the brain brain MRI brain magnetic resonance imaging MRI of the brain A medical examination performed using of magnetic resonance imaging to image the chest. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the chest chest MRI chest magnetic resonance imaging MRI of the chest Radiation therapy in which high-energy beams are delivered to the tumor from outside of the body. 2019-04-26T19:28:21Z NCIT:C15751 EBRT external beam RT external beam radiotherapeutics external beam radiotherapy external-beam radiation External radiation therapy external beam radiation therapy Radiation therapy in which high-energy beams are delivered to the tumor from outside of the body. NCIT:C15751 EBRT external beam RT A type of radiation therapy in which radioactive material is placed inside the body, into a tumor or body cavity. 2019-04-26T19:28:57Z NCIT:C15195 Brachytherapy Internal radiation brachytherapy internal radiation radiation brachytherapy internal radiation therapy A type of radiation therapy in which radioactive material is placed inside the body, into a tumor or body cavity. NCIT:C15195 A medical examination performed using of magnetic resonance imaging to image the breast. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 Nuclear magnetic resonance imaging of the breast breast MRI breast magnetic resonance imaging MRI of the breast Use of an organonitrogen heterocyclic antibiotic that contains a beta-lactam ring. 2019-08-29T18:00:40Z beta-lactams therapy CHEBI:27933 beta-lactam antibacterial drug therapy beta-lactam antibacterial drug treatment beta-lactam antibiotic agent therapy beta-lactam antibiotic therapy treatment with a beta-lactam antibacterial drug treatment with a beta-lactam antibacterial medication treatment with a beta-lactam antibacterial therapy treatment with a beta-lactam antibiotic agent treatment with a beta-lactam antibiotic drug treatment with a beta-lactam antibiotic medication treatment with a beta-lactam antibiotic therapy treatment with beta-lactam antibiotic beta-lactam antibacterial agent therapy Treatment with a pharmaceutical agent that inhibits the movement of calcium across through calcium channels in the cell membrane, preventing or decreasing the amount of calcium able to enter the cell. These drugs are used for their chronotropic, antihypertensive and vasodilatory effects. 2019-09-27T19:41:29Z CHEBI:38215 NCIT:C333 Ca2+ channel antagonist therapy Ca2+ channel blocker therapy calcium channel antagonist drug therapy calcium channel antagonist therapy calcium channel blocker drug therapy calcium channel blocker therapy treatment with calcium channel blocker treatment with calcium channel blocker drug treatment with calcium channel blocker medication treatment with calcium channel blocking drug treatment with calcium channel blocking medication One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools. calcium channel blocking agent therapy Ca2+ channel antagonist therapy Ca2+ channel blocker therapy One of a class of drugs that acts by selective inhibition of calcium influx through cell membranes or on the release and binding of calcium in intracellular pools. CHEBI:38215 Treatment with a drug that inhibits the action of N-methyl-D-aspartate (NMDA) receptors. 2019-10-01T19:23:17Z CHEBI:60643 N-methyl-D-aspartate receptor antagonist therapy NMDA receptor antagonist drug treatment NMDA receptor antagonist therapy NMDA receptor antagonist treatment NMDA receptor blocker therapy treatment with NMDA blockade drug treatment with NMDA blockade medication treatment with NMDA blockade therapy treatment with NMDA blockers treatment with NMDA receptor antagonist They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs. NMDA receptor antagonist therapy They tend to induce a state known as dissociative anesthesia, marked by catalepsy, amnesia, and analgesia, while side effects can include hallucinations, nightmares, and confusion. Due to their psychotomimetic effects, many NMDA receptor antagonists are used as recreational drugs. CHEBI:60643 Use of medication for the treatment of Attention Deficit Hyperactivity Disorder (ADHD). 2019-10-02T15:59:55Z ADHD drug therapy ADHD drug treatment Attention Deficit Hyperactivity Disorder drug therapy Attention Deficit Hyperactivity Disorder drug treatment drug therapy for ADHD ADHD agent therapy Use of medication for the treatment of Attention Deficit Hyperactivity Disorder (ADHD). http://orcid.org/0000-0001-7941-2961 Use of stimulant medication (usually amphetamines) for treatment of Attention Deficit Hyperactivity Disorder (ADHD). 2019-10-02T16:01:46Z stimulant ADHD drug treatment stimulant Attention Deficit Hyperactivity Disorder agent therapy stimulant Attention Deficit Hyperactivity Disorder drug treatment stimulant drug therapy for ADHD stimulant drug treatment for ADHD stimulant ADHD agent therapy Use of stimulant medication (usually amphetamines) for treatment of Attention Deficit Hyperactivity Disorder (ADHD). http://orcid.org/0000-0001-7941-2961 Treatment with a medication that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. 2019-10-02T18:41:07Z CHEBI:50949 NCIT:C94725 SSRI drug therapy SSRI drug treatment selective serotonin reuptake inhibitor drug therapy selective serotonin reuptake inhibitor drug treatment serotonin uptake inhibitor therapy treatment with SSRI treatment with SSRI agent treatment with selective serotonin reuptake inhibitor agent treatment with selective serotonin reuptake inhibitor drug treatment with selective serotonin reuptake inhibitor medication treatment with serotonin uptake inhibitor Any agent that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. Increased level in the synaptic cleft prolongs the action of 5-HT on the postsynaptic receptor. This type of agent is typically used as an antidepressant and in the treatment of anxiety disorders and some personality disorders. They are also typically effective and used in treating some cases of insomnia. selective serotonin reuptake inhibitor agent therapy Treatment with a medication that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. NCIT:C94725 Any agent that increases the extracellular level of the neurotransmitter serotonin (5-HT) by inhibiting its reuptake into the presynaptic cell. Increased level in the synaptic cleft prolongs the action of 5-HT on the postsynaptic receptor. This type of agent is typically used as an antidepressant and in the treatment of anxiety disorders and some personality disorders. They are also typically effective and used in treating some cases of insomnia. NCIT:C94725 Treatment with colony-stimulating factors (CSF) can help the blood-forming tissue recover from the effects of chemotherapy and radiation therapy. These factors include interleukin-3 (IL-3), granulocyte colony-stimulating factor (G-CSF), macrophage colony-stimulating factor (M-CSF), and granulocyte-macrophage colony-stimulating factor (GM-CSF). 2019-10-08T17:41:54Z NCIT:C387 CSF agent therapy recombinant colony stimulating factor drug therapy recombinant colony-stimulating factor treatment recombinant hematopoietic colony-stimulating factor drug treatment colony stimulating factor agent therapy Treatment with colony-stimulating factors (CSF) can help the blood-forming tissue recover from the effects of chemotherapy and radiation therapy. These factors include interleukin-3 (IL-3), granulocyte colony-stimulating factor (G-CSF), macrophage colony-stimulating factor (M-CSF), and granulocyte-macrophage colony-stimulating factor (GM-CSF). NCIT:C387 CSF agent therapy 2019-10-08T18:06:31Z NCIT:C1287 G-CSF treatment granulocyte-colony stimulating factor treatment therapy recombinant colony-stimulating factor 3 treatment therapy recombinant granulocyte colony stimulating factor agent therapy recombinant granulocyte colony-stimulating factor drug treatment rhG-CSF therapy granulocyte colony stimulating factor agent therapy G-CSF treatment rhG-CSF therapy 2019-10-08T18:37:29Z erythropoietin modulating treatment erythropoietin regulating agent therapy Use of a recombinant therapeutic agent which is chemically identical to or similar to the endogenous glycoprotein erythropoietin (Epo). Epo promotes the differentiation and maturation of hematopoietic progenitors into erythrocytes; is a mitogen and a chemoattractant for endothelial cells; stimulates activated and differentiated B-cells and enhances B-cell immunoglobulin production and proliferation; and is hypoxia-inducible. 2019-10-08T18:38:34Z erythrocyte colony stimulating factor agent therapy erythropoietin therapy CHEBI:81579 NCIT:C477 ESA therapy hematopoietin treatment therapy recombinant EPO treatment recombinant erythropoietin drug therapy recombinant erythropoietin treatment treatment with erythropoietin stimulating agent treatment with erythropoietin stimulating medication erythropoietin stimulating agent therapy ESA therapy recombinant EPO treatment Use of a drug that inhibits erythropoietin, a glycoprotein hormone that controls erythropoiesis (red blood cell production). 2019-10-08T18:49:31Z CHEBI:91025 EPO inhibitor agent therapy EPO inhibitor drug treatment erythropoietin inhibitor drug treatment erythropoietin inhibitor therapy treatment with erythropoietin inhibitor erythropoietin inhibitor agent therapy EPO inhibitor agent therapy EPO inhibitor drug treatment A drug that prevents fibrinolysis or lysis of a blood clot or thrombus. 2019-10-08T19:21:34Z CHEBI:48675 antifibrinolytic drug treatment antifibrinolytic agent therapy A drug that prevents fibrinolysis or lysis of a blood clot or thrombus. CHEBI:48675 A synthetic analogue of vasopressin in which 3-mercaptopropionic acid replaces the cysteine residue at position 1 and D-arginine replaces the residue at position 8. An antidiuretic, it increases urine concentration and decreases urine production, and is used (usually as the trihydrate of the acetic acid salt) to prevent and control excessive thirst, urination, and dehydration caused by injury, surgery, and certain medical conditions. It is also used in the diagnosis and treatment of cranial diabetes insipidus and in tests of renal function. 2019-10-08T19:26:15Z CHEBI:4450 NCIT:C61701 1-(3-mercaptopropionic acid)-8-D-arginine-vasopressin, 1-deamino-8-D-arginine vasopressin drug treatment 1-deamino-8-D-arginine vasopressin agent therapy 1-desamino-8-D-arginine vasopressin agent therapy DDAVP agent therapy desmopresina agent therapy desmopressin drug treatment desmopressine agent therapy desmopressinum agent therapy desmopressin agent therapy A synthetic analogue of vasopressin in which 3-mercaptopropionic acid replaces the cysteine residue at position 1 and D-arginine replaces the residue at position 8. An antidiuretic, it increases urine concentration and decreases urine production, and is used (usually as the trihydrate of the acetic acid salt) to prevent and control excessive thirst, urination, and dehydration caused by injury, surgery, and certain medical conditions. It is also used in the diagnosis and treatment of cranial diabetes insipidus and in tests of renal function. CHEBI:4450 The surgical removal (cutting out) of part or all of a structure or organ. 2019-12-27T17:21:50Z excision NCIT:C15232 abscission surgical removal surgical excision Surgical removal (cutting out or off) without replacement of all of a body part or structure. 2019-12-27T17:45:26Z resection surgical resection Taking or cutting out solid matter from a body part. The solid matter contained in the definition may be an abnormal byproduct of a biological function or a foreign body. It may be embedded in a body part, or in the lumen of a tubular body part. The solid matter may or may not have been previously broken into pieces. 2020-01-02T19:00:34Z extirpation surgical extirpation Taking or cutting out solid matter from a body part. The solid matter contained in the definition may be an abnormal byproduct of a biological function or a foreign body. It may be embedded in a body part, or in the lumen of a tubular body part. The solid matter may or may not have been previously broken into pieces. ICD-10-PCS A surgical procedure by which tissue or an organ (usually containing a tumor) is removed without rupture from a specific anatomic site. 2020-01-06T16:44:59Z enucleation surgical enucleation A surgical procedure by which tissue or an organ (usually containing a tumor) is removed without rupture from a specific anatomic site. NCIT:C48601 A surgical procedure that places something in the human body. 2020-01-06T18:21:08Z NCIT:C51982 implantation A surgical procedure that places something in the human body. NCIT:C51982 The removal of material from the surface of an object by vaporization, chipping, or other erosive process. 2020-01-06T19:26:24Z NCIT:C20985 https://doi.org/10.1016/B978-0-12-370610-2.50011-8 ablation therapy The removal of material from the surface of an object by vaporization, chipping, or other erosive process. https://doi.org/10.1016/B978-0-12-370610-2.50011-8 Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by light amplification by stimulated emission of radiation. 2020-01-06T19:30:40Z NCIT:C111241 photoablation therapy laser ablation therapy Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by light amplification by stimulated emission of radiation. NCIT:C111241 Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by chemical means. 2020-01-06T19:35:01Z NCIT:C111157 chemical ablation Removal, separation, detachment, extirpation, or eradication of a body part, pathway, or function by chemical means. NCIT:C111157 The use of extreme cold to damage or destroy a body part, pathway, or function. The procedure is performed using small cryogenic probes during surgery, and has recently been applied to solitary sporadic renal tumor lesions. 2020-01-06T19:45:30Z NCIT:C15215 cryoablation therapy cryosurgical ablation therapy cryosurgery The use of extreme cold to damage or destroy a body part, pathway, or function. The procedure is performed using small cryogenic probes during surgery, and has recently been applied to solitary sporadic renal tumor lesions. NCIT:C15215 Thermal ablation refers to the destruction of tissue by extreme hyperthermia or hypothermia. 2020-01-06T19:50:11Z NCIT:C15670 thermal ablation therapy Thermal ablation refers to the destruction of tissue by extreme hyperthermia or hypothermia. NCIT:C15670 2020-01-08T17:26:31Z pain management Hydrotherapy is the external or internal use of water in any of its forms (water, ice, steam) for health promotion or treatment of various diseases with various temperatures, pressure, duration, and site. 2020-01-08T17:32:42Z OMIT:0008013 PMID:24926444 hydropathy hydrotherapy treatment water therapy water cure hydrotherapy Hydrotherapy is the external or internal use of water in any of its forms (water, ice, steam) for health promotion or treatment of various diseases with various temperatures, pressure, duration, and site. PMID:24926444 Thermal hydrotherapy uses external or internal use of water in any of its forms (water, ice, steam) at temperatures above or below room temperature for health promotion or treatment of various diseases with various temperatures, pressure, duration, and site. 2020-01-08T17:39:29Z hydro-thermal therapy hydrothermal therapy thermal water therapy bathing in thermal waters thermal hydrotherapy Washing out a hollow organ by flushing with a fluid. 2020-01-08T17:42:19Z NCIT:C38068 OMIT:0008013 lavage therapeutic irrigation Washing out a hollow organ by flushing with a fluid. NCIT:C38068 Therapy where a substantial part of the body is immersed in warm water to produce a variety of therapeutic effects. 2020-01-08T18:05:56Z hot bath therapy warm water bath therapy hyperthermic immersion therapy warm water shower therapy warm water immersion therapy Therapy where a substantial part of the body is immersed in warm water to produce a variety of therapeutic effects. PMID:24926444 Therapy where a substantial part of the body is immersed in cold water to produce a variety of therapeutic effects. 2020-01-08T18:06:06Z CWI therapy ice bath therapy cold water immersion therapy CWI therapy A form of treatment where a limb or significant portion of the body is immersed in hot water immediately followed by the immersion into cold water. This procedure is repeated several times. 2020-01-08T18:06:31Z contrast water therapy 2020-01-08T18:07:42Z aquatic exercise therapy A minimally-invasive procedure that permits sampling of breast ductal fluids for cytopathologic analysis. 2020-01-08T19:03:16Z NCIT:C51969 breast duct lavage A minimally-invasive procedure that permits sampling of breast ductal fluids for cytopathologic analysis. NCIT:C51969 Washing out the bronchi and alveoli by flushing with a fluid. 2020-01-08T19:03:33Z NCIT:C51913 bronchoaveolar lavage Washing out the bronchi and alveoli by flushing with a fluid. NCIT:C51913 A minimally invasive procedure that permits sampling of peritoneal fluid for cytopathologic analysis. 2020-01-08T19:03:46Z NCIT:C159340 peritoneal washing peritoneal lavage A minimally invasive procedure that permits sampling of peritoneal fluid for cytopathologic analysis. NCIT:C159340 The process in which the nasal cavity is washed to flush out mucus and debrise from the nose and sinuses with water or saline. 2020-01-08T19:04:02Z nasal irrigation nasal washing nasal lavage Avoid the administration or use of therapeutic procedure. 2020-01-12T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid therapeutic procedure avoiding therapeutic procedure therapeutic procedure avoidance Avoid the administration or use of diagnostic procedure. 2020-01-12T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid diagnostic procedure avoiding diagnostic procedure diagnostic procedure avoidance Avoid the administration or use of preventative therapeutics. 2020-01-12T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid preventative therapeutics avoiding preventative therapeutics preventative therapeutics avoidance The implantation of a piece of mechanical or electronic equipment that is useful for prevention, diagnosis, monitoring, or treatment of disease or other conditions. 2020-01-20T14:58:18Z ERO:0001092 NCIT:C16830 implantation of a medical device medical instrument implantation medical machine implantation medical device implantation Implantation of a battery-powered device that is placed under the skin (typically in the left upper chest) with electrode wires that lead into the heart (typically lodging in the apex or septum of the right ventricle). The device can detect abnormal heart rhythms and deliver low-energy or high-energy shocks to interrupt malignant arrhythmia and thereby prevent sudden death. 2020-01-20T16:54:00Z NCIt:C93238 UMLS_CUI:C0162589 ICD placement automated implantable cardioverter defibrillator placement implantable cardioverter-defibrillator implantation implantable cardioverter-defibrillator placement ICD placement The resection or complete surgical removal of a nerve. 2020-01-20T17:09:07Z surgical denervation Left cardiac sympathetic denervation (LCSD) is a surgical antiadrenergic intervention with a strong antiarrhythmic effect. LCSD consists in the removal of the left thoracic sympathetic chain and paravertebral ganglia from T1 to T4. 2020-01-20T17:11:04Z PMID:30972341 LCSD left cardiac sympathetic denervation Left cardiac sympathetic denervation (LCSD) is a surgical antiadrenergic intervention with a strong antiarrhythmic effect. LCSD consists in the removal of the left thoracic sympathetic chain and paravertebral ganglia from T1 to T4. PMID:30972341 LCSD 2020-01-20T17:50:35Z MeSH:D019637 Any procedure relating to the branch of medicine dealing with the correction of deformities of bones or muscles. orthopaedic procedure orthopedic procedure Evaluation with a surgeon who focuses on the preservation, investigation and restoration of the form and function of the extremities, spine and associated structures by medical, surgical and physical means. This specialist is involved with the care of patients whose musculoskeletal problems include congenital deformities, trauma, infections, tumors, metabolic disturbances of the musculoskeletal system, deformities, injuries and degenerative diseases of the spine, hands, feet, knee, hip, shoulder and elbow in children and adults. An orthopaedic surgeon is also concerned with primary and secondary muscular problems and the effects of central or peripheral nervous system lesions of the musculoskeletal system. 2020-01-20T17:50:52Z consultation with orthopedic surgeon orthopaedic consult orthopedic consult orthopedic surgeon consultation orthopedic surgeon referral orthopedist consultation referral to orthopedic surgeon referral to orthopedist orthopedic surgeon evaluation Evaluation with a surgeon who focuses on the preservation, investigation and restoration of the form and function of the extremities, spine and associated structures by medical, surgical and physical means. This specialist is involved with the care of patients whose musculoskeletal problems include congenital deformities, trauma, infections, tumors, metabolic disturbances of the musculoskeletal system, deformities, injuries and degenerative diseases of the spine, hands, feet, knee, hip, shoulder and elbow in children and adults. An orthopaedic surgeon is also concerned with primary and secondary muscular problems and the effects of central or peripheral nervous system lesions of the musculoskeletal system. abms.org A surgical procedure to treat and correct deformities, diseases, and injuries to the skeletal system, its articulations, and associated structures. 2020-01-20T17:51:02Z NCIT:C16186 orthopedic surgical procedure orthopedic surgery A surgical procedure to treat and correct deformities, diseases, and injuries to the skeletal system, its articulations, and associated structures. NCIT:C16186 obsolete orthopedic consultation false Orthotic services provide prescription insoles, braces, splints, callipers, footwear, spinal jackets and helmets which help people recover from or avoid injury, or live with lifelong conditions. 2020-01-20T18:01:00Z orthotic services The recommendation of the use of an orthosis or multiple orthoses, which are externally applied device used to modify the structural and functional characteristics of the neuromuscular and skeletal system. 2020-01-20T18:02:48Z PMID:26835739 orthoses usage orthotic device usage The recommendation of the use of an orthosis or multiple orthoses, which are externally applied device used to modify the structural and functional characteristics of the neuromuscular and skeletal system. PMID:26835739 A procedure where a healthcare provider reviews a patient's medical history, examines the patient, and makes recommendations as to care and treatment. 2020-01-20T18:30:15Z medical professional consultation medical professional examination An appraisal or evaluation of a patient's condition by a clinician that is based on a physical exam, medical history, and the patient's account of symptoms. medical professional evaluation An appraisal or evaluation of a patient's condition by a clinician that is based on a physical exam, medical history, and the patient's account of symptoms. PMID:19567008 NCIT:C25305 Increase in the longest dimension of a bone to correct anatomical deficiencies, congenital, traumatic, or as a result of disease. The lengthening is not restricted to long bones. The usual surgical methods are internal fixation and distraction. 2020-01-21T19:47:30Z MeSH:D001852 OMIT:0003210 limb lengthening procedure leg lengthening bone lengthening procedure Increase in the longest dimension of a bone to correct anatomical deficiencies, congenital, traumatic, or as a result of disease. The lengthening is not restricted to long bones. The usual surgical methods are internal fixation and distraction. MeSH:D001852 A bone fixation technique using an external fixator for lengthening limbs, correcting pseudarthroses and other deformities, and assisting the healing of otherwise hopeless traumatic or pathological fractures and infections, such as chronic osteomyelitis. 2020-01-21T19:52:10Z MeSH:D018889 Ilizarov technique Ilizarov procedure A bone fixation technique using an external fixator for lengthening limbs, correcting pseudarthroses and other deformities, and assisting the healing of otherwise hopeless traumatic or pathological fractures and infections, such as chronic osteomyelitis. MeSH:D018889 Bone lengthening by gradual mechanical distraction. An external fixation device produces the distraction across the bone plate. The technique was originally applied to long bones but in recent years the method has been adapted for use with mandibular implants in maxillofacial surgery. 2020-01-21T20:01:15Z MeSH:D019857 distraction osteogenesis Bone lengthening by gradual mechanical distraction. An external fixation device produces the distraction across the bone plate. The technique was originally applied to long bones but in recent years the method has been adapted for use with mandibular implants in maxillofacial surgery. MeSH:D019857 A measurement performed in a clinical setting using clinician's observations and instrument data to inform patient care and research. 2020-01-21T20:29:43Z CMO:0000000 PMID:2647562 clinical assessment clinical measurement A measurement performed in a clinical setting using clinician's observations and instrument data to inform patient care and research. PMID:2647562 An assessment of body temperature. 2020-01-21T20:35:51Z CMO:0000015 GeneReviews:NBK331 body temperature measurement The act of assessing an individual's current temperature, heart rate, respiratory rate, pulse oxygenation, and blood pressure. 2020-01-21T20:43:33Z NCIT:C49672 VSTEST vital signs assessment vital signs measurement The act of assessing an individual's current temperature, heart rate, respiratory rate, pulse oxygenation, and blood pressure. NCIT:C49672 VSTEST An assessment of the number of heartbeats per unit time, usually expressed as beats per minute. 2020-01-21T20:47:05Z CMO:0000002 NCIT:C49677 HR measurement heart rate assessment heart rate measurement HR measurement Assessment and recording of arterial pulses in any of a number of locations. The observer should note its intensity, rate, rhythm, and if any blood vessel tenderness, tortuosity, or nodularity exists. 2020-01-21T20:59:19Z GeneReveiws:NBK350 pulse assessment The rate of breathing (inhalation and exhalation) measured within in a unit time, usually expressed as breaths per minute. 2020-01-21T21:04:00Z CMO:0000289 NCIT:C49678 respiratory rate assessment The rate of breathing (inhalation and exhalation) measured within in a unit time, usually expressed as breaths per minute. NCIT:C49678 Procedure to evaluate the structure and/or function of the cardiovascular system. 2020-01-21T21:09:50Z CMO:0000001 NCIT:C100084 cardiovascular measurement cardiovascular diagnostic procedure Measurement of the pressure on the walls of the vessels as blood moves around the body. Systolic blood pressure is the pressure when the heart beats – while the heart muscle is contracting (squeezing) and pumping oxygen-rich blood into the blood vessels. Diastolic blood pressure is the pressure on the blood vessels when the heart muscle relaxes. The diastolic pressure is always lower than the systolic pressure. 2020-01-21T21:13:22Z CMO:0000003 https://www.ncbi.nlm.nih.gov/books/NBK279251 blood pressure assessment blood pressure monitoring blood pressure measurement Monitoring blood pressure with a sphygmomanometer and a stethoscope to hear blood flow. 2020-01-22T15:29:56Z MMO:0000055 NCIT:C69318 PMID:20937442 VSO:0000001 ausculatory sphygmomanometer blood pressure measurement auscultatory blood pressure measurement process auscultatory blood pressure monitoring Although the auscultatory method using mercury sphygmomanometer is regarded as the ‘gold standard’ for office blood pressure measurement, widespread implementation of the ban in use of mercury sphygmomanometers continues to diminish the role of this technique. auscultatory blood pressure measurement Although the auscultatory method using mercury sphygmomanometer is regarded as the ‘gold standard’ for office blood pressure measurement, widespread implementation of the ban in use of mercury sphygmomanometers continues to diminish the role of this technique. PMID:20937442 A blood pressure measurement using a sphygmomanometer and an electronic pressure sensor (transducer) that detects blood flow by the presence of oscillations in the cuff pressure. 2020-01-22T20:49:15Z NCIT:C69319 PMID:20937442 VSO:0000026 oscillometric blood pressure measurement A method for monitoring blood pressure without requiring instruments introduced into the body. 2020-01-22T21:01:49Z NCIT:C69319 PMID:20937442 VSO:0000024 non-invasive blood presure measurement noninvasive blood pressure measurement An intra-arterial method of monitoring blood pressure. 2020-01-22T21:18:39Z VSO:0000023 invasive blood pressure measurement Any form of treatment that acts to improve or assist with respiratory function. 2020-01-23T15:55:17Z NCIT:C15322 respiratory therapy Any form of treatment that acts to improve or assist with respiratory function. NCIT:C15322 A set of maneuvers or medical procedures performed to prevent and relieve airway obstruction. This ensures an open pathway for gas exchange between a patient's lungs and the atmosphere. 2020-01-23T15:56:57Z MeSH:D058109 airway management A set of maneuvers or medical procedures performed to prevent and relieve airway obstruction. This ensures an open pathway for gas exchange between a patient's lungs and the atmosphere. PMID:18675024 Removal of an endotracheal tube from the patient. 2020-01-23T16:07:45Z MeSH:D060666 NCIT:C50819 airway extubation tracheal extubation endotracheal extubation Removal of an endotracheal tube from the patient. MeSH:D060666 A procedure involving placement of a tube into the trachea through the mouth or nose in order to provide a patient with oxygen and anesthesia. 2020-01-23T16:16:19Z MeSH:D007442 NCIT:C116648 airway intubation intratracheal intubation tracheal intubation endotracheal intubation A procedure involving placement of a tube into the trachea through the mouth or nose in order to provide a patient with oxygen and anesthesia. MeSH:D007442 Any method of artificial breathing that employs mechanical or non-mechanical means to force the air into and out of the lungs. Artificial respiration or ventilation is used in individuals who have stopped breathing or have respiratory insufficiency to increase their intake of oxygen (O2) and excretion of carbon dioxide (CO2). 2020-01-23T16:34:17Z artificial ventilation mechanical ventilation artificial respiration Surgical formation of an opening into the trachea through the neck, or the opening so created. 2020-01-23T16:48:07Z Tracheostomy and tracheotomy are sometimes used interchangeably, but tracheotomy is simply a surgical incision of the trachea. tracheostomy Surgical formation of an opening into the trachea through the neck, or the opening so created. MeSH:D014139 Tracheostomy and tracheotomy are sometimes used interchangeably, but tracheotomy is simply a surgical incision of the trachea. MeSH:D014140 A manual method for maintaining oxygenation using a mask. 2020-01-23T17:41:09Z bag-mask ventilation mask ventilation Techniques for administering artificial respiration without the need for intratracheal intubation. 2020-01-23T17:52:50Z MeSH:D063087 non-invasive ventilation noninvasive ventilation Techniques for administering artificial respiration without the need for intratracheal intubation. MeSH:D063087 Ventilatory support system using frequencies from 60-900 cycles/min or more. Three types of systems have been distinguished on the basis of rates, volumes, and the system used. 2020-01-23T17:57:32Z MeSH:D006612 high frequency oscillation ventilation high frequency positive pressure ventilation high-frequency ventilation Ventilatory support system using frequencies from 60-900 cycles/min or more. Three types of systems have been distinguished on the basis of rates, volumes, and the system used. MeSH:D006612 A technique of mechanical ventilation in which the lungs are insufflated with an oxygenated perfluorochemical liquid rather than an oxygen-containing gas mixture. 2020-01-23T18:01:24Z MeSH:D021061 liquid-assisted ventilation liquid ventilation A technique of mechanical ventilation in which the lungs are insufflated with an oxygenated perfluorochemical liquid rather than an oxygen-containing gas mixture. PMID:22043370 A method of mechanical ventilation in which pressure is maintained to increase the volume of gas remaining in the lungs at the end of expiration, thus reducing the shunting of blood through the lungs and improving gas exchange. 2020-01-23T18:06:14Z MeSH:D011175 positive control ventilation positive controlled respiration positive end expiratory pressure technique positive pressure respiration positive pressure ventilation positive-controlled ventilation positive-pressure respiration positive-pressure ventilation positive controlled ventilation A method of mechanical ventilation in which pressure is maintained to increase the volume of gas remaining in the lungs at the end of expiration, thus reducing the shunting of blood through the lungs and improving gas exchange. MeSH:D011175 Assisted ventilation by applying intermittent subatmospheric pressure around the thorax, abdomen, or airway and periodically expand the chest wall and inflate the lungs. 2020-01-23T18:22:46Z iron lung ventilation portalung ventilation MeSH:D015919 negative-pressure ventilation negative-pressure respiration A form of non-invasive mechanical pressure support ventilation that uses a time-cycled change of the applied positive airway pressure level to support spontaneous breathing activity. 2020-01-23T18:27:45Z MeSH:D007385 NCIT:C124039 BiPAP ventilation biphasic positive airway pressure ventilation bilevel positive airway pressure ventilation A form of non-invasive mechanical pressure support ventilation that uses a time-cycled change of the applied positive airway pressure level to support spontaneous breathing activity. NCIT:C124039 BiPAP ventilation A form of non-invasive mechanical pressure support ventilation that uses a continuous positive airway pressure level to support spontaneous breathing activity. 2020-01-23T18:31:36Z MeSH:D045422 NCIT:C124040 CPAP ventilation nCPAP ventilation nasal continuous positive airway pressure ventilation continuous positive airway pressure ventilation A form of non-invasive mechanical pressure support ventilation that uses a continuous positive airway pressure level to support spontaneous breathing activity. NCIT:C124040 CPAP ventilation nCPAP ventilation A rehabilitation therapy for removal of copious mucus secretion from the lung of patients with diseases. The patient's head is placed in a downward incline (so the trachea is inferior to the affected area) for 15 to 20 minute sessions. 2020-01-23T19:45:07Z MeSH:D015916 postural respiratory drainage pulmonary postural drainage postural drainage A respiratory support system used to remove mucus and clear airway by oscillating pressure on the chest. 2020-01-23T20:18:02Z MeSH:D035641 external chest wall oscillation high-frequency chest compression high-frequency chest wall oscillation chest wall oscillation A respiratory support system used to remove mucus and clear airway by oscillating pressure on the chest. MeSH:D035641 Application of a life support system that circulates the blood through an oxygenating system, which may consist of a pump, a membrane oxygenator, and a heat exchanger. 2020-01-23T20:23:16Z MeSH:D015199 ECLS treatment ECMO treatment extracorporeal life support extracorporeal membrane oxygenation Application of a life support system that circulates the blood through an oxygenating system, which may consist of a pump, a membrane oxygenator, and a heat exchanger. MeSH:D015199 ECLS treatment ECMO treatment Chest physical therapy (CPT or Chest PT) is an airway clearance technique (ACT) to drain the lungs, and may include percussion (clapping), vibration, deep breathing, and huffing or coughing. 2020-01-23T20:32:18Z CPT Chest PT chest physical therapy chest physiotherapy The insertion of a cannula or tube into a hollow body organ. 2020-01-23T20:44:41Z ERO:0001108 MeSH:D007440 NCIT:C37981 intubation procedure The insertion of a cannula or tube into a hollow body organ. NCIT:C37981 The removal of a previously inserted tube from a hollow organ or passageway, often from the airway. 2020-01-23T20:48:40Z NCIT:C50819 extubation procedure The removal of a previously inserted tube from a hollow organ or passageway, often from the airway. NCIT:C50819 Use of medical ultrasonography in pregnancy where sound waves are used to create a real-time visual image of the developing fetus in the uterus. Imaging can include the mother's ovaries and uterus as well. 2020-01-24T19:29:52Z obstetric sonography prenatal ultrasound procedure obstetric ultrasonography A clinical recommendation to avoid or refrain from certain behaviors in order to maintain health or ameliorate symptoms. 2020-01-29T17:35:05Z behavior avoidance for therapeutic purposes cognitive and behavioral intervention avoidance An appraisal or evaluation of a patient's condition by a clinician that is based on a physical exam, medical history, and the patient's account of symptoms. 2020-03-04T17:09:05Z NCIT:C25305 clinical examination medical examination An appraisal or evaluation of a patient's condition by a clinician that is based on a physical exam, medical history, and the patient's account of symptoms. NCIT:C25305 PMID:19567008 A systemic evaluation of the body and its functions using visual inspection, palpation, percussion and auscultation. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. 2020-03-04T17:45:04Z physical examination A systemic evaluation of the body and its functions using visual inspection, palpation, percussion and auscultation. The purpose is to determine the presence or absence of physical signs of disease or abnormality for an individual's health assessment. NCIT:C20989 A test or diagnostic examination to assess the health status and well being of the fetus. 2020-03-17T18:13:46Z antenatal examination prenatal exam prenatal examination NCIT:C92714 examination of the fetus fetal assessment fetal evaluation fetal exam foetal assessment foetal examination fetal examination A test or diagnostic examination to assess the health status and well being of the fetus. NCIT:C92714 Testing of fetal DNA during pregnancy to determine if the fetus has chromosomal aberrations, fetal aneuploidy, or other detectable genetic disorders. 2020-03-17T18:55:32Z fetal genetic testing foetal genetic screening prenatal genetic screening prenatal genetic testing A genetic test to whether a healthy person harbors a recessive mutation in one of their copies of a gene or genes. 2020-03-17T20:04:20Z carrier screening genetic carrier screening A test that analyzes small fragments of DNA that are circulating in a pregnant woman’s blood to determine the risk that the fetus will be born with genetic abnormalities. 2020-03-17T20:22:26Z NIPT noninvasive prenatal screening noninvasive prenatal testing NIPT A diverse set of techniques used to identify the molecular basis of genetic disease prenatally. Examples of molecular genetic tests include: genotyping to detect specific pathogenic variants; sequencing of a gene to detect pathogenic variants; amplification or hybridization methods (e.g., qPCR, array CGH, MLPA) to detect copy number variants involving one or more genes; methylation-specific techniques to detect epigenetic changes that influence gene expression; and exome and genome sequencing. 2020-03-18T19:16:15Z GeneReviews:NBK5191 prenatal molecular genetic testing A diverse set of techniques used to identify the molecular basis of genetic disease prenatally. Examples of molecular genetic tests include: genotyping to detect specific pathogenic variants; sequencing of a gene to detect pathogenic variants; amplification or hybridization methods (e.g., qPCR, array CGH, MLPA) to detect copy number variants involving one or more genes; methylation-specific techniques to detect epigenetic changes that influence gene expression; and exome and genome sequencing. GeneReviews:NBK5191 A diverse set of techniques used to identify the molecular basis of genetic disease. Examples of molecular genetic tests include: genotyping to detect specific pathogenic variants; sequencing of a gene to detect pathogenic variants; amplification or hybridization methods (e.g., qPCR, array CGH, MLPA) to detect copy number variants involving one or more genes; methylation-specific techniques to detect epigenetic changes that influence gene expression; and exome and genome sequencing. 2020-03-18T19:19:07Z molecular genetic testing A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. 2020-03-19T19:24:04Z NCIT:C52009 amniocentisis A prenatal diagnostic procedure in which a small sample of amniotic fluid is removed from the uterus by a needle inserted into the abdomen. This procedure is used to detect various genetic abnormalities in the fetus and/or the sex of the fetus. NCIT:C52009 Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. 2020-03-19T19:39:48Z surgical aspiration procedure Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. NCIT:C15631 A prenatal test in which a sample of chorionic villi is removed from the placenta for testing. The sample can be taken through the cervix (transcervical) or the abdominal wall (transabdominal). Mayo Clinic 2020-03-19T19:51:26Z NCIT:C92755 CVS chorionic villus biopsy The biopsy of placental tissue containing the chorionic villi from the maternal uterus in early pregnancy to diagnose fetal genetic defects. chorionic villus sampling CVS The biopsy of placental tissue containing the chorionic villi from the maternal uterus in early pregnancy to diagnose fetal genetic defects. NCIT:C92755 A procedure conducted during pregnancy for the presence of Gardnerella vaginalis, Ureaplasma urealyticum, Mycoplasma hominis, Mobiluncus, Prevotella and anaerobic bacteria. 2020-03-19T20:17:55Z NCIT:C92740 BV testing bacterial vaginosis screening BV testing A test for the presence of fetal fibronectin in the cervico-vaginal area that is used to predict preterm birth. 2020-03-19T20:22:14Z NCIT:C92786 FBNCTFT fFN testing fetal fibronectin assessment fetal fibronectin testing A test for the presence of fetal fibronectin in the cervico-vaginal area that is used to predict preterm birth. NCIT:C92786 FBNCTFT fFN testing Screening with a swab from the vaginal and rectal areas in late pregnancy to test for the presence of Group B streptococcal infection. 2020-03-19T20:47:28Z NCIT:C92805 GBS beta-hemolytic strep culture screening broup B Beta-hemolytic streptococcus screening group B strep screening prenatal group B streptococcus screening Screening with a swab from the vaginal and rectal areas in late pregnancy to test for the presence of Group B streptococcal infection. NCIT:C92805 GBS An ultrasonic examination of the fetus in the late first trimester to measure the clear space at the back of the fetal neck to assess risk of genetic or cardiac abnormalities. 2020-03-19T21:03:16Z NCIT:C92837 NT testing nuchal translucency ultrasound screening nuchal translucency screening An ultrasonic examination of the fetus in the late first trimester to measure the clear space at the back of the fetal neck to assess risk of genetic or cardiac abnormalities. NCIT:C92837 NT testing A screening measurement in which the maternal blood levels of alpha-fetoprotein, unconjugated estriol, human chorionic gonadotrophin and Inhibin A are calculated. These are then evaluated in relation to the mother's age, weight and fetal gestational age. 2020-03-19T21:11:02Z NCIT:C92865 quadruple marker testing quad test assessment A screening measurement in which the maternal blood levels of alpha-fetoprotein, unconjugated estriol, human chorionic gonadotrophin and Inhibin A are calculated. These are then evaluated in relation to the mother's age, weight and fetal gestational age. NCIT:C92865 The determination of the number of eosinophils in a blood sample. 2020-03-26T19:53:41Z NCIT:C64550 EOS cell count eosinophil count The determination of the number of eosinophils in a blood sample. NCIT:C64550 EOS cell count The determination of the amount of granulocytes present in a sample. 2020-03-26T19:56:24Z NCIT:C96654 polymorphonuclear leukocyte count granulocyte count The determination of the amount of granulocytes present in a sample. NCIT:C96654 The determination of the absolute number of basophils in a blood sample. 2020-03-26T20:00:33Z NCIT:C64470 basophil cell count total basophil count basophil count The determination of the absolute number of basophils in a blood sample. NCIT:C64470 The determination of the number of lymphocytes in a blood sample. 2020-03-26T20:07:56Z NCIT:C51949 lymphocyte count The determination of the number of lymphocytes in a blood sample. NCIT:C51949 A procedure by which biological material is obtained from a subject for testing, diagnostic, treatment, or research purposes. 2020-03-27T15:53:08Z NCIT:C70700 clinical specimen collection clinical biospecimen collection obsolete swab-based biospecimen collection false Measuring a person's own body temperature usually at home using any of a number of types of thermometers. 2020-03-29T18:25:39Z self-reported temperature measurement at home temperature measurement self-reported fever measurement self body temperature measurement A characteristic that can be objectively measured and serves as an indicator for the inflammatory response. It could be used to indicate the normal inflammatory processes, pathogenic processes, state of health or disease, the risk for disease development and/or prognosis, or responsiveness to a particular therapeutic intervention. 2020-03-29T18:32:41Z inflammatory biomarker measurement inflammatory biomarker assessment Assay based assessment of a serum sample for detection and concentration (mg/L) C-reactive protein. 2020-03-29T18:33:44Z CRP measurement C-reactive protein (CRP) measurement is a measurement of the level of C-reactive protein in the blood. Levels are known to rise in response to inflammation, CRP is therefore used as a clinical measure of inflammation. The measurement is used in the process of clinical diagnosis as high levels of CRP are associated with cardiovascular disease, diabetes and hypertension and in some cancers. C-reactive protein biomarker assessment Assay based assessment of a serum sample for detection and concentration (mg/L) C-reactive protein. PMID:11238291 CRP measurement C-reactive protein (CRP) measurement is a measurement of the level of C-reactive protein in the blood. Levels are known to rise in response to inflammation, CRP is therefore used as a clinical measure of inflammation. The measurement is used in the process of clinical diagnosis as high levels of CRP are associated with cardiovascular disease, diabetes and hypertension and in some cancers. EFO:0004458 Detection of circultating interleukin-6, which stimulates the inflammatory and auto-immune processes in many diseases. 2020-03-29T18:44:31Z IL-6 level assessment IL-6 measurement A quantification of interleukin-6, a pro-inflammatory and anti-inflammatory cytokine. interleukin-6 biomarker measurement IL-6 level assessment IL-6 measurement A quantification of interleukin-6, a pro-inflammatory and anti-inflammatory cytokine. EFO:0004810 A chemokine that can be objectively measured and serves as an indicator for the inflammatory response. 2020-03-30T15:51:58Z cytokine biomarker measurement Cytokines are small, nonstructural proteins, including interleukins, chemokines, interferons, and tumor necrosis factors, which have a multitude of pleiotropic effects in various organs [1]. They are released in a number of paracrine, autocrine, or endocrine pathways and have been implicated in a variety of infections and immune system-affecting disorders by both proinflammatory and anti-inflammatory mechanisms. Macrophages and T lymphocytes (T-cells) are the primary producers of cytokines which may have predominantly pro-inflammatory (inflammation-promoting)(IL-1alpha, IL-1beta, IL-2, IL-6, Il-8, IL-12, TNF-alpha, IFN-gamma) or anti-inflammatory (inflammation-suppressive)(IL-4, IL-5, IL-10, TGF-beta) abilities. cytokine biomarker assessment Cytokines are small, nonstructural proteins, including interleukins, chemokines, interferons, and tumor necrosis factors, which have a multitude of pleiotropic effects in various organs [1]. They are released in a number of paracrine, autocrine, or endocrine pathways and have been implicated in a variety of infections and immune system-affecting disorders by both proinflammatory and anti-inflammatory mechanisms. PMID:28487810 Macrophages and T lymphocytes (T-cells) are the primary producers of cytokines which may have predominantly pro-inflammatory (inflammation-promoting)(IL-1alpha, IL-1beta, IL-2, IL-6, Il-8, IL-12, TNF-alpha, IFN-gamma) or anti-inflammatory (inflammation-suppressive)(IL-4, IL-5, IL-10, TGF-beta) abilities. PMID:24962838 Detection of interleukin-1 beta levels, an IL-1 cytokine family protein, secreted by macrophages and a mediator of inflammatory response. 2020-03-30T16:03:54Z IL-1 beta assessment interleukin-1 beta biomarker measurement Detection of interleukin-1 alpha, a mediator of the inflammatory response. 2020-03-30T16:05:46Z IL-1 alpha assessment IL-1 alpha testing interleukin-1 alpha biomarker measurement Detection of interleukin-2, a mediator of inflammatory response. 2020-03-30T16:08:32Z IL-2 level assessment IL-2 testing interleukin-2 biomarker measurement Detection of interleukin-8 levels, a mediator of inflammatory response. 2020-03-30T16:09:36Z IL-8 level assessment IL-8 testing interleukin-8 biomarker measurement Detection of interleukin-12 levels, an inflammatory cytokine. 2020-03-30T16:24:01Z IL-12 assessment IL-12 level testing interleukin-12 biomarker measurement Detection of TNF-alpha levels, a cytokine involved in systemic inflammation. 2020-03-30T16:28:04Z TNF-alpha assessment TNF-alpha level testing tumor necrosis factor-alpha biomarker measurement Detection of interferon-gamma, a cytokine that indicates an inflammatory response. 2020-03-30T16:31:18Z INF-gamma assessment INF-gamma levels testing interferon-gamma biomarker measurement Detection of interleukin-4, a cytokine identified as an inflammation suppressant. 2020-03-30T18:59:24Z IL-4 measurement IL-4 testing IL4 assessment interleukin-4 biomarker measurement Detection of interleukin-5, a cytokine identified as an inflammation suppressant. 2020-03-30T19:04:15Z IL-5 measurement IL-5 testing IL5 assessment interleukin-5 biomarker measurement Detection of interleukin-10, a cytokine identified as an inflammation suppressant. 2020-03-30T19:05:58Z IL-10 measurement IL-10 testing IL10 assessment Interleukin-10 biomarker measurement Detection of tumor necrosis factor-beta (TNF-beta), a cytokine identified as an inflammation suppressant. 2020-03-30T19:07:19Z TNF-beta measurement TNF-beta testing TNFbeta assessment tumor necrosis factor-beta biomarker measurement Detection of serum levels of amyloid A (SAA) in response to inflammation. 2020-03-30T19:37:28Z SAA biomarker measurement serum amyloid A biomarker assessment A clinical laboratory procedure designed for the quantification of an organic or inorganic chemical within a biological specimen required for diagnostics or monitoring of treatments. 2020-03-30T19:49:21Z NCIT:C49237 clincal chemistry test clinical chemistry measurement testing clinical chemistry testing clinical chemistry assessment A quantitative measurement for assessing the amount of glucose present in a blood sample. 2020-03-30T19:58:59Z NCIT:C92744 blood glucose measurement blood glucose testing blood surgar testing blood glucose assessment A quantitative measurement for assessing the amount of glucose present in a blood sample. NCIT:C92744 Glucose Plasma Concentration (GPC) measurement is an essential diagnostic modality for different types of carbohydrate metabolism derangements including diabetes mellitus. 2020-03-30T20:02:19Z NCIT:C41376 plasma glucose measurement Glucose Plasma Concentration (GPC) measurement is an essential diagnostic modality for different types of carbohydrate metabolism derangements including diabetes mellitus. The disordered carbohydrate metabolism that underlies diabetes manifests as hyperglycemia. Plasma glucose concentrations in healthy individuals vary with age. Normal fasting plasma glucose intervals (in the morning after an overnight fast) in children are 3.3 - 5.6 mmol/L (60-100 mg/dL); adult range - 4.1- 5.9 mmol/L (74-106 mg/dL). GPCs are approximately 11% higher than whole blood if the hematocrit is normal. Glucose concentrations in heparinized plasma are reported to be 5% lower than in serum. plasma glucose assessment Glucose Plasma Concentration (GPC) measurement is an essential diagnostic modality for different types of carbohydrate metabolism derangements including diabetes mellitus. The disordered carbohydrate metabolism that underlies diabetes manifests as hyperglycemia. Plasma glucose concentrations in healthy individuals vary with age. Normal fasting plasma glucose intervals (in the morning after an overnight fast) in children are 3.3 - 5.6 mmol/L (60-100 mg/dL); adult range - 4.1- 5.9 mmol/L (74-106 mg/dL). GPCs are approximately 11% higher than whole blood if the hematocrit is normal. Glucose concentrations in heparinized plasma are reported to be 5% lower than in serum. NCIT:C41376 A quantitative measurement of the amount of glucose present in a sample of blood, obtained from a source that has abstained from nutrition, typically at least 8 hours prior to the sample collection time. 2020-03-30T20:05:54Z NCIT:C80400 FBS measurement fasting blood glucose measurement fasting blood sugar measurement testing fasting blood glucose assessment A quantitative measurement of the amount of glucose present in a sample of blood, obtained from a source that has abstained from nutrition, typically at least 8 hours prior to the sample collection time. NCIT:C80400 A technique to collect sputum by inhaling hypertonic saline through an oxygen mask in order to induce sputum. 2020-03-30T20:17:26Z induced sputum collection A technique to collect sputum by inhaling hypertonic saline through an oxygen mask in order to induce sputum. PMID:32171389 A method of examining structures within the body by scanning them with X rays and using a computer to construct a series of cross-sectional scans along a single axis. 2020-03-30T20:32:28Z NCIT:C17204 CAT scan CT CT scan computerized axial tomography computed tomography procedure A method of examining structures within the body by scanning them with X rays and using a computer to construct a series of cross-sectional scans along a single axis. NCIT:C17204 Use of a drug that lower the level of glucose in the blood. 2020-03-31T00:42:37Z CHEBI:35526 hypoglycaemic drug therapy hypoglycemic agent therapy hypoglycemic drug therapy treatment with hypoglycemic agent treatment with hypoglycemic drug treatment with hypoglycemic medication hypoglycemic agent therapy Treatment of retroviral infections with medications that target the virus directly, limiting the ability of infected cells to produce new virus particles. 2020-03-31T00:49:23Z NCIT:C94631 ART anti-retroviral therapy treatment with an anti-retroviral medication treatment with an antiretroviral drug treatment with an antiretroviral medication antiretroviral therapy Treatment of retroviral infections with medications that target the virus directly, limiting the ability of infected cells to produce new virus particles. NCIT:C94631 The process of gathering information regarding a person's medical history. 2020-03-31T00:59:49Z patient assessment NCIT:C146918 medical history collection medical history taking The process of gathering information regarding a person's medical history. NCIT:C146918 Determination if a patient's background or demographic characteristics makes the patient susceptible to disease. 2020-03-31T01:03:49Z patient demographic characteristics assessment Determination if patient's travel history may impact current health. 2020-03-31T01:05:10Z patient travel risk assessment A questionnaire designed to determine if patient's travel history may impact current health. 2020-03-31T01:05:32Z patient travel risk questionnaire Determination if the patient may have been exposed to something which would impact the health of the patient. 2020-03-31T01:11:38Z patient environmental exposure assessment A test that measures the amount of oxygen and carbon dioxide in the blood. It may also be used to determine the pH of the blood. 2020-03-31T19:11:20Z NCIT:C71252 blood gas measurement testing blood gas test arterial blood gas measurement pH and blood gas measurements are used to detect and monitor ventilation, oxygenation, and acid-base disturbances. blood gas assessment pH and blood gas measurements are used to detect and monitor ventilation, oxygenation, and acid-base disturbances. PMID:33371 The determination of the unmeasured anions (those other than the chloride and bicarbonate anions) present in a sample. 2020-03-31T19:16:41Z NCIT:C74685 anion gap measurement testing anion gap assessment The determination of the unmeasured anions (those other than the chloride and bicarbonate anions) present in a sample. NCIT:C74685 A quantitative measurement of the amount of calcium present in a sample, usually serum or urine. 2020-03-31T19:19:43Z NCIT:C64488 calcium measurement calcium assessment A quantitative measurement of the amount of an electrolyte present in urine or serum. 2020-03-31T19:32:42Z NCIT:C74946 electrolyte measurement electrolyte assessment A quantitative measurement of the amount of an electrolyte present in serum. 2020-03-31T19:33:45Z electrolytes- serum testing serum electrolyte measurement serum electrolyte assessment A quantitative measurement of the amount of an electrolyte present in urine. 2020-03-31T19:34:22Z electrolytes- urine testing urine eletrolyte measurement urine eletrolyte assessment Any laboratory procedure for growing microorganisms. 2020-03-31T20:08:52Z NCIT:C25300 microbial culture procedure Any laboratory procedure for growing microorganisms. NCIT:C25300 A type of mechanical ventilation using endotracheal intubation. 2020-03-31T20:23:41Z invasive ventilation A time-triggered, pressure-limited, inverse-ratio mode of ventilation that provides continuous distending airway pressure with intermittent release phases 2020-04-01T20:00:59Z APRV airway pressure release ventilation A time-triggered, pressure-limited, inverse-ratio mode of ventilation that provides continuous distending airway pressure with intermittent release phases PMID:29641221 APRV A technique that detects a particular nucleic acid sequence in order to identify a pathogen (organism or virus) in blood, tissue, urine, or other bodily fluids. 2020-04-02T20:59:07Z NAT nucleic acid testing clinical nucleic acid testing NAT A tecnique that uses an amplification of nucleic acids to detect a pathogen. Some amplification methods include polymerase chain reaction (PCR), strand displacement assay (SDA), or transcription mediated assay (TMA) to detect a virus, bacteria or other pathogen. 2020-04-02T21:17:28Z NCIT:C20055 NAAT nucleic acid amplification procedure Any of various amplification and detection strategies applied to detection of virus contamination in donor blood. Specifically designed to detect recently infected individuals during the latency period before seroconversion. nucleic acid amplification testing NAAT Any of various amplification and detection strategies applied to detection of virus contamination in donor blood. Specifically designed to detect recently infected individuals during the latency period before seroconversion. NCIT:C20055 A type of nucleic acid amplification test in which sample DNA is exposed to a single temperature in the presence of multiple sets of primers and a polymerase with replication and high strand displacement activity. This test negates the need for thermal cyclers and may be a low cost alternative to PCR. 2020-04-02T21:43:07Z NCIT:C102661 loop-mediated isothermal amplification procedure loop-mediated isothermal amplification testing A type of nucleic acid amplification test in which sample DNA is exposed to a single temperature in the presence of multiple sets of primers and a polymerase with replication and high strand displacement activity. This test negates the need for thermal cyclers and may be a low cost alternative to PCR. NCIT:C102661 A technique that detects a particular DNA sequence in order to identify a pathogen (organism or virus) in blood, tissue, urine, or other bodily fluids. 2020-04-03T00:29:00Z DNA detection examination DNA detection procedure DNA detection testing DNA detection kit testing clinical DNA detection testing A technique that detects a particular RNA sequence in order to identify a pathogen (organism or virus) in blood, tissue, urine, or other bodily fluids. 2020-04-03T00:30:09Z RNA detection examination RNA detection procedure RNA detection testing RNA detection kit testing clinical RNA detection testing A clinical assay that amplifies and quantifies a specific DNA molecule based on in tissue, blood, sputum, urine, or any other bodily fluid to detect the presence of a pathogen. It enables both detection and quantification of one or more specific sequences in a DNA sample. 2020-04-03T00:38:02Z NCIT:C51962 OBI:0000893 clinical qPCR testing clinical real-time RT-PCR procedure real-time PCR procedure for clinical use clinical real-time PCR testing A method to measure very small amounts of RNA transcripts as cDNA targets from tissue, blood, sputum or other body fluids. 2020-04-03T00:47:00Z NCIT:C28408 OBI:0000911 clinical quantitative RT-PCR procedure clinical quantitative RT-PCR testing clinical quantitative reverse transcription PCR procedure clinical quantitative reverse transcription PCR testing A procedure producing an image on a radiosensitive surface by x-ray radiation that has penetrated and passed through a structure in order to diagnose or treat a patient. 2020-04-07T15:49:43Z NCIT:C38101 NCIT:C60727 X-ray imaging procedure radiogram imaging procedure radiographic imaging procedure radiographic procedure radiography radiography imaging procedure radiograph imaging procedure The process of taking a thorough history and physical exam to determine if a patient has been exposed to an infectious disease. Close attention is paid to travel history, environmental exposures, and vaccination history. 2020-04-07T18:27:36Z infectious disease screening The administration of oxygen to an individual, usually to aid in respiration by means of a mask. 2020-04-07T19:00:52Z oxygen support therapy with mask supplemental oxygen therapy with mask The administration of oxygen to an individual, usually to aid in respiration by means of a nasal cannula. 2020-04-07T19:01:10Z oxygen support therapy with nasal cannula supplemental oxygen therapy with nasal cannula Therapy using a substance used in the treatment of hypotension. A vasopressor agent increases reduced blood pressure. 2020-04-07T19:23:15Z CHEBI:137431 NCIT:C126567 antihypotensive agent drug therapy antihypotensive agent therapy treatment with antihypotensive agent treatment with antihypotensive drug treatment with antihypotensive medication treatment with vasopressor agent treatment with vasopressor medication vasopressor support therapy vasopressor agent therapy Treatments that substitute for the blood-filtering function of the kidneys. 2020-04-07T19:42:23Z MeSH:D017582 NCIT:C126400 RRT kidney replacement therapy It includes dialysis (hemodialysis or peritoneal dialysis), hemofiltration, and hemodiafiltration. Kidney transplant may also be considered a renal replacement therapy. renal replacement therapy RRT A procedure to remove toxic substances from the blood that is used in patients with end-stage chronic kidney disease or acute kidney failure. This includes hemodialysis and peritoneal dialysis. 2020-04-07T19:57:22Z NCIT:C15221 dialysis renal dialysis A therapeutic procedure used in patients with kidney failure. It involves the extracorporeal removal of harmful wastes and fluids from the blood using a dialysis machine. Following the dialysis, the blood is returned to the body. 2020-04-07T20:03:50Z NCIT:C15248 hemodialysis A therapeutic procedure used in patients with kidney failure. It involves the extracorporeal removal of harmful wastes and fluids from the blood using a dialysis machine. Following the dialysis, the blood is returned to the body. NCIT:C15248 A form of dialysis that uses the peritoneum as a membrane across which the infused dialysate exchanges nutrients for waste products that are removed when the fluid is exchanged. 2020-04-07T20:04:03Z NCIT:C15297 peritoneal dialysis A form of dialysis that uses the peritoneum as a membrane across which the infused dialysate exchanges nutrients for waste products that are removed when the fluid is exchanged. NCIT:C15297 A laboratory procedure that tests the function of an endocrine organ and measures the amount of a hormone present in a sample. 2020-04-07T20:40:24Z NCIT:C74971 endocrine testing A laboratory procedure that tests the function of an endocrine organ and measures the amount of a hormone present in a sample. NCIT:C74971 A term that refers to a chemistry test measuring a specific protein or enzyme in the peripheral blood or body fluid. 2020-04-07T20:51:38Z NCIT:C64430 protein measurement enzyme measurement protein assessment A term that refers to a chemistry test measuring a specific protein or enzyme in the peripheral blood or body fluid. NCIT:C64430 The determination of the amount of the procalcitonin in a sample. 2020-04-07T21:30:45Z NCIT:C103430 procalcitonin level measurement procalcitonin level testing procalcitonin testing A substance produced in response to bacterial infections and tissue injury. procalcitonin assessment The determination of the amount of the procalcitonin in a sample. NCIT:C103430 A quantification of a fibrin degradation product in blood used in the diagnosis of thrombosis. 2020-04-07T21:37:45Z NCIT:C82621 D dimer level testing D-dimer measurement fibrin degradation fragment testing fragment D-dimer testing D-dimer assessment A quantitative measurement of the amount of phosphate present in a sample of serum. 2020-04-07T21:53:04Z NCIT:C61028 serum phosphate measurement serum phosphorus measurement serum phosphate assessment A quantitative measurement of the amount of phosphate present in a sample of serum. NCIT:C61028 Testing blood serum for the presence of specifc antibody or antibodies to a specific antigen. Often used when an infection is suspected. 2020-04-08T14:34:24Z serology assay serology testing A highly sensitive technique for detecting and measuring antigens or antibodies in a solution; the solution is run over a surface to which immobilized antibodies specific to the substance have been attached, and if the substance is present, it will bind to the antibody layer, and its presence is verified and visualized with an application of antibodies that have been tagged in some way. 2020-04-08T14:51:34Z NCIT:C16553 OBI:0000661 enzyme linked immunosorbent assay testing enzyme-linked immunosorbent assay clinical ELISA testing A highly sensitive technique for detecting and measuring antigens or antibodies in a solution; the solution is run over a surface to which immobilized antibodies specific to the substance have been attached, and if the substance is present, it will bind to the antibody layer, and its presence is verified and visualized with an application of antibodies that have been tagged in some way. NCIT:C16553 A type of lateral flow assay that qualitatively detect IgG and IgM antibodies of an infectious disease within human serum, plasma or whole blood in vitro. 2020-04-08T15:03:41Z rapid IgM-IgG testing rapid IgM-IgG combined antibody testing A procedure using a paper-based platform for the detection and quantification of analytes in complex mixtures, where the sample is placed on a test device for clinical use. 2020-04-08T15:06:47Z LFA testing lateral flow immuno assay lateral flow immunoassay clinical lateral flow assay testing A procedure using a paper-based platform for the detection and quantification of analytes in complex mixtures, where the sample is placed on a test device for clinical use. PMID:27365041 LFA testing Any of several immunoassay methods that use an enzyme covalently linked to an antigen or antibody as a label and are typically used for diagnostics or disease progression. 2020-04-08T15:17:14Z NCIT:C17455 clinical immunoassay 2020-04-08T15:46:23Z clinical immunofluorescence assay testing A technique for analyzing or identifying proteins immobilized on a filter by complementary reaction with specific antibodies. 2020-04-08T15:46:38Z NCIT:C17638 OBI:0001978 clinical Western blot assay clinical immunoblot assay testing A technique for analyzing or identifying proteins immobilized on a filter by complementary reaction with specific antibodies. NCIT:C17638 The measurement of the ratio of oxygenated hemoglobin to total hemoglobin in the blood. 2020-04-08T18:45:55Z NCIT:C60832 oxygen saturation measurement The measurement of the ratio of oxygenated hemoglobin to total hemoglobin in the blood. NCIT:C60832 A non-invasive method that provides estimates of arterial oxyhemoglobin saturation by utilizing selected wavelengths of light to determine the saturation of oxyhemoglobin. 2020-04-08T18:54:34Z NCIT:C38085 pulse ox measurement pulse oximetry A non-invasive method that provides estimates of arterial oxyhemoglobin saturation by utilizing selected wavelengths of light to determine the saturation of oxyhemoglobin. NCIT:C38085 A therapy of replenishing bodily fluids lost through sweating, bleeding, fluid shifts or other pathological processes, such as sepsis. 2020-04-08T19:29:53Z fluid resuscitation therapy fluid replacement therapy Prone positioning improves ventilation-perfusion matching (transferring delivered oxygen into the bloodstream more efficiently) and keeps alveolar units open and evenly distributed at end-expiration (improving gas exchange and preventing ventilator-induced lung injury). 2020-04-08T19:45:40Z ventilation with proning Prone positioning improves ventilation-perfusion matching (transferring delivered oxygen into the bloodstream more efficiently) and keeps alveolar units open and evenly distributed at end-expiration (improving gas exchange and preventing ventilator-induced lung injury). https://pulmccm.org/ards-review/prone-positioning-ards-ats-sccm/ A procedure of surgical placement of a catheter, which lumen is usually occupied by a trocar, into the central vein (internal jugular, subclavian, and femoral often used) or veins, to provide vascular access for measurement of hemodynamic variables that cannot be measured accurately by noninvasive means. It also can be used to deliver medications that were too potent or too toxic to be administered through peripheral access, for parenteral nutrition delivery; and for placing wires and pulmonary artery catheters. Central veins are usually cannulated percutaneously. The procedure is associated with many adverse events and has to be performed or supervised by an experienced physician. 2020-04-08T20:12:41Z NCIT:C40972 central line insertion central line placement central venous access catheter insertion central venous line insertion cvc insertion central venous cannula insertion A procedure of surgical placement of a catheter, which lumen is usually occupied by a trocar, into the central vein (internal jugular, subclavian, and femoral often used) or veins, to provide vascular access for measurement of hemodynamic variables that cannot be measured accurately by noninvasive means. It also can be used to deliver medications that were too potent or too toxic to be administered through peripheral access, for parenteral nutrition delivery; and for placing wires and pulmonary artery catheters. Central veins are usually cannulated percutaneously. The procedure is associated with many adverse events and has to be performed or supervised by an experienced physician. NCIT:C40972 A thin catheter inserted into an artery to monitor blood pressure directly and obtain blood samples. 2020-04-08T20:20:40Z a-line insertion art-line placement arterial line placement arterial catheter line insertion Allows delivery of positive-pressure ventilation with a tight-fitting nasal or facial mask that is attached to a continuous positive airway pressure (CPAP) or a bilevel positive airway pressure (BiPAP) machine. 2020-04-27T20:57:00Z NIPPV non-invasive positive pressure ventilation noninvasive positve-pressure ventilation NIPPV Nutrition intervention for nutrition counseling is a supportive process, characterized by a collaborative counselor–patient/client relationship to establish food, nutrition and physical activity priorities, goals, and individualized action plans that acknowledge and foster responsibility for self-care to treat an existing condition and promote health. 2020-04-28T16:03:29Z http://orcid.org/0000-0002-7463-6306 dietary counseling nutritional counseling nutrition counseling Nutrition intervention for nutrition counseling is a supportive process, characterized by a collaborative counselor–patient/client relationship to establish food, nutrition and physical activity priorities, goals, and individualized action plans that acknowledge and foster responsibility for self-care to treat an existing condition and promote health. Reference: Academy of Nutrition and Dietetics. Nutrition Terminology Reference Manual (eNCPT): Dietetics Language for Nutrition Care 2014, Nutrition Intervention/Terms and Definitions/Nutrition Counseling (C), page-064, http://ncpt.webauthor.com An in-depth evaluation of an individual's food and nutrient intake, lifestyle, and medical history designed to help the individual either maintain their health status or attain a healthier status. 2020-04-28T16:12:44Z NCIT:C15286 http://orcid.org/0000-0002-7463-6306 dietary assessment nutritional assessment nutrition assessment An in-depth evaluation of an individual's food and nutrient intake, lifestyle, and medical history designed to help the individual either maintain their health status or attain a healthier status. NCIT:C15286 A therapy utilizing an inhaled substance that produces loss of consciousness. 2020-05-26T16:13:05Z anesthetic gas therapy gas anesthetic drug therapy inhalation anaesthetic drug therapy inhalation anaesthetic medication therapy inhalation anaesthetic therapy inhalation anesthesia treatment inhalation anesthetic drug therapy inhalation anesthetic medication therapy inhalation anesthetic treatment inhalation anesthetic utilization treatment with inhalation anaesthetic inhalation anesthetic therapy A therapy utilizing an intravenous substance that produces loss of consciousness. 2020-05-26T18:19:32Z IV anaesthetic agent therapy IV anesthetic agent therapy i.v. anesthetic agent therapy i.v. anesthetic drug therapy i.v. anesthetic drug treatment i.v. anesthetic medication therapy intravenous anaesthetic agent therapy intravenous anaesthetic therapy intravenous anesthesia treatment intravenous anesthetic drug therapy intravenous anesthetic medication therapy treatment with intravenous anaesthetic intravenous anesthetic agent therapy A superficial loss of sensation in conjunctiva, mucous membranes, or skin, produced by direct application of local anesthetic solutions, ointments, gels or sprays. 2020-05-26T18:25:03Z topical anaesthetic agent therapy topical anaesthetic drug treatment topical anaesthetic therapy topical anesthesia treatment topical anesthetic drug therapy topical anesthetic medication treatment treatment with topical anaesthetic topical anesthetic agent therapy A superficial loss of sensation in conjunctiva, mucous membranes, or skin, produced by direct application of local anesthetic solutions, ointments, gels or sprays. PMID:26702198 Use of an agent that modulates the physiologic angiogenesis process. 2020-05-26T19:04:03Z CHEBI:50926 angiogenesis modulating agent therapy angiogenesis modulating drug treatment angiogenesis modulating medication therapy treatment with angiogenesis modulating agent angiogenesis modulating agent therapy Use of an agent that induces or stimulates the physiologic angiogenesis process. 2020-05-26T19:05:59Z CHEBI:50927 angiogenesis inducing agent therapy angiogenesis inducing drug treatment angiogenesis inducing medication therapy treatment with angiogenesis inducing agent angiogenesis inducing agent therapy Use of a compound that promotes the growth of new blood vessels from pre-existing vessels. 2020-05-26T19:22:45Z CHEBI:72571 pro-angiogenic agent therapy pro-angiogenic drug treatment pro-angiogenic medication therapy pro-angiogenic medication treatment proangiogenic agent therapy treatment with pro-angiogenic agent pro-angiogenic agent therapy A therapy used to neutralize stomach acidity. 2020-05-26T19:41:56Z CHEBI:65265 antacid drug therapy antacid medication therapy antacid therapy treatment with antacid antacid agent therapy A therapy used to treat or ameliorate peptic ulcer or irritation of the gastrointestinal tract. 2020-05-26T20:00:43Z CHEBI:49201 anti-ulcer drug therapy anti-ulcer medication treatment treatment with anti-ulcer agent treatment with anti-ulcer drug treatment with anti-ulcer medication anti-ulcer agent therapy Treatment of allergic reactions with medications. 2020-05-26T20:23:47Z CHEBI:50857 allergy drug therapy allergy drug treatment allergy medication therapy anti-allergic agent therapy anti-allergic drug therapy anti-allergic drug treatment anti-allergic medication therapy anti-allergic medication treatment treatment with allergy medication treatment with an allergy drug treatment with anti-allergic agent allergy agent therapy Usage of a drug to treat asthma. 2020-05-26T20:37:22Z CHEBI:49167 anti-asthma drug therapy anti-asthma drug treatment anti-asthmatic drug therapy asthma medication therapy drug treatment of asthma treatment with anti-asthmatic drug anti-asthmatic agent therapy Treatment with a drug which acts to reduce estrogenic activity in the body, either by reducing the amount of estrogen or by reducing the activity of whatever estrogen is present. 2020-05-26T21:17:28Z CHEBI:50739 CHEBI:50751 anti estrogen agent therapy anti-estrogen drug therapy anti-estrogen medication treatment anti-oestrogen agent therapy estrogen antagonist therapy estrogen receptor modulator therapy treatment with anti-estrogen agent treatment with anti-estrogen drug treatment with anti-estrogen medication treatment with anti-oestrogen medication treatment with antiestrogen medication treatment with antioestrogen medication treatment with estrogen antagonist treatment with estrogen receptor modulator anti-estrogen agent therapy Use of a compound which can be used to treat or alleviate the symptoms of dyskinesia. 2020-05-27T14:13:29Z CHEBI:66956 anti-dyskinesia agent therapy anti-dyskinesia drug therapy anti-dyskinesia medication therapy anti-dyskinetic drug therapy anti-dyskinetic medication therapy antidyskinesia agent therapy antidyskinesia drug therapy antidyskinetic drug therapy antidyskinetic medication therapy treatment with an anti-dyskinesia drug treatment with an antidyskinetic drug treatment with anti-dyskinesia medication treatment with anti-dyskinetic drug treatment with anti-dyskinetic medication treatment with antidyskinesia agent treatment with antidyskinesia drug treatment with antidyskinesia medication treatment with antidyskinetic medication anti-dyskinesia agent therapy Treatment with an antiviral agent that destroys or inhibits the replication of the herpes simplex virus. 2020-05-28T13:49:36Z CHEBI:64952 Treatment of HSV with drug Treatment of HSV with medication Treatment of herpes simplex virus with medication Treatment with anti-HSV drug Treatment with anti-HSV medication Treatment with anti-herpes simplex virus drug Treatment with anti-herpes simplex virus medication anti-HSV agent therapy anti-HSV drug therapy anti-HSV drug treatment anti-HSV medication therapy anti-herpes simplex virus agent therapy anti-herpes simplex virus drug therapy anti-herpes simplex virus drug treatment anti-herpes simplex virus medication therapy treatment with anti-HSV agent anti-HSV agent therapy Treatment with an antiviral agent that destroys or inhibits the replication of the herpes simplex virus-1. 2020-05-28T14:07:27Z CHEBI:64953 anti-HSV-1 agent therapy anti-herpes simplex virus 1 drug therapy anti-herpes simplex virus 1 medication treatment treatment for HSV-1 with medication treatment with anti-HSV-1 agent treatment with anti-HSV-1 drug treatment with anti-HSV-1 medication anti-HSV-1 agent therapy Treatment with an antiviral agent that destroys or inhibits the replication of the herpes simplex virus-2. 2020-05-28T14:07:27Z 2020-05-28T14:20:29Z CHEBI:64954 anti-HSV-2 agent therapy anti-herpes simplex virus 2 drug therapy anti-herpes simplex virus 2 medication treatment treatment for HSV-2 with medication treatment with anti-HSV-2 agent treatment with anti-HSV-2 drug treatment with anti-HSV-2 medication anti-HSV-2 agent therapy Use of a natural or synthetic analog of the hormones secreted by the adrenal gland as a type of anti-inflammatory treatment. 2020-05-28T15:10:35Z CHEBI:50858 corticosteroid therapy corticosteroid treatment treatment with corticosteroid treatment with corticosteroid agent treatment with corticosteroid drug treatment with corticosteroid medication treatment with corticosteroid therapy corticosteroid injection treatment oral corticosteroid drug treatment corticosteroid agent therapy Treatment to induce vomiting and nausea usually administered in emergency situations after ingestion of a toxin. 2020-05-28T18:31:36Z CHEBI:149552 emetic drug therapy emetic medication therapy emetic therapy treatment with an emetic drug treatment with an emetic medication treatment with an emetic therapy treatment with emetic emetic agent therapy Treatment with a drug to alleviate rheumatoid arthritis and its symptoms. 2020-05-28T18:46:29Z CHEBI:35842 anti-rheumatic agent therapy anti-rheumatic drug therapy anti-rheumatic medication therapy antirheumatic drug therapy antirheumatic drug treatment antirheumatic medication therapy treatment with anti-rheumatic agent treatment with anti-rheumatic drug treatment with anti-rheumatic medication treatment with antirheumatic agent treatment with antirheumatic drug treatment with antirheumatic medication antirheumatic agent therapy 2020-05-28T19:11:27Z CHEBI:52206 biochemical role therapy treatment with biochemical role molecular pathway modifying agent therapy Use of an inhibitor that interferes with the action of enzyme acetylcholinesterase, which helps breaking down of acetylcholine into choline and acetic acid 2020-05-28T19:16:31Z AChE inhibitor drug treatment AChE inhibitor medication treatment EC 3.1.1.7 (acetylcholinesterase) inhibitor therapy acetylcholinesterase inhibitor agent therapy acetylcholinesterase inhibitor drug therapy treatment with EC 3.1.1.7 (acetylcholinesterase) inhibitor acetylcholinesterase inhibitor therapy Treatment that uses drugs to stop the growth of cancer cells, either by killing the cells or by stopping them from dividing. Chemotherapy may be given by mouth, injection, or infusion, or on the skin, depending on the type and stage of the cancer being treated. It may be given alone or with other treatments, such as surgery, radiation therapy, or biologic therapy. 2020-05-29T20:29:34Z anti-neoplastic chemotherapy antineoplastic chemotherapy NCRO:0000233 cancer chemotherapeutic agent treatment cytotoxic antineoplastic agent therapy cytotoxic antineoplastic medication therapy cytotoxic cancer treatment treatment with cancer chemotherapeutic agent treatment with cancer chemotherapeutic drug treatment with cancer chemotherapeutic medication Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity. cancer chemotherapy Treatment that uses drugs to stop the growth of cancer cells, either by killing the cells or by stopping them from dividing. Chemotherapy may be given by mouth, injection, or infusion, or on the skin, depending on the type and stage of the cancer being treated. It may be given alone or with other treatments, such as surgery, radiation therapy, or biologic therapy. https://www.cancer.gov/publications/dictionaries/cancer-terms/def/chemotherapy Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity. NCIT:C15632 The use of synthetic or naturally-occurring chemicals for the treatment of diseases. 2020-06-02T13:10:41Z NCIT:C15632 OGMS:0000113 chemotherapeutic agent treatment chemotherapeutic drug treatment treatment with a chemotherapeutic agent treatment with a chemotherapeutic drug treatment with a chemotherapeutic medication Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity. chemotherapy The use of synthetic or naturally-occurring chemicals for the treatment of diseases. NCIT:C15632 Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity. NCIT:C15632 A therapy using a compound or agent that combines with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. 2020-06-02T18:44:24Z CHEBI:23924 enzyme inhibitor drug treatment enzyme inhibitor medication treatment enzyme inhibitor therapy treatment with enzyme inhibitor treatment with enzyme inhibitor agent treatment with enzyme inhibitor drug treatment with enzyme inhibitor medication treatment with enzyme inhibitor therapy enzyme inhibitor agent therapy Use of a drug which increases blood glucose level. 2020-06-02T20:39:40Z CHEBI:76916 hyperglycemic agent therapy treatment with hyperglycemic agent treatment with hyperglycemic drug treatment with hyperglycemic medication hyperglycemic agent therapy Treatment with a cardiovascular drug that prevents atherogenesis, the accumulation of lipid-containing plaques on the innermost layers of the arteries. 2020-06-03T14:37:54Z CHEBI:50855 anti-atherogenic agent therapy antiatherogenic agent therapy antiatherogenic drug therapy treatment with anti-atherogenic agent treatment with anti-atherogenic drug treatment with anti-atherogenic medication treatment with anti-atherogenic therapy treatment with antiatherogenic agent treatment with antiatherogenic drug treatment with antiatherogenic medication antiatherogenic agent therapy Treatment with a cardiovascular drug that prevents atherosclerosis, a disease in which the inside of an artery narrows due to the build-up of plaque. 2020-06-03T14:51:06Z CHEBI:145947 anti-atherosclerotic agent therapy antiatherosclerotic agent therapy antiatherosclerotic drug therapy treatment with anti-atherosclerosis drug treatment with anti-atherosclerosis medication treatment with anti-atherosclerosis therapy treatment with anti-atherosclerotic agent treatment with anti-atherosclerotic drug treatment with anti-atherosclerotic medication treatment with antiatherosclerotic agent treatment with antiatherosclerotic drug treatment with antiatherosclerotic medication antiatherosclerotic agent therapy Use of a drug that inhibits angiotensin-converting enzyme (ACE), an enzyme that catalyzes the conversion of angiotensin I to angiotensin II. Inhibition of ACE results in a reduction in angiotensin II and angiotensin II-induced aldosterone secretion, causing vasodilation and natriuresis. 2020-06-04T17:31:19Z CHEBI:147289 NCIT:C247 Treatment with ACE inhibitor Treatment with angiotensin-converting enzyme inhibitor angiotensin-converting enzyme inhibitor therapy ACE inhibitor therapy Treatment with a class of agents that act by selectively inhibiting angiotensin II receptor activation in the renin-angiotensin-aldosterone system. 2020-06-04T17:31:52Z CHEBI:61016 NCIT:C66930 ARB therapy angiotensin receptor antagonist therapy treatment with ARB treatment with angiotensin II receptor antagonist treatment with angiotensin II receptor blocker treatment with angiotensin receptor antagonist A pharmaceutical agent that selectively inhibits angiotensin II receptor activation in the renin-angiotensin-aldosterone system reducing production and secretion of aldosterone, amongst other actions. The combined effects result in reduction of blood pressure. It is primarily used for the reduction of proteinuria and the treatment of hypertension in cases where the patient is intolerant of ACE inhibitor therapy. Angiotensin II receptor antagonists bind to and block the activation of angiotensin II type 1 (AT1) receptors, thereby reducing production and secretion of aldosterone, amongst other actions. The combined effects result in reduction of blood pressure. Although this class of agents is also used in diabetic nephropathy (kidney damage due to diabetes) and congestive heart failure, it is primarily used for the treatment of hypertension in cases where the patient is intolerant of ACE inhibitor therapy. angiotensin-receptor blocker therapy A pharmaceutical agent that selectively inhibits angiotensin II receptor activation in the renin-angiotensin-aldosterone system reducing production and secretion of aldosterone, amongst other actions. The combined effects result in reduction of blood pressure. It is primarily used for the reduction of proteinuria and the treatment of hypertension in cases where the patient is intolerant of ACE inhibitor therapy. NCIT:C66930 Angiotensin II receptor antagonists bind to and block the activation of angiotensin II type 1 (AT1) receptors, thereby reducing production and secretion of aldosterone, amongst other actions. The combined effects result in reduction of blood pressure. Although this class of agents is also used in diabetic nephropathy (kidney damage due to diabetes) and congestive heart failure, it is primarily used for the treatment of hypertension in cases where the patient is intolerant of ACE inhibitor therapy. NCIT:C66930 2020-06-04T17:32:06Z Treatment with a group of pharmaceutical drugs used primarily in treatment of essential hypertension. These drugs inhibit the first and rate-limiting step of the renin–angiotensin–aldosterone system, namely the conversion of angiotensinogen to angiotensin I. renin inhibitor therapy Use of a drug that inhibits angiotensin-converting enzyme (ACE) 1, an enzyme that catalyzes the conversion of angiotensin I to angiotensin II. 2020-06-04T18:03:38Z CHEBI:35457 EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor therapy Treatment with ACE-1 inhibitor Treatment with ACE1 inhibitor angiotensin-converting enzyme-1 inhibitor therapy peptidyl-dipeptidase A inhibitor therapy treatment with EC 3.4.15.1 (peptidyl-dipeptidase A) inhibitor treatment with angiotensin I-converting enzyme inhibitor ACE 1 inhibitor therapy Use of a drug that inhibits angiotensin-converting enzyme (ACE) 2, an enzyme that catalyzes the conversion of angiotensin I to angiotensin II. 2020-06-04T18:17:34Z EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitor therapy Treatment with ACE-2 inhibitor angiotensin-converting enzyme-2 inhibitor therapy angiotensin-converting enzyme2 inhibitor therapy treatment with EC 3.4.17.23 (angiotensin-converting enzyme 2) inhibitor treatment with hACE2 inhibitor ACE 2 inhibitor therapy Use of a drug that selectively binds to and inhibits metabotropic glutamate receptors. 2020-06-05T20:18:05Z CHEBI:63963 metabotropic glutamate receptor antagonist therapy treatment with mGluR antagonist treatment with metabotropic glutamate receptor antagonist treatment with metabotropic glutamate receptor blockade treatment with metabotropic glutamate receptor blocker metabotropic glutamate receptor antagonist therapy Use of a drug that modulates the action of N-methyl-D-aspartate (NMDA) receptors. 2020-06-08T17:47:39Z Treatment with NMDA receptor modulator NMDA receptor modulator agent therapy 2020-06-08T17:48:19Z AMPA-targeting agent therapy Use of a drug that selectively binds to and regulates metabotropic glutamate receptors (mGluR). 2020-06-08T17:48:54Z treatment with mGluR modulator treatment with metabotropic glutamate receptor modulator metabotropic glutamate receptor–targeting agent therapy Use of a drug that activates the action of N-methyl-D-aspartate (NMDA) receptors. 2020-06-08T18:14:26Z CHEBI:64571 NMDA receptor agonist therapy treatment with NMDA receptor agonist NMDA receptor agonist therapy Use of a drug that selectively binds to and activates AMPA receptors. 2020-06-09T13:52:30Z CHEBI:64102 AMPA receptor agonist therapy Treatment with AMPA receptor agonist treatment with AMPA receptor agonist AMPA receptor agonist therapy Use of a drug that selectively binds to and inhibits AMPA receptors. 2020-06-09T13:52:48Z CHEBI:71014 AMPA receptor antagonist therapy Treatment with AMPA receptor antagonist Treatment with AMPA receptor blockade Treatment with AMPA receptor blocker treatment with AMPA receptor antagonist AMPA receptor antagonist therapy 2020-06-09T15:32:19Z CHEBI:55323 anti-diarrheal agent therapy antidiarrhoeal agent therapy antidiarrhoeal drug therapy treatment with anti-diarrheal drug treatment with antidiarrheal agent treatment with antidiarrheal medication treatment with antidiarrhoeal drug antidiarrheal agent therapy An evaluation by healthcare provider who is a specialist in a particular medical area. 2020-07-01T18:18:19Z specialty medical professional consultation specialty medical professional evaluation medical specialist evaluation An evaluation by an allergist-immunologist who diagnoses and manages disorders involving immune system conditions such as asthma, anaphylaxis, rhinitis and eczema as well as adverse reactions to drugs, foods and insect stings. An allergist-immunologist also manages immune deficiency diseases and problems related to autoimmune disease, organ transplantation or malignancies of the immune system. 2020-07-01T18:29:08Z allergy and immunologist consultation allergy and immunologist doctor consultation allergy and immunologist doctor evaluation allergy and immunologist evaluation allergy and immunology specialist consultation consultation with allergy and immunologist referral to allergist and immunologist allergist consultation allergist doctor consultation allergist doctor evaluation allergist evaluation consultation with allergist allergy and immunology specialist evaluation An evaluation by an allergist-immunologist who diagnoses and manages disorders involving immune system conditions such as asthma, anaphylaxis, rhinitis and eczema as well as adverse reactions to drugs, foods and insect stings. An allergist-immunologist also manages immune deficiency diseases and problems related to autoimmune disease, organ transplantation or malignancies of the immune system. ABMS.org An evaluation by a physician who provides anesthesia for patients undergoing surgical, obstetric, diagnostic or therapeutic procedures while monitoring the patient's condition and supporting vital organ functions. The anesthesiologist also diagnoses and treats acute, chronic and/or cancer pain as well as provides resuscitation and medical management for patients with critical illnesses and severe injuries. 2020-07-01T18:42:19Z NCIT:C93067 anesthesiologist consultation anesthesiologist evaluation anesthesiology doctor consultation anesthesiology doctor evaluation anesthesiology specialist consultation consultation with anesthesiologist referral to anesthesiologist anesthesiology specialist evaluation An evaluation by a physician who provides anesthesia for patients undergoing surgical, obstetric, diagnostic or therapeutic procedures while monitoring the patient's condition and supporting vital organ functions. The anesthesiologist also diagnoses and treats acute, chronic and/or cancer pain as well as provides resuscitation and medical management for patients with critical illnesses and severe injuries. abms.org An evaluation by an anesthesiologist who specializes in Pediatric Anesthesiology. This specialist provides anesthesia for neonates, infants, children and adolescents undergoing surgical, diagnostic or therapeutic procedures as well as appropriate pre- and post-operative care, advanced life support, and acute pain management. 2020-07-01T18:48:51Z consultation with pediatric anesthesiologist pediatric anesthesiologist consultation pediatric anesthesiologist evaluation pediatric anesthesiology specialist consultation pediatric anesthesiology specialist evaluation An evaluation by a colon and rectal surgeon who diagnoses and treats various diseases of the small intestine, colon, rectum, anal canal and perianal area including the organs and tissues related with primary intestinal diseases (liver, urinary and female reproductive system). This specialist treats conditions such as hemorrhoids, fissures (painful tears in the anal lining), abscesses and fistulas (infections located around the anus and rectum). A colon and rectal surgeon diagnoses and treats problems of the intestine and colon such as cancer, polyps (precancerous growths) and inflammatory conditions. 2020-07-01T19:08:36Z colon and rectal surgeon consultation colon and rectal surgeon evaluation colon and rectal surgery specialist consultation colorectal surgeon consultation colorectal surgeon evaluation consultation with colon and rectal surgeon consultation with colon and rectal surgery specialist consultation with colorectal surgeon referral to a colon and rectal surgeon referral to colorectal surgeon colon and rectal surgery specialist evaluation An evaluation by a colon and rectal surgeon who diagnoses and treats various diseases of the small intestine, colon, rectum, anal canal and perianal area including the organs and tissues related with primary intestinal diseases (liver, urinary and female reproductive system). This specialist treats conditions such as hemorrhoids, fissures (painful tears in the anal lining), abscesses and fistulas (infections located around the anus and rectum). A colon and rectal surgeon diagnoses and treats problems of the intestine and colon such as cancer, polyps (precancerous growths) and inflammatory conditions. abms.org An evaluation by a physician with training and expertise in the diagnosis and medical/surgical management of diseases of the skin, hair and nails, and mucous membranes. 2020-07-01T19:12:58Z consultation with a dermatologist dermatologist consultation dermatologist evaluation dermatology specialist consultation referral to a dermatologist dermatology specialist evaluation An evaluation by a physician with training and expertise in the diagnosis and medical/surgical management of diseases of the skin, hair and nails, and mucous membranes. abms.org An evaluation by a physician who specializes in immediate decision making and action necessary to prevent death or any further disability both in the pre-hospital setting by directing emergency medical technicians and in the emergency department. This specialist provides immediate recognition, evaluation, care, stabilization and disposition of a generally diversified population of adult and pediatric patients in response to acute illness and injury. 2020-07-01T19:23:12Z assessment by emergency medicine specialist emergency medicine specialist assessment emergency room doctor evaluation emergency medicine specialist evaluation An evaluation by a physician who specializes in immediate decision making and action necessary to prevent death or any further disability both in the pre-hospital setting by directing emergency medical technicians and in the emergency department. This specialist provides immediate recognition, evaluation, care, stabilization and disposition of a generally diversified population of adult and pediatric patients in response to acute illness and injury. abms.org An evaluation by a physician who provides front-line health care that is accessible, high quality, comprehensive and continuous over time for people of all ages, life stages, backgrounds and conditions. The specialists care for individuals and for entire families, from birth through the end of life, including a broad range of preventive care; healthy lifestyle counseling; mental health care; care of acute illnesses; management of chronic diseases, including patients with multi-morbidity. When needed, they also provide referral and coordination of care with other specialists. 2020-07-01T19:39:31Z consultation with family medicine specialist family medicine specialist consultation family medicine specialist evaluation An evaluation by a physician who provides front-line health care that is accessible, high quality, comprehensive and continuous over time for people of all ages, life stages, backgrounds and conditions. The specialists care for individuals and for entire families, from birth through the end of life, including a broad range of preventive care; healthy lifestyle counseling; mental health care; care of acute illnesses; management of chronic diseases, including patients with multi-morbidity. When needed, they also provide referral and coordination of care with other specialists. abms.org An evaluation by a physician with special knowledge of the aging process and special skills in the diagnostic, therapeutic, preventive and rehabilitative aspects of illness in the elderly. This specialist cares for geriatric patients in the patient’s home, the office, long-term care settings such as nursing homes, and the hospital. 2020-07-01T19:52:16Z assessment by geriatric medicine specialist consultation with geriatric medicine specialist evaluation by geriatric medicine specialist geriatric medicine specialist consultation referral to geriatric medicine specialist geriatric medicine specialist evaluation An evaluation by a physician with special knowledge of the aging process and special skills in the diagnostic, therapeutic, preventive and rehabilitative aspects of illness in the elderly. This specialist cares for geriatric patients in the patient’s home, the office, long-term care settings such as nursing homes, and the hospital. abms.org An evaluation by a physician who specializes in Hospice and Palliative Medicine who provides care to prevent and relieve the suffering experienced by patients with life-limiting illnesses. This specialist works with an interdisciplinary hospice or palliative care team to optimize quality of life while addressing the physical, psychological, social and spiritual needs of both patient and family. 2020-07-01T19:53:31Z consultation with hospice and palliative medicine specialist hospice and palliative medicine specialist consultation referral to hospice and palliative medicine specialist assessment by palliative care specialist consultation with palliative care specialist evaluation by palliative care specialist palliative care specialist consultation palliative care specialist evaluation palliative care specialist referral referral to palliative care specialist hospice and palliative medicine specialist evaluation An evaluation by a physician who diagnoses and treats patients experiencing problems with acute or chronic pain, or pain related to cancer, in both hospital and outpatient settings and coordinates care needs with other specialists. 2020-07-01T19:56:48Z assessment by pain medicine specialist consultation with pain medicine specialist evaluation by pain medicine specialist pain medicine specialist consultation referral to a pain medicine specialist pain medicine specialist evaluation An evaluation by a physician who diagnoses and treats patients experiencing problems with acute or chronic pain, or pain related to cancer, in both hospital and outpatient settings and coordinates care needs with other specialists. abms.org An evaluation a specialist focuses on preventing, diagnosing, and treating injuries related to participating in sports and/or exercise. In addition to the study of those fields that focus on prevention, diagnosis, treatment, and management of injuries, Sports Medicine specialists also deal with illnesses and diseases that might have effects on health and physical performance. 2020-07-01T19:59:07Z consultation with sports medicine specialist referral to a sports medicine specialist sports medicine specialist consultation sports medicine specialist evaluation An evaluation a specialist focuses on preventing, diagnosing, and treating injuries related to participating in sports and/or exercise. In addition to the study of those fields that focus on prevention, diagnosis, treatment, and management of injuries, Sports Medicine specialists also deal with illnesses and diseases that might have effects on health and physical performance. abms.org An evaluation with a specialist who has expertise in the diagnosis and management of clinical conditions that occur during sleep, that disturb sleep, or that are affected by disturbances in the wake-sleep cycle. This specialist is skilled in the analysis and interpretation of comprehensive polysomnography, and well versed in emerging research and management of a sleep laboratory. 2020-07-01T20:01:47Z assessment by sleep medicine specialist assessment by sleep specialist consultation with sleep medicine specialist consultation with sleep specialist evaluation by sleep medicine specialist evaluation by sleep specialist referral to sleep medicine specialist referral to sleep specialist sleep medicine specialist consultation sleep specialist assessment sleep specialist consultation sleep specialist evaluation sleep specialist referral sleep study evaluation sleep medicine specialist evaluation An evaluation with a specialist who has expertise in the diagnosis and management of clinical conditions that occur during sleep, that disturb sleep, or that are affected by disturbances in the wake-sleep cycle. This specialist is skilled in the analysis and interpretation of comprehensive polysomnography, and well versed in emerging research and management of a sleep laboratory. abms.org An evalutation by a personal physician who provides long-term, comprehensive care in the office and in the hospital, managing both common and complex illnesses of adolescents, adults and the elderly. Internists are trained in the diagnosis and treatment of cancer, infections and diseases affecting the heart, blood, kidneys, joints and the digestive, respiratory and vascular systems. Internists are also trained in the essentials of primary care internal medicine, which incorporates an understanding of disease prevention, wellness, substance abuse, mental health and effective treatment of common problems of the eyes, ears, skin, nervous system and reproductive organs. 2020-07-01T20:07:16Z consultation with internal medicine specialist consultation with internist internal medicine specialist consultation internist consultation internist evaluation referral to an internal medicine specialist referral to an internist internal medicine specialist evaluation An evalutation by a personal physician who provides long-term, comprehensive care in the office and in the hospital, managing both common and complex illnesses of adolescents, adults and the elderly. Internists are trained in the diagnosis and treatment of cancer, infections and diseases affecting the heart, blood, kidneys, joints and the digestive, respiratory and vascular systems. Internists are also trained in the essentials of primary care internal medicine, which incorporates an understanding of disease prevention, wellness, substance abuse, mental health and effective treatment of common problems of the eyes, ears, skin, nervous system and reproductive organs. abms.org An evaluation with a multidisciplinary health care specialist trained in the unique physical, psychological and social characteristics of adolescents, their health care problems and needs. 2020-07-01T20:13:15Z adolescent medicine specialist consultation adolescent medicine specialist evaluation assessment by adolescent medicine specialist consultation with adolescent medicine specialist evaluation by adolescent medicine specialist referral to adolescent medicine specialist adolescent medicine specialist evaluation An evaluation with a multidisciplinary health care specialist trained in the unique physical, psychological and social characteristics of adolescents, their health care problems and needs. abms.org An evaluation by an internist who specializes in diseases of the heart and blood vessels and manages complex cardiac conditions, such as heart attacks and life-threatening, abnormal heartbeat rhythms. 2020-07-01T20:16:52Z assessment by cardiologist cardiologist consultation cardiologist evaluation cardiologist referral cardiovascular disease internist consultation cardiovascular disease internist evaluation consultation with cardiologist consultation with cardiovascular disease internist consultation with internal medicine cardiovascular disease specialist evaluation by cardiologist internal medicine cardiovascular disease specialist consultation referral to cardiologist referral to cardiovascular disease internist cardiovascular disease internist evaluation An evaluation by an internist who specializes in diseases of the heart and blood vessels and manages complex cardiac conditions, such as heart attacks and life-threatening, abnormal heartbeat rhythms. abms.org An evaluation by a specialist who specializes in intricate technical procedures to evaluate heart rhythms and determine appropriate treatment. 2020-07-01T20:30:10Z consultation with clinical cardiac electrophysiologist consultation with clinical cardiac electrophysiology specialist internal medicine clinical cardiac electrophysiologist consultation internal medicine clinical cardiac electrophysiology specialist consultation internal medicine clinical cardiac electrophysiology specialist evaluation referral to a clinical electrophysiologist clinical cardiac electrophysiologist evaluation An evaluation by a specialist who specializes in intricate technical procedures to evaluate heart rhythms and determine appropriate treatment. abms.org 2020-07-01T20:35:47Z consultation with critical care medicine internist consultation with internal medicine critical care medicine specialist internal medicine critical care medicine consultation internal medicine critical care medicine evaluation referral to critical care internist critical care medicine internist evaluation An evaluation with an internist who specializes in the diagnosis and management of disorders of hormones and their actions, metabolic disorders, and neoplasia of the endocrine glands. This specialist cares for patients with diabetes mellitus, thyroid disorders, disorders of calcium and bone, hyperlipidemia, obesity and nutritional disorders, pituitary disorders, reproductive and gonadal disorders, adrenal diseases, and endocrine hypertension. 2020-07-01T20:43:06Z consultation with endocrinologist consultation with endocrinology, diabetes and metabolism specialist endocrinologist consultation endocrinology, diabetes and metabolism specialist consultation endocrinology, diabetes and metabolism specialist evaluation referral to endocrinologist endocrinologist evaluation An evaluation with an internist who specializes in the diagnosis and management of disorders of hormones and their actions, metabolic disorders, and neoplasia of the endocrine glands. This specialist cares for patients with diabetes mellitus, thyroid disorders, disorders of calcium and bone, hyperlipidemia, obesity and nutritional disorders, pituitary disorders, reproductive and gonadal disorders, adrenal diseases, and endocrine hypertension. abms.org An evaluation with an internist who specializes in diagnosis and treatment of diseases of the digestive organs including the stomach, bowels, liver and gallbladder. This specialist treats conditions such as abdominal pain, ulcers, diarrhea, cancer and jaundice and performs complex diagnostic and therapeutic procedures using endoscopes to visualize internal organs. 2020-07-01T20:46:33Z consultation with gastroenterologist consultation with gastroenterology specialist gastroenterologist consultation gastroenterology specialist evaluation referral to gastroenterologist gastroenterologist evaluation An evaluation with an internist who specializes in diagnosis and treatment of diseases of the digestive organs including the stomach, bowels, liver and gallbladder. This specialist treats conditions such as abdominal pain, ulcers, diarrhea, cancer and jaundice and performs complex diagnostic and therapeutic procedures using endoscopes to visualize internal organs. abms.org An evaluation by an internist with additional training who specializes in diseases of the blood, spleen and lymph. This specialist treats conditions such as anemia, clotting disorders, sickle cell disease, hemophilia, leukemia and lymphoma. 2020-07-01T21:00:28Z consultation with hematologist hematologist consultation hematology specialist consultation hematology specialist evaluation referral to hematologist hematologist evaluation An evaluation by an internist with additional training who specializes in diseases of the blood, spleen and lymph. This specialist treats conditions such as anemia, clotting disorders, sickle cell disease, hemophilia, leukemia and lymphoma. abms.org An evaluation by an internist who deals with infectious diseases of all types and in all organ systems. Infectious disease specialists may also have expertise in preventive medicine and travel medicine. 2020-07-02T17:10:50Z consultation with infectious disease specialist infectious disease specialist consultation infectious disease specialist evaluation referral to infectious disease internist infectious disease internist evaluation An evaluation by an internist who deals with infectious diseases of all types and in all organ systems. Infectious disease specialists may also have expertise in preventive medicine and travel medicine. abms.org An evaluation by an internist who specializes in the diagnosis and treatment of all types of cancer and other benign and malignant tumors. This specialist decides on and administers therapy for these malignancies, as well as consults with surgeons and radiotherapists on other treatments for cancer. 2020-07-02T17:50:50Z consultation with medical oncologist consultation with medical oncology internist medical oncologist consultation medical oncology internist consultation medical oncology internist evaluation referral to oncologist medical oncologist evaluation An evaluation by an internist who specializes in the diagnosis and treatment of all types of cancer and other benign and malignant tumors. This specialist decides on and administers therapy for these malignancies, as well as consults with surgeons and radiotherapists on other treatments for cancer. abms.org An evaluation by an internist who treats disorders of the kidney, high blood pressure, fluid and mineral balance, and dialysis of body wastes when the kidneys do not function. This specialist consults with surgeons about kidney transplantation. 2020-07-02T18:23:18Z consultation with nephrologist consultation with nephrology internist nephrologist consultation nephrology internist consultation nephrology internist evaluation referral to nephrologist nephrologist evaluation An evaluation by an internist who treats disorders of the kidney, high blood pressure, fluid and mineral balance, and dialysis of body wastes when the kidneys do not function. This specialist consults with surgeons about kidney transplantation. abms.org An evaluation by an internist who treats diseases of the lungs and airways. The specialist diagnoses and treats cancer, pneumonia, pleurisy, asthma, occupational and environmental diseases, bronchitis, sleep disorders, emphysema and other complex disorders of the lungs. 2020-07-02T18:32:06Z consultation with pulmonary disease internist consultation with pulmonary disease specialist consultation with pulmonologist pulmonary disease internist consultation pulmonary disease internist evaluation pulmonologist consultation referral to pulmonologist pulmonologist evaluation An evaluation by an internist who treats diseases of the lungs and airways. The specialist diagnoses and treats cancer, pneumonia, pleurisy, asthma, occupational and environmental diseases, bronchitis, sleep disorders, emphysema and other complex disorders of the lungs. abms.org An evaluation by an internist who treats diseases of joints, muscle, bones and tendons. This specialist diagnoses and treats arthritis, back pain, muscle strains, common athletic injuries and collagen diseases. 2020-07-02T19:00:04Z consultation with rheumatologist consultation with rheumatology internist referral to rhematologist rheumatologist consultation rheumatology internist consultation rheumatology internist evaluation rheumatology specialist consultation rheumatology specialist evaluation rheumatologist evaluation An evaluation by an internist who treats diseases of joints, muscle, bones and tendons. This specialist diagnoses and treats arthritis, back pain, muscle strains, common athletic injuries and collagen diseases. abms.org An evaluation with a specialist who directs and interprets a wide range of specialized, laboratory biochemical genetic analyses relevant to the diagnosis and management of inherited metabolic disorders. The specialist acts as a consultant regarding laboratory diagnosis on a broad range of inborn errors of metabolism. 2020-07-02T20:14:07Z clinical biochemical geneticist consultation consultation with clinical biochemical geneticist referral to a clinical biochemical geneticist clinical biochemical geneticist evaluation An evaluation with a specialist who directs and interprets a wide range of specialized, laboratory biochemical genetic analyses relevant to the diagnosis and management of inherited metabolic disorders. The specialist acts as a consultant regarding laboratory diagnosis on a broad range of inborn errors of metabolism. abms.org An evaluation with a specialist who provides comprehensive diagnostic, management, therapeutic, and counseling services for individuals and families at risk for clinical disorders with a genetic basis. The specialist is trained to evaluate individuals of all ages for hereditary conditions. 2020-07-02T20:16:59Z clinical geneticist consultation clinical geneticist evaluation clinical genetics and genomics specialist consultation consultation with clinical geneticist consultation with clinical genetics and genomics specialist referral to a clinical geneticist clinical genetics and genomics specialist evaluation An evaluation with a specialist who provides comprehensive diagnostic, management, therapeutic, and counseling services for individuals and families at risk for clinical disorders with a genetic basis. The specialist is trained to evaluate individuals of all ages for hereditary conditions. abms.org An evaluation or consultation by a diplomate certified in Laboratory Genetics and Genomics who directs and interprets both clinical cytogenetic and molecular genetic analyses relevant to the diagnosis and management of human genetic disease. This specialist acts as a consultant in laboratory diagnoses for a broad range of molecular and chromosomal-based disorders, including both inherited and acquired conditions. 2020-07-02T20:29:00Z clinical laboratory geneticist evaluation An evaluation or consultation by a diplomate certified in Laboratory Genetics and Genomics who directs and interprets both clinical cytogenetic and molecular genetic analyses relevant to the diagnosis and management of human genetic disease. This specialist acts as a consultant in laboratory diagnoses for a broad range of molecular and chromosomal-based disorders, including both inherited and acquired conditions. abms.org Evaluation by this specialist provides care for adult and pediatric patients in the treatment of pain or pathological processes that may modify the function or activity of the central nervous system (e.g., brain, hypophysis, and spinal cord), the peripheral nervous system (e.g., cranial, spinal, and peripheral nerves), the autonomic nervous system, the supporting structures of these systems (e.g., meninges, skull & skull base, and vertebral column), and their vascular supply (e.g., intracranial, extracranial, and spinal vasculature). 2020-07-08T15:24:04Z NCIT:C17722 consultation with neurological surgeon consultation with neurological surgery specialist consultation with neurosurgeon neurological surgeon consultation neurological surgeon evaluation neurological surgery specialist consultation neurosurgeon consultation neurosurgeon evaluation referral to neurosurgeon neurological surgery specialist evaluation Evaluation by this specialist provides care for adult and pediatric patients in the treatment of pain or pathological processes that may modify the function or activity of the central nervous system (e.g., brain, hypophysis, and spinal cord), the peripheral nervous system (e.g., cranial, spinal, and peripheral nerves), the autonomic nervous system, the supporting structures of these systems (e.g., meninges, skull & skull base, and vertebral column), and their vascular supply (e.g., intracranial, extracranial, and spinal vasculature). abms.org An evaluation by a specialist that uses molecular tracers (usually labeled with radioactive atoms) for diagnosis and therapy. 2020-07-08T17:46:13Z consultation with nuclear medicine specialist nuclear medicine specialist consultation referral to nuclear medicine specialist These labeled tracers are most often used to produce images that provide information about organ function, as well as cellular function on a molecular level (molecular imaging). Molecular imaging can be combined with anatomical imaging by using specialized cameras. The most common diagnostic applications of Nuclear Medicine include the early detection of coronary artery disease, cancer diagnosis and staging and the evaluation of the effect of cancer treatment. The fusion of molecular and anatomical information increases diagnostic accuracy and changes medical management. Radioactive materials are also used to treat a variety of health problems, including thyroid disorders and cancer. nuclear medicine specialist evaluation An evaluation by a specialist that uses molecular tracers (usually labeled with radioactive atoms) for diagnosis and therapy. abms.org These labeled tracers are most often used to produce images that provide information about organ function, as well as cellular function on a molecular level (molecular imaging). Molecular imaging can be combined with anatomical imaging by using specialized cameras. The most common diagnostic applications of Nuclear Medicine include the early detection of coronary artery disease, cancer diagnosis and staging and the evaluation of the effect of cancer treatment. The fusion of molecular and anatomical information increases diagnostic accuracy and changes medical management. Radioactive materials are also used to treat a variety of health problems, including thyroid disorders and cancer. abms.org An evaluation with a specialist who focuses on the health of women before, during and after childbearing years, diagnosing and treating conditions of the reproductive system and associated disorders. 2020-07-08T17:53:55Z OB/GYN specialist consultation OB/GYN specialist evaluation consultation OB/GYN specialist consultation obstetrician/gynecologist consultation with obstetrics and gynecology specialist obstetrician/gynecologist consultation obstetrician/gynecologist evaluation obstetrics and gynecology specialist consultation obstetrics/gynecology specialist consultation obstetrics/gynecology specialist evaluation referral to OB/GYN specialist obstetrics and gynecology specialist evaluation An evaluation with a specialist who focuses on the health of women before, during and after childbearing years, diagnosing and treating conditions of the reproductive system and associated disorders. abms.org An evaluation by a specialist focused on the medical and surgical care of the eyes. Ophthalmologists are the only physicians medically trained to manage the complete range of the eye and vision care. They can prescribe glasses and contact lenses, dispense medications, diagnose and treat eye conditions and diseases and perform surgeries. 2020-07-08T20:14:31Z consultation with ophthalmologist ophthalmologist consultation ophthalmologist referral ophthalmology specialist consultation ophthalmology specialist evaluation referral to ophthalmologist referral to ophthalmology specialist referral to optometrist ophthalmologist evaluation An evaluation by a specialist focused on the medical and surgical care of the eyes. Ophthalmologists are the only physicians medically trained to manage the complete range of the eye and vision care. They can prescribe glasses and contact lenses, dispense medications, diagnose and treat eye conditions and diseases and perform surgeries. abms.org An evaluation by a specialist who has expertise in the surgical and medical care for all structures of the musculoskeletal system directly affected by participation in sporting activity. This specialist is proficient in areas including conditioning, training and fitness, athletic performance and the impact of dietary supplements, pharmaceuticals, and nutrition on performance and health, coordination of care within the team setting utilizing other health care professionals, field evaluation and management, soft tissue biomechanics and injury healing and repair. Knowledge and understanding of the principles and techniques of rehabilitation, athletic equipment and orthotic devices enables the specialist to prevent and manage athletic injuries. 2020-07-08T20:31:50Z consultation with sports medicine orthopedic surgeon referral to sports medicine orthopedic surgeon referral to sports medicine orthopedist sports medicine orthopedic surgeon consultation sports medicine orthopedic surgeon evaluation sports medicine orthopedist consultation sports medicine orthopedist referral sports medicine orthopedist evaluation An evaluation by a specialist who has expertise in the surgical and medical care for all structures of the musculoskeletal system directly affected by participation in sporting activity. This specialist is proficient in areas including conditioning, training and fitness, athletic performance and the impact of dietary supplements, pharmaceuticals, and nutrition on performance and health, coordination of care within the team setting utilizing other health care professionals, field evaluation and management, soft tissue biomechanics and injury healing and repair. Knowledge and understanding of the principles and techniques of rehabilitation, athletic equipment and orthotic devices enables the specialist to prevent and manage athletic injuries. abms.org An evaluation by a specialist with expertise in the surgical, medical and rehabilitative care of patients with diseases, injuries, and disorders affecting the hand, wrist and forearm. 2020-07-08T20:34:54Z consultation with hand surgeon consultation with orthopedic hand surgeon hand surgeon consultation referral to hand surgeon referral to orthopedic hand surgeon Common conditions treated by a hand surgeon include carpal tunnel syndrome, trigger fingers, ganglia (lumps), sports injuries to the hand and wrist, and hand injuries involving cut tendons, nerves and arteries. Hand Surgeons may be General Surgeons, Orthopedic Surgeons or Plastic Surgeons who have received additional training in this area. hand surgeon evaluation An evaluation by a specialist with expertise in the surgical, medical and rehabilitative care of patients with diseases, injuries, and disorders affecting the hand, wrist and forearm. abms.org Common conditions treated by a hand surgeon include carpal tunnel syndrome, trigger fingers, ganglia (lumps), sports injuries to the hand and wrist, and hand injuries involving cut tendons, nerves and arteries. Hand Surgeons may be General Surgeons, Orthopedic Surgeons or Plastic Surgeons who have received additional training in this area. abms.org An evaluation by a specialist who provides medical and/or surgical therapy or prevention of diseases, allergies, neoplasms, deformities, disorders and/or injuries of the ears, nose, sinuses, throat, respiratory and upper alimentary systems, face, jaws and the other head and neck systems. 2020-07-09T16:10:20Z consultation by otolaryngology specialist consultation with head and neck surgeon consultation with otolaryngologist evaluation by otolaryngologist head and neck surgeon consultation head and neck surgeon evaluation head and neck surgeon referral otolaryngologist consultation otolaryngologist referral otolaryngology specialist consultation otolaryngology specialist evaluation otolaryngology specialist referral referral to head and neck surgeon referral to otolaryngologist Head and neck oncology, facial plastic and reconstructive surgery and the treatment of disorders of hearing and voice are fundamental areas of expertise. otolaryngologist evaluation An evaluation by a specialist who provides medical and/or surgical therapy or prevention of diseases, allergies, neoplasms, deformities, disorders and/or injuries of the ears, nose, sinuses, throat, respiratory and upper alimentary systems, face, jaws and the other head and neck systems. abms.org Head and neck oncology, facial plastic and reconstructive surgery and the treatment of disorders of hearing and voice are fundamental areas of expertise. abms.org An evaluation by a specialist concerned with the physical, emotional, and social health of children from birth to young adulthood. 2020-07-09T17:48:27Z evaluation by pediatrician pediatrician consultation Pediatric care encompasses a broad spectrum of health services ranging from preventive health care to the diagnosis and treatment of acute and chronic diseases. Pediatricians understand the many factors that affect the growth and development of children. They understand that children are not simply small adults. Children change rapidly, and they must be approached with an appreciation for their stage of physical and mental development. pediatrician evaluation An evaluation by a specialist concerned with the physical, emotional, and social health of children from birth to young adulthood. abms.org Pediatric care encompasses a broad spectrum of health services ranging from preventive health care to the diagnosis and treatment of acute and chronic diseases. Pediatricians understand the many factors that affect the growth and development of children. They understand that children are not simply small adults. Children change rapidly, and they must be approached with an appreciation for their stage of physical and mental development. abms.org An evaluation with a specialist who possesses special skills, training and experience to foster understanding and promotion of optimal development of children and families through research, education, clinical care and advocacy efforts. This physician assists in the prevention, diagnosis and management of developmental difficulties and problematic behaviors in children and in the family dysfunctions that compromise children’s development. 2020-07-09T18:05:01Z consultation with developmental-behavior pediatrician developmental-behavior pediatrician consultation developmental-behavior pediatrician referral referral to developmental-behavior pediatrician developmental-behavior pediatrician evaluation An evaluation with a specialist who possesses special skills, training and experience to foster understanding and promotion of optimal development of children and families through research, education, clinical care and advocacy efforts. This physician assists in the prevention, diagnosis and management of developmental difficulties and problematic behaviors in children and in the family dysfunctions that compromise children’s development. abms.org An evaluation by a specialist who provides expert care to infants, children and adolescents who have diseases that result from an abnormality in the endocrine glands (glands which secrete hormones). These diseases include diabetes mellitus, growth failure, unusual size for age, early or late pubertal development, birth defects, the genital region and disorders of the thyroid, the adrenal and pituitary glands. 2020-07-09T18:48:58Z assessment by pediatric endocrinologist consultation with pediatric endocrinologist evaluation by pediatric endocrinologist pediatric endocrinologist consultation pediatric endocrinologist referral referral to pediatric endocrinologist pediatric endocrinologist evalutation An evaluation by a specialist who provides expert care to infants, children and adolescents who have diseases that result from an abnormality in the endocrine glands (glands which secrete hormones). These diseases include diabetes mellitus, growth failure, unusual size for age, early or late pubertal development, birth defects, the genital region and disorders of the thyroid, the adrenal and pituitary glands. abms.org Evaluation by a specialist who provides comprehensive care to patients with cardiovascular problems. This specialist is skilled in selecting, performing, and evaluating the structural and functional assessment of the heart and blood vessels, and the clinical evaluation of cardiovascular disease. 2020-07-09T18:54:16Z assessment by pediatric cardiologist consultation with pediatric cardiologist evaluation by pediatric cardiologist pediatric cardiologist consultation pediatric cardiologist referral referral to pediatric cardiologist pediatric cardiologist evaluation Evaluation by a specialist who provides comprehensive care to patients with cardiovascular problems. This specialist is skilled in selecting, performing, and evaluating the structural and functional assessment of the heart and blood vessels, and the clinical evaluation of cardiovascular disease. abms.org Evaluation by a specialist who treats patients with disorders or disabilities in the muscles, bones, and nervous system, including neck or back pain, sports and work injuries, stroke, brain injury, spinal cord injury, spasticity, and any other disability or disorder that affects function. 2020-07-09T19:45:07Z assessment by physiatrist assessment by physical medicine and rehabilitation specialist consultation by physiatrist consultation with physical medicine and rehabilitation specialist evaluation by physical medicine and rehabilitation specialist physiatrist assessment physiatrist consultation physiatrist referral physical medicine and rehabilitation specialist assessment physical medicine and rehabilitation specialist consultation physical medicine and rehabilitation specialist evaluation physical medicine and rehabilitation specialist referral referral to physiatrist Treatment modalities by a physiatrist may include medications, injections, therapeutic exercise, electrodiagnosis, and any equipment required for daily activities. physiatrist evaluation Evaluation by a specialist who treats patients with disorders or disabilities in the muscles, bones, and nervous system, including neck or back pain, sports and work injuries, stroke, brain injury, spinal cord injury, spasticity, and any other disability or disorder that affects function. abms.org Treatment modalities by a physiatrist may include medications, injections, therapeutic exercise, electrodiagnosis, and any equipment required for daily activities. abms.org An evaluation with a specialist who focuses on the repair, reconstruction or replacement of physical defects of form or function involving the skin, musculoskeletal system, craniomaxillofacial structures, hand, extremities, breast and trunk and external genitalia or cosmetic enhancement of these areas of the body. 2020-07-09T19:54:01Z consultation with plastic surgeon evaluation by plastic surgeon plastic surgeon assessment plastic surgeon consultation plastic surgeon referral plastic surgeon evaluation An evaluation with a specialist who focuses on the repair, reconstruction or replacement of physical defects of form or function involving the skin, musculoskeletal system, craniomaxillofacial structures, hand, extremities, breast and trunk and external genitalia or cosmetic enhancement of these areas of the body. abms.org Evaluation by a physician who specializes in the evaluation and treatment of mental, addictive and emotional disorders. 2020-07-09T20:37:35Z assessment by psychiatrist consult with psychiatrist evaluation by psychiatrist psychiatrist assessment psychiatrist consultation psychiatrist referral referral to psychiatrist psychiatrist evaluation Evaluation by a physician who specializes in the evaluation and treatment of mental, addictive and emotional disorders. abms.org Evaluation by a physician who specializes in the evaluation and treatment of mental, addictive and emotional disorders in children and adolescence. 2020-07-09T20:41:16Z assessment by child and adolescent psychiatrist assessment by child psychiatrist child and adolescent psychiatrist assessment child and adolescent psychiatrist consultation child and adolescent psychiatrist referral child psychiatrist assessment child psychiatrist evaluation child psychiatrist referral consultation with child and adolescent psychiatrist consultation with child psychiatrist evaluation by child and adolescent psychiatrist referral to child and adolescent psychiatrist referral to child psychiatrist child and adolescent psychiatrist evaluation Evaluation by a physician who specializes in the evaluation and treatment of mental, addictive and emotional disorders in children and adolescence. abms.org An evaluation a specialist who treats all types of disease or impaired function of the brain, spinal cord, peripheral nerves, muscles and autonomic nervous system, as well as the blood vessels that relate to these structures. 2020-07-10T16:33:00Z consultation with neurologist neurologist assessment neurologist consultation neurologist referral referral to neurologist neurologist evaluation An evaluation a specialist who treats all types of disease or impaired function of the brain, spinal cord, peripheral nerves, muscles and autonomic nervous system, as well as the blood vessels that relate to these structures. abms.org Evaluation with a specialist who diagnose and treat all types of disease or impaired function of the brain, spinal cord, peripheral nerves, muscles and autonomic nervous system, as well as the blood vessels that relate to these structures in infants, children, and adolescents. They also have special competence in genetic and metabolic problems, malformation, retardation and other neurodevelopmental problems of childhood. 2020-07-10T18:35:13Z assessment by pediatric neurologist child neurologist assessment child neurologist consultation consultation with child neurologist consultation with pediatric neurologist evaluation by child neurologist pediatric neurologist assessment pediatric neurologist consultation pediatric neurologist evaluation referral to child neurologist referral to pediatric neurologist child neurologist evaluation Evaluation with a specialist who diagnose and treat all types of disease or impaired function of the brain, spinal cord, peripheral nerves, muscles and autonomic nervous system, as well as the blood vessels that relate to these structures in infants, children, and adolescents. They also have special competence in genetic and metabolic problems, malformation, retardation and other neurodevelopmental problems of childhood. abms.org Evaluation by a specialist who uses imaging methodologies to diagnose and manage patients and provide therapeutic options. 2020-07-10T19:06:21Z assessment by radiologist evaluation by radiologist radiologist assessment radiologist evaluation Evaluation by a specialist who uses imaging methodologies to diagnose and manage patients and provide therapeutic options. abms.org Evaluation by an expert in the diagnosis and care of patients with diseases and disorders affecting the abdomen, digestive tract, endocrine system, breast, skin and blood vessels. A general surgeon is also trained in the treatment of patients who are injured or critically ill, and in the care of pediatric and cancer patients. General surgeons are skilled in the use of minimally invasive techniques and endoscopies. 2020-07-10T19:33:25Z assessment by general surgeon consultation with general surgeon evaluation by general surgeon general surgeon assessment general surgeon consultation general surgeon evaluation general surgeon evaluation Evaluation by an expert in the diagnosis and care of patients with diseases and disorders affecting the abdomen, digestive tract, endocrine system, breast, skin and blood vessels. A general surgeon is also trained in the treatment of patients who are injured or critically ill, and in the care of pediatric and cancer patients. General surgeons are skilled in the use of minimally invasive techniques and endoscopies. abms.org An evaluation by a specialist who performs preoperative, operative, and postoperative management of patients with disorders of the arterial, venous and lymphatic systems, excluding vessels of the brain and the heart. 2020-07-10T19:54:59Z assessment by vascular surgeon evaluation by vascular surgeon referral by vascular surgeon vascular surgeon assessment vascular surgeon consultation vascular surgeon referral vascular surgeon evaluation Evaluation by a specialist who focuses on the operative, perioperative, and surgical critical care of patients with acquired and congenital pathologic conditions within the chest. 2020-07-10T20:40:44Z assessment by thoracic and cardiac surgeon assessment by thoracic surgeon consultation with thoracic and cardiac surgeon consultation with thoracic surgeon evaluation by thoracic and cardiac surgeon evaluation by thoracic surgeon referral to thoracic and cardiac surgeon referral to thoracic surgeon thoracic and cardiac surgeon assessment thoracic and cardiac surgeon consultation thoracic and cardiac surgeon referral thoracic surgeon assessment thoracic surgeon evaluation thoracic surgeon referral thoracic and cardiac surgeon evaluation Evaluation by a specialist who focuses on the operative, perioperative, and surgical critical care of patients with acquired and congenital pathologic conditions within the chest. abms.org An evaluation by a specialist that focuses on diagnosing and treating disorders of the urinary tracts of males and females, and on the reproductive system of males. This specialist manages non-surgical problems such as urinary tract infections and benign prostatic hyperplasia, as well as surgical problems such as the surgical management of cancers, the correction of congenital abnormalities, and correcting stress incontinence. 2020-07-10T20:44:20Z assessment by genitourinary surgeon assessment by urologist consultation with genitourinary surgeon consultation with urologist evaluation by genitourinary surgeon evaluation by urologist genitourinary surgeon consultation genitourinary surgeon evaluation referral to genitourinary surgeon referral to urologist urologist assessment urologist consultation urologist referral urologist evaluation An evaluation by a specialist that focuses on diagnosing and treating disorders of the urinary tracts of males and females, and on the reproductive system of males. This specialist manages non-surgical problems such as urinary tract infections and benign prostatic hyperplasia, as well as surgical problems such as the surgical management of cancers, the correction of congenital abnormalities, and correcting stress incontinence. abms.org 2020-07-13T17:01:27Z psychiatry and neurology specialist evaluation Assessment by a specialist who has expertise in the diagnosis and preoperative, operative, and postoperative management of patient care. 2020-07-13T17:57:48Z surgeon evaluation Assessment by a specialist who has expertise in the diagnosis and preoperative, operative, and postoperative management of patient care. abms.org A procedure, also known as sonohysterography or saline infusion sonography, using a minimally invasive ultrasound technique to view the inside of the uterus. Sterile saline is injected into the endometrial cavity thereby distending the endometrial cavity, providing good visualization of the anatomic structures within. 2020-07-16T14:18:41Z NCIT:C38066 diagnostic hysterosonography medical hysterosonography sonohysterography saline infusion sonography hysterosonography A procedure, also known as sonohysterography or saline infusion sonography, using a minimally invasive ultrasound technique to view the inside of the uterus. Sterile saline is injected into the endometrial cavity thereby distending the endometrial cavity, providing good visualization of the anatomic structures within. NCIT:C38066 An invasive procedure in which sound waves (called ultrasound) are bounced off of vascular tissues from within the vessel and the echoes produce a picture (sonogram). 2020-07-16T14:31:24Z NCIT:C99535 IVUS diagnostic intravascular ultrasound intravascular sonography intravascular ultrasound medical intravascular ultrasonography intravascular ultrasonography An invasive procedure in which sound waves (called ultrasound) are bounced off of vascular tissues from within the vessel and the echoes produce a picture (sonogram). NCIT:C99535 IVUS A technique in which sound waves are sent out by an ultrasound probe that has been inserted in the vagina and a computer uses the ultrasound echoes to create an image of the female genital tract. The test can be performed to evaluate women with infertility problems, abnormal bleeding, sources of unexplained pain, congenital malformations of the uterus and ovaries, and possible tumors and infection. 2020-07-16T14:38:38Z NCIT:C17644 TVS TVU diagnostic transvaginal ultrasound medical transvaginal sonography transvaginal sonography transvaginal ultrasound transvaginal ultrasound examination transvaginal ultrasonography A technique in which sound waves are sent out by an ultrasound probe that has been inserted in the vagina and a computer uses the ultrasound echoes to create an image of the female genital tract. The test can be performed to evaluate women with infertility problems, abnormal bleeding, sources of unexplained pain, congenital malformations of the uterus and ovaries, and possible tumors and infection. NCIT:C17644 TVS TVU A procedure that uses sound waves to create a video image of the pelvic organs and tissues. A small, lubricated probe placed into the rectum releases sound waves, which create echoes as they enter a pelvic organ. The echoes that bounce back are sent to a computer that translates the pattern of echoes into a picture of the specific organ under examination. This procedure is most often used to evaluate the prostate gland. 2020-07-16T14:46:48Z NCIT:C18315 ERUS TRUS diagnostic transrectal ultrasound endorectal sonography endorectal ultrasound endorectal ultrsonography medical transrectal ultrasound transrectal sonography transrectal ultrasound transrectal ultrasound examination transrectal ultrasonography A procedure that uses sound waves to create a video image of the pelvic organs and tissues. A small, lubricated probe placed into the rectum releases sound waves, which create echoes as they enter a pelvic organ. The echoes that bounce back are sent to a computer that translates the pattern of echoes into a picture of the specific organ under examination. This procedure is most often used to evaluate the prostate gland. NCIT:C18315 ERUS TRUS An evaluation or treatment by a professional who provides a range of diagnostic, technical, therapeutic, and support services in connection with health care. This is care provided by health care practitioners who are distinct providers from dentistry, nursing, medicine, and pharmacy health care professionals. 2020-10-06T17:59:44Z allied health clnicians support allied health practitioner consultation allied health practitioner evaluation allied health professional consultation assessment by allied health professional consulationat with allied health professional consultation with allied health practitioner evaluation by allied health professional evaluation managed by allied health professional support by allied health clinicians allied health professional evaluation An evaluation or assessment by a health professional trained to help people who are ill or disabled learn to manage their daily activities. 2020-10-06T19:51:46Z OT assessment OT consult OT eval OT evaluation OT treatment assessment by occupational therapist evaluation by occupational therapist managed by occupational therapist occupational therapist assessment occupational therapist consultation occupational therapist management occupational therapist treatment treatment by OT treatment by occupational therapist occupational therapist evaluation OT assessment OT consult OT eval OT evaluation OT treatment treatment by OT An assessment by a professional who works to prevent, assess, diagnose, and treat speech, language, social communication, congnitive-communication, and swallowing disorders. 2020-10-08T15:24:36Z assessment with speech therapist consult with speech therapist evaluation by speech and language therapist speech and language pathologist evaluation speech and language therapist evaluation speech therapist assessment speech therapist consultation speech therapist evaluation speech-language pathologist assessment speech-language pathologist examination speech/language pathologist evaluation speech/language therapist evaluation speech-language pathologist evaluation An assessment by a professional who works to prevent, assess, diagnose, and treat speech, language, social communication, congnitive-communication, and swallowing disorders. asha.org An assessment by a trained non-medical health professional who specializes in the identification, testing, habilitation and rehabilitation of hearing loss and other auditory and balance disorders. Particularly, an audiologist may be involved in diagnostic and screening procedures to determine hearing deficits, as well as in assessment of amplification devices and instruction in their care, training in speechreading, and may serve as consultant to government and industry on issues concerning environmental, noise-induced hearing loss. 2020-10-08T20:20:40Z NCIT:C51804 assessment by audiologist audilogic assessment audiologic evaluation audiology evaluation audiology examination evaluation by audiologist treatment by audiologist audiologist evaluation A therapy derived from fibric acid that lowers serum LDL cholesterol levels by activating peroxisome proliferator activated receptor alpha (PPARa). 2020-11-17T21:12:47Z NCIT:C98150 fibrate dyslipidemic agent therapy fibrate antilipidemic agent therapy Therapy using a highly charged polymeric agent to bind bile acids in the gastrointestinal tract and prevent their reabsorption from the gut. The bound bile acids are excreted with the feces and plasma cholesterol is converted to bile acid to reestablish normal bile acid levels, resulting in a lowering of plasma cholesterol concentrations. 2020-11-17T21:21:54Z bile-acid sequestrant agent therapy bile-acid sequestrant therapy treatment with bile-acid sequestrant bile acid sequestrant therapy Therapy that inhibits HMG-CoA reductase inhibitor. 2020-11-17T21:37:04Z EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor therapy hydroxymethylglutaryl-CoA reductase inhibitor therapy statin agent therapy treatment with EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor treatment with statins HMG-CoA reductase inhibitor therapy Treatment with an agent that works through, or mimics, the action of niacin. 2020-11-17T21:45:22Z CHEBI:15940 NCIT:C98151 niacin-based antilipidemic agent niacin agent therapy treatment with niacin An antilipidemic agent that works through, or mimics, the action of niacin to increase HDL-C levels by blocking hepatic uptake of apolipoprotein A-1 and decreasing HDL clearance. The use of free niacin is limited by its side effects of skin flushing (i.e., redness, itching, burning, and paresthesias) nicotinic acid agent therapy An antilipidemic agent that works through, or mimics, the action of niacin to increase HDL-C levels by blocking hepatic uptake of apolipoprotein A-1 and decreasing HDL clearance. The use of free niacin is limited by its side effects of skin flushing (i.e., redness, itching, burning, and paresthesias) NCIT:C98151 Treatment with a diuretic agent that produces diuresis without increasing potassium excretion. 2020-11-18T16:10:36Z NCIT:C49186 treatment with potassium-sparing diuretic Potassium sparing diuretics are generally either aldosterone antagonists and thus prevent the aldosterone-mediated promotion of sodium and water retention, or are epithelial sodium channel blockers and prevent the exchange of potassium for sodium in the distal convoluted tubule. These agents cause diuresis without increasing potassium secretion and thus do not cause hypokalemia. potassium-sparing diuretic agent therapy Potassium sparing diuretics are generally either aldosterone antagonists and thus prevent the aldosterone-mediated promotion of sodium and water retention, or are epithelial sodium channel blockers and prevent the exchange of potassium for sodium in the distal convoluted tubule. These agents cause diuresis without increasing potassium secretion and thus do not cause hypokalemia. NCIT:C49186 Treatment with a benzothiadiazide derivative or other thiazide-like agent with diuretic and anti-hypertensive activity. 2020-11-18T16:16:04Z NCIT:C49185 treatment with thiazide diuretic agent Thiazide diuretics inhibit the sodium-chloride transporter in the distal tubule in the kidneys, thereby suppressing sodium and chloride reabsorption from the distal convoluted tubules (DCT) and increasing the excretion of sodium, chloride, potassium and water. In addition, thiazide diuretics decrease excretion of calcium and uric acid. These agents cause vasodilation possibly by activating calcium-activated potassium channels in vascular smooth muscle and inhibiting various carbonic anhydrases in vascular tissue. thiazide diuretic agent therapy Thiazide diuretics inhibit the sodium-chloride transporter in the distal tubule in the kidneys, thereby suppressing sodium and chloride reabsorption from the distal convoluted tubules (DCT) and increasing the excretion of sodium, chloride, potassium and water. In addition, thiazide diuretics decrease excretion of calcium and uric acid. These agents cause vasodilation possibly by activating calcium-activated potassium channels in vascular smooth muscle and inhibiting various carbonic anhydrases in vascular tissue. NCIT:C49185 Treatment with sulfonamide urea derivatives with antihyperglycemic activity. 2020-11-18T16:22:03Z NCIT:C97936 sulfonylurea antidiabetic agent therapy treatment with sulfonylurea treatment with sulfonylurea agent Sulphonylurea antidiabetic agents bind to sulfonylurea receptor type 1 (SUR1), the subunit of ATP-sensitive inwardly-rectifier potassium (IKATP) channels on the membranes of pancreatic beta cells, thereby blocking the inward current flow (influx) of positively charged K+ ions into the cell. This results in tonic membrane depolarization, and induces a calcium ion influx through voltage-sensitive calcium channels; increased intracellular calcium ion levels trigger exocytosis of insulin-containing granules. This eventually induces secretion of insulin. The IKATP channels found in pancreatic islets are complexes of four IKATP 6.2 and four SUR1 subunits. In addition, some sulfonylureas of larger molecular size may increase the sensitivity of peripheral tissues to insulin mediated through peroxisome proliferator-activated receptor gamma (PPARgamma). sulfonylurea agent therapy Sulphonylurea antidiabetic agents bind to sulfonylurea receptor type 1 (SUR1), the subunit of ATP-sensitive inwardly-rectifier potassium (IKATP) channels on the membranes of pancreatic beta cells, thereby blocking the inward current flow (influx) of positively charged K+ ions into the cell. This results in tonic membrane depolarization, and induces a calcium ion influx through voltage-sensitive calcium channels; increased intracellular calcium ion levels trigger exocytosis of insulin-containing granules. This eventually induces secretion of insulin. The IKATP channels found in pancreatic islets are complexes of four IKATP 6.2 and four SUR1 subunits. In addition, some sulfonylureas of larger molecular size may increase the sensitivity of peripheral tissues to insulin mediated through peroxisome proliferator-activated receptor gamma (PPARgamma). NCIT:C97936 Treatment with estrogens or estrogen/progesterone after menopause or ovariectomy to prevent pathological effects of decreased estrogen production. 2020-11-19T16:03:14Z MHT menopausal hormone replacement therapy postmenopausal hormone therapy menopausal hormone therapy Treatment with estrogens or estrogen/progesterone after menopause or ovariectomy to prevent pathological effects of decreased estrogen production. NCIT:C15599 Techniques for analysis of chromosomal and subchromosomal properties and structures, such as those to diagnose, classify, screen for, or manage genetic diseases and abnormalities. 2020-11-19T19:13:57Z NCIT:C18280 cytogenetic study cytogenetic testing cytogenetic analysis Techniques for analysis of chromosomal and subchromosomal properties and structures, such as those to diagnose, classify, screen for, or manage genetic diseases and abnormalities. NCIT:C18280 A test to detect chromosomal breakage or aberrations (breaks, gaps, rearrangements, radials, exchanges, endoreduplications) in peripheral blood cells after culture with a T-cell mitogen and a DNA clastogenic (cross-linking) agent, such as diepoxybutane (DEB) or mitomycin C (MMC). 2020-11-19T19:24:16Z Chromosome Breakage Analysis (DEB/MMC) DEB/MMC testing chromosomal breakage testing induced chormosomal breakage testing chromosomal breakage analysis A test to detect chromosomal breakage or aberrations (breaks, gaps, rearrangements, radials, exchanges, endoreduplications) in peripheral blood cells after culture with a T-cell mitogen and a DNA clastogenic (cross-linking) agent, such as diepoxybutane (DEB) or mitomycin C (MMC). PMID:25006279 Transfer of multipotent hematopoietic stem cells, usually derived from bone marrow, peripheral blood, or umbilical cord blood into the body. 2020-11-19T19:56:02Z HPSCT HSCT hematopoietic stem cell transplantation HPSCT HSCT The transplantation of fecal bacteria, via enema, colonoscopy, or other method, from a healthy individual to a recipient. 2020-11-19T20:03:04Z FMT fecal material transplantation fecal transplantation stool transplantation fecal microbiota transplantation The transplantation of fecal bacteria, via enema, colonoscopy, or other method, from a healthy individual to a recipient. NCIT:C118643 FMT The removal of T-cells from the donor's hematopoietic stem cell specimen prior to its transfusion into the recipient. 2020-11-19T20:07:15Z NCIT:C116468 T cell-depleted hematopoietic stem cell transplantation The removal of T-cells from the donor's hematopoietic stem cell specimen prior to its transfusion into the recipient. NCIT:C116468 Administration of high doses of chemotherapy or radiation therapy, as well as immunosuppressive therapy, to a transplant recipient prior to a bone marrow or hematopoietic stem cell transplant. Conditioning destroys the patient's abnormal blood cells or cancer, as well as slows the patient's immune response against the donor bone marrow (graft rejection). 2020-11-19T20:12:40Z NCIT:C64468 conditioning regimen transplant conditioning Administration of high doses of chemotherapy or radiation therapy, as well as immunosuppressive therapy, to a transplant recipient prior to a bone marrow or hematopoietic stem cell transplant. Conditioning destroys the patient's abnormal blood cells or cancer, as well as slows the patient's immune response against the donor bone marrow (graft rejection). NCIT:C64468 The systematic collection, analysis, and interpretation of health data on an ongoing basis. 2020-11-19T20:25:20Z NCIT:C15719 clinical surveilance The systematic collection, analysis, and interpretation of health data on an ongoing basis. NCIT:C15719 Removal of a small amount of liquid bone marrow through a needle. 2020-11-19T20:31:02Z bone marrow aspiration procedure bone marrow aspiration The pathologic analysis of samples of bone marrow obtained by bone marrow biopsy and bone marrow aspiration. 2020-11-19T20:33:41Z bone marrow testing bone marrow monitoring bone marrow examination The determination of the amount of degree, quality or condition of cells present in a sample. 2020-11-19T20:39:47Z NCIT:C111153 cellularity grade measurement cellularity indexing cellularity measurement The determination of the amount of degree, quality or condition of cells present in a sample. NCIT:C111153 The sampling and analysis of non-solid biological tissue often through rapid and non-invasive methods, which allows the assessment in real-time of the evolving landscape of cancer. 2020-11-19T20:45:40Z solid tumor monitoring liquid biopsy The sampling and analysis of non-solid biological tissue often through rapid and non-invasive methods, which allows the assessment in real-time of the evolving landscape of cancer. PMID:32580740 The injection of whole blood or a blood component directly into the bloodstream. 2020-11-19T20:58:55Z transfusion NCIT:C15192 OGMS:0000145 transfusion of blood products blood component transfusion blood transfusion The injection of whole blood or a blood component directly into the bloodstream. NCIT:C15192 Any form of treatment that is introduced into the body via a blood vessel, a muscle, or the spinal cord. 2020-11-19T21:01:00Z NCIT:C15388 infusion infusion procedure Any form of treatment that is introduced into the body via a blood vessel, a muscle, or the spinal cord. NCIT:C15388 Avoid sexual intercourse without the use of precautions to prevent conception or the transmission of sexually transmitted diseases. 2020-11-19T21:20:20Z avoid unprotected sexual intercourse Vaccination against human papillomavirus infection. 2020-11-19T21:22:47Z VO:0000667 HPV vaccination human papillomavirus vaccination Addition of vitamin b12 to the diet for adequate and complete nutrition. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of vitamin b12 supplementation of vitamin b12 vitamin b12 supplemental intake vitamin b12 vitamin b12 supplementation Addition of vitamin B to the diet for adequate and complete nutrition. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of vitamin B supplementation of vitamin B vitamin B supplemental intake vitamin B vitamin B supplementation Intake of nutrients intravenously. 2020-11-30T16:40:53Z parenteral nutrition intake Intake of nutrients intravenously as well as enterically. 2020-11-30T16:43:26Z partial parenteral nutrition intake Intravenous nutrition intake administered via vein access in a limb. 2020-11-30T16:45:00Z PPN intake peripheral parenteral nutrition intake Intravenous nutrition administration via the central vein. 2020-11-30T16:46:01Z CVN intake central venous nutrition intake A recommendation to alter dietary intake where 30% or less of the calories come from fat. 2020-11-30T17:13:24Z NCBI:NBK553097 low fat diet intake Recommendation of a specific diet to adhere to prevent, relieve, or alleviate symptoms. 2020-11-30T17:15:20Z prescriptive dietary intake A recommendation to alter a standard diet from 2-3 large meals per day to many frequent smaller meals throughout the day. 2020-11-30T17:19:06Z frequent small meals recommendation small meal size recommendation A recommendation to maintain a vegetarian diet for health reasons. 2020-11-30T17:26:23Z vegetarian diet intake prescriptive vegetarian diet intake Dietary recommendation to closely control the amount of carbohydrates consumed. 2020-11-30T17:38:43Z NCBI:NBK537084 Very low-carbohydrate (< 10% carbohydrates) or 20-50 gm/day Low-carbohydrate (<26% carbohydrates) or less than < 130 gm/day Moderate-carbohydrate (26%-44%) High-carbohydrate (45% or greater) carbohydrate controlled diet intake Very low-carbohydrate (< 10% carbohydrates) or 20-50 gm/day Low-carbohydrate (<26% carbohydrates) or less than < 130 gm/day Moderate-carbohydrate (26%-44%) High-carbohydrate (45% or greater) NCBI:NBK537084 A dietary recommendation to restrict the amount of carbohydrates consumed. 2020-11-30T17:41:20Z carbohydrate restrictive diet intake low carbohydrate diet intake carbohydrate-restricted diet intake A recommendation to consume food low in purine content. 2020-11-30T17:50:25Z low intake of purine-rich diet low intake of purine-rich food purine restrictive diet intake low purine diet intake A recommendation to adhere to Dietary Approaches to Stop Hypertension (DASH) diet. The diet promotes consumption of vegetables and fruits, lean meat and dairy products, and the inclusion of micronutrients and the reduction of sodium in the diet to about 1500 mg/day. 2020-11-30T18:26:25Z dietary approaches to stop hypertension diet intake DASH diet intake A recommendation to adhere to Dietary Approaches to Stop Hypertension (DASH) diet. The diet promotes consumption of vegetables and fruits, lean meat and dairy products, and the inclusion of micronutrients and the reduction of sodium in the diet to about 1500 mg/day. NCBI:NBK482514 Exclusively feeding an infant formula in efforts to prevent allergic reactions, intolerances, or communication of diseases (i.e. HIV) through feeding human milk. 2020-11-30T18:51:35Z EFF exclusive formula feeding Exclusively feeding an infant formula in efforts to prevent allergic reactions, intolerances, or communication of diseases (i.e. HIV) through feeding human milk. PMID:23711175 EFF A diet low in poorly absorbed, fermentable, short chain carbohydrates including fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) intended to reduce bloating, abdominal pain, excessive flatus and altered bowel habit. 2020-11-30T19:48:31Z low FODMAP diet intake A diet low in poorly absorbed, fermentable, short chain carbohydrates including fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) intended to reduce bloating, abdominal pain, excessive flatus and altered bowel habit. PMID:28244669 Addition of iron to the diet by taking ferrous sulfate supplements. 2020-12-07T19:35:36Z slow release iron supplementation ferrous sulfate supplementation A type of MRI that takes a series of images of an organ in quick succession and statistically analyzes the differences between the images. 2019-04-26T20:04:29Z NCIT:C17958 Functional MRI fMRI functional magnetic resonance imaging procedure A type of MRI that takes a series of images of an organ in quick succession and statistically analyzes the differences between the images. NCIT:C17958 Functional MRI fMRI Gene therapy involves the use of nucleic acids (DNA or RNA) for the treatment, cure or prevention of human disorders. 2019-05-07T16:28:50Z NCIT:C15238 SCDO:0001344 DNA therapy gene therapies gene transfer procedure genetic therapy gene therapy Gene therapy involves the use of nucleic acids (DNA or RNA) for the treatment, cure or prevention of human disorders. PMID:24106209 The goal of immunotherapy is to induce anti-disease (usually tumor) responses by reprogramming and augmenting immune surveillance, and reducing immune suppression. 2019-05-07T16:32:45Z NCIT:C15262 OGMS:0000114 immune therapy immunologically directed therapy immunotherapy procedure The goal of immunotherapy is to induce anti-disease (usually tumor) responses by reprogramming and augmenting immune surveillance, and reducing immune suppression. PMID:29242097 2019-05-15T16:33:57Z alcohol deterrent drug treatment alcohol deterrent agent therapy 2019-05-15T16:44:49Z smoking cessation drug treatment smoking cessation agent therapy An agent that binds to but does not activate an opioid receptor thereby blocking the actions of endogenous or exogenous opioid receptor agonists. 2019-05-15T16:45:09Z CHEBI:60605 NCIT:C681 opiate antagonist agent therapy opioid antagonist drug treatment opioid antagonist agent therapy An agent that binds to but does not activate an opioid receptor thereby blocking the actions of endogenous or exogenous opioid receptor agonists. CHEBI:60605 The determination of the number of red blood cells, white blood cells, and platelets in a blood sample. 2019-05-16T18:09:14Z NCIT:C28133 CBC complete blood count full blood count blood cell count The determination of the number of red blood cells, white blood cells, and platelets in a blood sample. NCIT:C28133 CBC The determination of the number of erythrocytes in a blood sample. 2019-05-16T18:18:55Z NCIT:C51946 RBC red blood cell count red cell count erythrocyte count The determination of the number of erythrocytes in a blood sample. NCIT:C51946 RBC The determination of the number of platelets in a blood sample, usually expressed as platelets per cubic millimeter (cmm) of whole blood. 2019-05-16T18:20:55Z NCIT:C51951 thrombocyte count platelet count The determination of the number of platelets in a blood sample, usually expressed as platelets per cubic millimeter (cmm) of whole blood. NCIT:C51951 2019-05-16T18:24:56Z A test to determine the number of neutrophils in a sample of blood. neutrophil count A test to determine the number of leukocytes in a sample of blood. 2019-05-16T18:25:40Z NCIT:C51948 WBC white blood cell count leukocyte count A test to determine the number of leukocytes in a sample of blood. NCIT:C51948 WBC 2019-06-12T14:22:47Z medical action avoidance Avoid the administration or use of aerobic exercise therapy. 2019-05-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid aerobic exercise therapy avoiding aerobic exercise therapy aerobic exercise therapy avoidance Inoculating an individual with either killed or live agents to prevent contraction of a disease. 2019-06-14T15:47:12Z EFO:0004292 IDOMAL:0001040 NCIT:C15258 VO:0000002 vaccination Inoculating an individual with either killed or live agents to prevent contraction of a disease. NCIT:C15258 Nutrition intake is the process of taking in of nutrients, especially by eating or drinking, considered in relation to the body’s dietary needs. 2019-07-23T18:14:54Z nutrient consumption nutrient intake nutrition consumption nutritional intake take nourishment dietary intake eating food consumption food intake ingesting nutrition intake Nutrition intake is the process of taking in of nutrients, especially by eating or drinking, considered in relation to the body’s dietary needs. http://orcid.org/0000-0001-7941-2961 Addition of vitamin supplement, prenatal to the diet for adequate and complete nutrition. 2019-07-23T19:56:32Z NCIT:C92860 antenatal supplementation antenatal vitamin supplement treatment antenatal vitamin treatment dietary supplementation of vitamin supplement, prenatal prenatal vitamin supplement treatment supplementation of vitamin supplement, prenatal treatment with prenatal supplements vitamin supplement, prenatal supplemental intake A vitamin enriched supplement containing higher doses for specific nutrients such as folic acid, intended for women before, during and after pregnancy and also during their lactating phase. vitamin supplement, prenatal prenatal vitamin supplementation A vitamin enriched supplement containing higher doses for specific nutrients such as folic acid, intended for women before, during and after pregnancy and also during their lactating phase. NCIT:C92860 A therapy utilizing a substance that produces loss of consciousness. 2019-07-24T15:53:13Z CHEBI:38869 general anaesthetic agents therapy general anaesthetic medication therapy general anaesthetic therapy general anaesthetics therapy general anesthesia therapy general anesthesia treatment general anesthetic medication therapy general anesthetics therapy treatment with general anaesthetic general anesthetic agent therapy Use of a drug or therapy to treat or prevent microbial infections. 2019-07-24T16:13:47Z CHEBI:36043 antimicrobial drug therapy antimicrobial drug treatment antimicrobial treatment treatment with an anti-microbial agent treatment with an anti-microbial drug treatment with an anti-microbial medication treatment with an antimicrobial agent treatment with an antimicrobial drug treatment with an antimicrobial medication treatment with antimicrobial drug antimicrobial agent therapy A loosely defined grouping of drugs that have effects on psychological function. 2019-07-24T19:33:44Z CHEBI:35471 psychoactive agent therapy psychoactive drug treatment psychopharmaceutical therapy psychotropic agent drug therapy psychotropic drug therapy psychotropic drug treatment treatment with psychotropic drug psychotropic agent therapy A loosely defined grouping of drugs that have effects on psychological function. CHEBI:35471 Treatment with a traditional grouping of drugs said to have a soothing or calming effect on mood, thought or behavior. 2019-07-24T19:39:15Z CHEBI:35473 ataractic agents tranquilisers tranquilising agents tranquilising drug tranquilizers tranquilizing agent tranquilizing drug tranquilizing drug therapy tranquilizing drugs treatment with tranquilizing drug tranquilizing agent therapy Therapy using any agent that acts on an adrenergic receptor or affects adrenergic signal transduction. 2019-07-25T14:32:48Z CHEBI:37962 NCIT:C29747 adrenergic agent drug treatment adrenergic agent therapy adrenergic drug therapy treatment with adrenergic agent treatment with adrenergic drug treatment with adrenergic medication adrenergic agent therapy An agent that selectively binds to and activates beta-adrenergic receptors. 2019-07-25T14:42:00Z CHEBI:35522 b-adrenergic agonist b-adrenergic receptor agonist beta adrenergic receptor agonist beta-adrenergic agonist beta-adrenergic agonist agent beta-adrenergic agonist drugs beta-adrenergic agonist therapy beta-adrenergic agonists beta-adrenergic receptor agonist drugs beta-adrenergic receptor agonist beta-adrenoceptor agonists treatment with beta-adrenergic agonist treatment with beta-adrenergic agonist agent treatment with beta-adrenergic agonist drug treatment with beta-adrenergic agonist medication beta-adrenergic agonist agent therapy An agent that selectively binds to and activates beta-adrenergic receptors. CHEBI:35522 The surgical removal (cutting out) of part or all of pharyngeal tonsil. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C51697 adenoid removal pharyngeal tonsil surgical removal removal of adenoids removal of nasopharyngeal tonsil removal of tonsil of Luschka removal of tonsilla pharyngealis adenoidectomy The surgical removal (cutting out) of part or all of adrenal gland. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 adrenal gland surgical removal adrenalectomy The surgical removal (cutting out) of part or all of tooth root. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 tooth root surgical removal apicoectomy The surgical removal (cutting out) of part or all of vermiform appendix. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C51687 appendicectomy appendix removal removal of appendix vermiform appendix surgical removal appendectomy The surgical removal (cutting out) of part or all of skeletal joint. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 removal of a joint skeletal joint surgical removal arthectomy The surgical removal (cutting out) of part or all of ear. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 ear surgical removal auriculectomy The surgical removal (cutting out) of part or all of synovial bursa. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 bursa removal removal of bursa synovial bursa surgical removal bursectomy The surgical removal (cutting out) of part or all of cardia of stomach. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 cardia of stomach surgical removal cardiectomy cardiectomy of stomach gastric cardiectomy The surgical removal (cutting out) of part or all of head. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 decapitation head surgical removal cephalectomy The surgical removal (cutting out) of part or all of uterine cervix. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 cervix removal removal of cervix uterine cervix surgical removal cervicectomy The surgical removal (cutting out) of part or all of gall bladder. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C51676 gall bladder surgical removal cholecystectomy The surgical removal (cutting out) of part or all of optic choroid. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 optic choroid surgical removal removal of choroid layer of they eye choroidectomy The surgical removal (cutting out) of part or all of clitoris. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 clitorectomy clitoris surgical removal clitoridectomy The surgical removal (cutting out) of part or all of colon. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C15209 colon surgical removal colectomy The surgical removal (cutting out) of part or all of cranium. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C51791 cranium surgical removal craniectomy The surgical removal (cutting out) of part or all of urinary bladder. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C15217 bladder removal removal of the bladder urinary bladder surgical removal Can mean the removal of the urinary bladder or the surgical removal of a cyst. cystectomy The surgical removal (cutting out) of part or all of bony vertebral centrum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 body of vertebrae removal bony vertebral centrum surgical removal corpus vertebra removal corpus vertebrae removal vertebral body removal vertebrectomy corpectomy The surgical removal (cutting out) of part or all of intervertebral disk. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C21009 intervertebral disk surgical removal removal of intervertebral disc removal of spinal disc discectomy The surgical removal (cutting out) of part or all of digestive tract diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 digestive tract diverticulum surgical removal digestive tract diverticulectomy The surgical removal (cutting out) of part or all of thyroid diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 thyroid diverticulum surgical removal thyroid diverticulectomy The surgical removal (cutting out) of part or all of hepatic diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 hepatic diverticulum surgical removal hepatic diverticulectomy The surgical removal (cutting out) of part or all of duodenum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 duodenum surgical removal enterectomy small bowel resection duodenectomy The surgical removal (cutting out) of part or all of sympathetic nerve trunk. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 sympathetic nerve trunk surgical removal endoscopic thoracic sympathectomy The surgical removal (cutting out) of part or all of esophagus. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 esophagus surgical removal oesophagectomy esophagectomy The surgical removal (cutting out) of part or all of stomach. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 stomach surgical removal gastrectomy The surgical removal (cutting out) of part or all of tongue. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 tongue surgical removal glossectomy The surgical removal (cutting out) of part or all of gonad. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 gonad surgical removal gonadectomy The surgical removal (cutting out) of part or all of liver. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 liver surgical removal hepatectomy The surgical removal (cutting out) of part or all of pituitary gland. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 hypophysis removal pituitary gland surgical removal hypophysectomy The surgical removal (cutting out) of part or all of uterus. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 uterus surgical removal hysterectomy The surgical removal (cutting out) of part or all of iris. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 iris surgical removal iridectomy The surgical removal (cutting out) of part or all of cornea. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 cornea surgical removal keratectomy The surgical removal (cutting out) of part or all of vertebra. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 vertebra surgical removal laminectomy The surgical removal (cutting out) of part or all of larynx. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 larynx surgical removal lymph node dissection laryngectomy The surgical removal (cutting out) of part or all of lymph node. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 lymph node surgical removal lymphadenectomy The surgical removal (cutting out) of part or all of breast. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 breast surgical removal mastectomy The surgical removal (cutting out) of part or all of kidney. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 kidney surgical removal nephrectomy The surgical removal (cutting out) of part or all of nerve. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 nerve surgical removal neurectomy The surgical removal (cutting out) of part or all of ovary. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 female gonad removal ovariectomy ovary surgical removal removal of female genitalia removal of female gonad removal of female reproductive system gonada removal of gonada of female oophorectomy The surgical removal (cutting out) of part or all of testis. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 castration orchidectomy removal of male genitalia gonad removal of testicles testis surgical removal orchiectomy The surgical removal (cutting out) of part or all of bone tissue. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 bone tissue surgical removal ostectomy The surgical removal (cutting out) of part or all of pancreas. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 pancreas surgical removal pancreatectomy The surgical removal (cutting out) of part or all of panniculus adiposus. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C51597 panniculus adiposus surgical removal abdominal panniculectomy The surgical removal (cutting out) of part or all of parathyroid gland. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 parathyroid gland surgical removal parathyroid removal parathyroidectomy The surgical removal (cutting out) of part or all of pineal body. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 pineal body surgical removal removal of pineal gland pinealectomy The surgical removal (cutting out) of part or all of lung. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 lung surgical removal pneumectomy pneumonectomy The surgical removal (cutting out) of part or all of skin of prepuce of penis. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 circumcision forskin removal skin of prepuce of penis surgical removal posthectomy The surgical removal (cutting out) of part or all of fallopian tube. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 fallopian tube surgical removal salpingectomy The surgical removal (cutting out) of part or all of spleen. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 spleen surgical removal splenectomy The surgical removal (cutting out) of part or all of synovial membrane of synovial joint. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 synovial membrane of synovial joint surgical removal synovectomy The surgical removal (cutting out) of part or all of thymus. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 thymus surgical removal thymectomy The surgical removal (cutting out) of part or all of thyroid gland. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 thyroid gland surgical removal thyroidectomy The surgical removal (cutting out) of part or all of palatine tonsil. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 palatine tonsil surgical removal tonsillectomy The surgical removal (cutting out) of part or all of eye trabecular meshwork. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 eye trabecular meshwork surgical removal trabeculectomy The surgical removal (cutting out) of part or all of vagina. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 vagina surgical removal vaginectomy The surgical removal (cutting out) of part or all of vas deferens. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 vas deferens surgical removal vasectomy The surgical removal (cutting out) of part or all of vitreous humor. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 vitreous humor surgical removal vitrectomy The surgical removal (cutting out) of part or all of mammalian vulva. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 mammalian vulva surgical removal vulvectomy The surgical removal (cutting out) of part or all of penis. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 penis surgical removal penectomy The surgical removal (cutting out) of part or all of Pulmonary bulla. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Pulmonary bulla surgical removal bullectomy The surgical removal (cutting out) of part or all of Hallux valgus. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C96171 Hallux valgus surgical removal bunion removal removal of bunion bunionectomy Surgical removal of an abnormal pouch of the lining of the small intestine (bowel). 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Meckel diverticulum surgical removal Meckel's diverticulectomy The surgical removal (cutting out) of part or all of Cardiac diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Cardiac diverticulum surgical removal cardiac diverticulectomy The surgical removal (cutting out) of part or all of Esophageal diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Esophageal diverticulum surgical removal esophageal diverticulectomy The surgical removal (cutting out) of part or all of Gastric diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Gastric diverticulum surgical removal gastric diverticulectomy The surgical removal (cutting out) of part or all of Renal diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Renal diverticulum surgical removal renal diverticulectomy The surgical removal (cutting out) of part or all of Bladder diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Bladder diverticulum surgical removal bladder diverticulectomy The surgical removal (cutting out) of part or all of Urethral diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Urethral diverticulum surgical removal uethral diverticulectomy The surgical removal (cutting out) of part or all of Fibrous cardiac diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Fibrous cardiac diverticulum surgical removal fibrous cardiac diverticulectomy The surgical removal (cutting out) of part or all of Muscular cardiac diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Muscular cardiac diverticulum surgical removal muscular cardiac diverticulectomy The surgical removal (cutting out) of part or all of Spinal meningeal diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Spinal meningeal diverticulum surgical removal spinal meningeal diverticulectomy The surgical removal (cutting out) of part or all of Coronary sinus diverticulum. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Coronary sinus diverticulum surgical removal coronary sinus diverticulectomy The surgical removal (cutting out) of part or all of Thromboembolism. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Thromboembolism surgical removal thromboembolectomy The surgical removal (cutting out) of part or all of Pulmonary embolism. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 Pulmonary embolism surgical removal pulmonary embolectomy The surgical removal (cutting out) of part or all of Arterial calcification. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C52002 Arterial calcification surgical removal endarterectomy The surgical removal (cutting out) of part or all of Neoplasm of the breast. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C15755 Neoplasm of the breast surgical removal breast segmental resection breast wide local lumpectomy of breast excision partial mastectomy tylectomy Surgery to remove abnormal tissue or cancer from the breast and a small amount of normal tissue around it. It is a type of breast-sparing surgery. NCIT:C15755 lumpectomy The surgical removal (cutting out) of part or all of Uterine leiomyoma. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C51645 Uterine leiomyoma surgical removal fiboroidectomy removal of uterine fibroids myomectomy The surgical removal (cutting out) of part or all of Arterial thrombosis. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2962 Arterial thrombosis surgical removal arterial thrombosis The surgical removal (cutting out) of part or all of Venous thrombosis. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2963 Venous thrombosis surgical removal venous thrombosis The surgical removal (cutting out) of part or all of Abnormal thrombosis. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2964 Abnormal thrombosis surgical removal removal of thrombosis thrombosis removal thrombosis The surgical removal (cutting out) of part or all of Neoplasm. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2965 Neoplasm surgical removal cancer removal removal of tumor tumor removal tumorectomy The surgical removal (cutting out) of part or all of gland. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 gland surgical removal adenectomy obsolete kidney ct false A medical requirement or recommendation to avoid abnormal phenotypes. 2020-09-15T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid phenotype abnormality abnormal phenotype avoidance A medical requirement or recommendation to avoid ketosis. 2020-09-15T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid ketosis ketosis avoidance A medical requirement or recommendation to avoid diabetes. 2020-09-15T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid diabetes diabetes avoidance A medical requirement or recommendation to avoid a febrile state. 2020-09-15T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid febrile state avoid fever fever avoidance A medical requirement or recommendation to avoid seizures. 2020-09-15T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid seizure Recommendation to avoid triggers known to cause seizures or take medicine to avoid seizures. seizure avoidance A medical requirement or recommendation to avoid hypotension. 2020-09-15T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid hypotension hypotension avoidance A medical requirement or recommendation to avoid hyperglycemia. 2020-09-15T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid hyperglycemia hyperglycemia avoidance A medical requirement or recommendation to avoid weight loss 2020-09-15T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid weight loss weight loss avoidance Removal of tissue from the kidney. 2020-06-23T20:39:14Z http://orcid.org/0000-0001-7941-2961 kidney biopsy biopsy of kidney The use of computed tomography to produce images of structures of the kidney. 2020-06-9T20:39:14Z http://orcid.org/0000-0001-7941-3010 CAT scan of kidney CT of kidney kidney CAT scan kidney CT examination kidney computed tomography kidney computerized axial tomography renal CAT scan renal CT kidney CT Addition of potassium atom to a the diet for complete nutrition support. 2020-11-17T02:36:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of potassium dietary supplementation of potassium atom potassium atom supplemental intake supplementation of potassium supplementation of potassium atom potassium supplementation 2020-11-17T11:00:00Z http://orcid.org/0000-0001-7941-2961 anticholesteremic drug therapy antihypercholesterolemic agent therapy cholesterol inhibitor therapy hypocholesteremic agent therapy treatment with anticholesteremic drug anticholesteric agent therapy Therapy with an agent that inhibits the function of the sodium-potassium-chloride (Na+, K+, Cl-) cotransporter system in the thick ascending limb of the loop of Henle, thereby inhibiting the reabsorption of sodium, potassium, and chloride ions. This leads to an increase in the excretion of sodium, potassium, chloride, calcium, magnesium, ammonium and water. 2020-11-17T11:00:00Z http://orcid.org/0000-0001-7941-2961 loop diuretic therapy treatment with loop diuretic loop diuretic agent therapy Avoid the administration or use of blood transfusion. 2020-11-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid blood transfusion avoiding blood transfusion blood transfusion avoidance Avoid the administration or use of radiograph imaging procedure. 2020-11-19T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid radiograph imaging procedure avoiding radiograph imaging procedure radiograph imaging procedure avoidance Addition of folic acid to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of folic acid folic acid supplemental intake supplementation of folic acid folic acid supplementation Addition of Vitamin to the diet for adequate and complete nutrition. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 Vitamin supplemental intake dietary supplementation of Vitamin supplementation of Vitamin supplementation with vitamin Vitamin vitamin supplementation Addition of nicotinic acid to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of nicotinic acid niacin supplementation nicotinic acid supplemental intake supplementation of nicotinic acid nicotinic acid supplementation Addition of pyridoxine to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of pyridoxine pyridoxine supplemental intake supplementation of pyridoxine pyridoxine supplementation A medical requirement or recommendation of avoiding the consumption of purine. 2020-11-30T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid purine intake avoiding dietary purine intake purine consumption avoidance purine restricted diet intake purine restriction dietary purine intake avoidance Addition of ascorbic acid to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 ascorbic acid supplemental intake dietary supplementation of ascorbic acid supplementation of ascorbic acid ascorbic acid supplementation Addition of sodium pyruvate to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of sodium pyruvate sodium pyruvate supplemental intake supplementation of sodium pyruvate sodium pyruvate supplementation Addition of fat-soluble vitamin to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of fat-soluble vitamin essential fat soluble vitamin supplementation fat-soluble vitamin supplemental intake supplementation of essential fat soluble vitamin supplementation of fat-soluble vitamin fat-soluble vitamin supplementation Addition of S-adenosyl-L-methionine to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 S-adenosyl-L-methionine supplemental intake SAM-e supplementation dietary supplementation of S-adenosyl-L-methionine supplementation of S-adenosyl-L-methionine S-adenosyl methionine supplementation Addition of isoleucine to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of isoleucine isoleucine supplemental intake supplementation of isoleucine isoleucine supplementation Addition of valine to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of valine supplementation of valine valine supplemental intake valine supplementation Addition of calcium atom to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 calcium atom supplemental intake dietary supplementation of calcium atom supplementation of calcium atom supplementation with calcium calcium supplementation Addition of calcium carbonate to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 calcium carbonate supplemental intake dietary supplementation of calcium carbonate supplementation of calcium carbonate calcium carbonate supplementation Addition of glucose to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of glucose glucose supplemental intake supplementation of glucose glucose supplementation Addition of docosahexaenoic acid to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 DHA supplementtion dietary supplementation of docosahexaenoic acid docosahexaenoic acid supplemental intake supplementation of docosahexaenoic acid supplementation with DHA docosahexaenoic acid supplementation Addition of omega-3 fatty acid to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of omega-3 fatty acid eicosapentaenoic acid supplementation omega-3 fatty acid supplemental intake supplementation of omega-3 fatty acid omega-3 fatty acid supplementation Addition of lutein to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of lutein lutein supplemental intake supplementation of lutein lutein supplementation Addition of ribose to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of ribose ribose supplemental intake supplementation of ribose ribose supplementation Addition of fluoride to a the diet for complete nutrition support. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of fluoride fluoride supplemental intake supplementation of fluoride fluoride supplementation Addition of dietary supplement, fibre to the diet for adequate and complete nutrition. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplement, fibre supplemental intake dietary supplementation of dietary supplement, fibre supplementation of dietary supplement, fibre supplementation with soluble fiber dietary supplement, fibre soluble fiber supplementation Addition of fish oil to the diet for adequate and complete nutrition. 2020-11-23T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of fish oil fish oil supplemental intake supplementation of fish oil fish oil fish oil supplementation Addition of magnesium atom to a the diet for complete nutrition support. 2020-11-30T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of magnesium atom magnesium atom supplemental intake magnesium supplemental intake supplementation of magnesium supplementation of magnesium atom magnesium supplementation A medical requirement or recommendation of avoiding cannabis consumption. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid cannabis consumption cessation of cannabis consumption cannabis consumption avoidance A medical requirement or recommendation of avoiding tobacco consumption. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid tobacco consumption cessation of tobacco consumption tobacco consumption avoidance A medical requirement or recommendation of avoiding smoking behavior. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid smoking behavior cessation of smoking behavior smoking behavior avoidance A medical requirement or recommendation of avoiding consumption of an addictive substance. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid consumption of an addictive substance cessation of consumption of an addictive substance consumption of an addictive substance avoidance A medical requirement or recommendation of avoiding agitation behavior. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid agitation behavior agitation avoidance A medical requirement or recommendation of avoiding fear/anxiety related behavior. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid fear/anxiety related behavior fear or anxiety avoidance A medical requirement or recommendation of avoiding sexual activity. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sexual activity sexual activity avoidance A medical requirement or recommendation of avoiding copulation. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid copulation copulation avoidance A medical requirement or recommendation of avoiding stress related behavior. 2020-01-28T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid stress related behavior stress avoidance A medical requirement or recommendation of avoiding the consumption of gluten. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 avoid gluten intake avoiding gluten intake celiac dietary intake gluten consumption avoidance gluten-free dietary intake Intake may interfere with disease treatment, prolong the recovery phase, or cause complications. gluten intake avoidance A medical requirement or recommendation of avoiding the consumption of liquid. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 avoid liquid intake avoiding liquid intake liquid consumption avoidance liquid intake avoidance A medical requirement or recommendation of avoiding the consumption of protein extract, concentrate or isolate. 2019-11-13T02:36:00Z http://orcid.org/0000-0001-7941-2961 avoid protein extract, concentrate or isolate intake avoiding protein extract, concentrate or isolate intake protein extract, concentrate or isolate consumption avoidance protein intake avoidance A medical requirement or recommendation of avoiding the consumption of fat or oil. 2019-11-13T02:36:00Z http://orcid.org/0000-0001-7941-2961 avoid fat or oil intake avoiding fat or oil intake fat or oil consumption avoidance limited fat dietary intake low fat dietary intake non-fat dietary intake fat or oil intake avoidance Addition of amino-acid betaine to a the diet for complete nutrition support. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 amino-acid betaine supplemental intake dietary supplementation of amino-acid betaine supplementation of amino-acid betaine supplementation with betaine betaine supplementation Addition of folates to a the diet for complete nutrition support. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of folates folates supplemental intake supplementation of folates supplementation with folate folate supplementation Addition of carnitine to a the diet for complete nutrition support. 2019-11-13T02:36:00Z http://orcid.org/0000-0001-7941-2961 carnitine supplemental intake dietary supplementation of carnitine supplementation of carnitine carnitine supplementation Addition of methionine to a the diet for complete nutrition support. 2019-11-13T02:36:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of methionine methionine supplemental intake supplementation of methionine methionine supplementation Addition of creatine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 creatine supplemental intake dietary supplementation of creatine supplementation of creatine creatine supplementation Addition of arginine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 arginine supplemental intake dietary supplementation of arginine supplementation of arginine arginine supplementation Addition of biotins to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 biotins supplemental intake dietary supplementation of biotins supplementation of biotins biotin supplementation Addition of chenodeoxycholic acid to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 chenodeoxycholic acid supplemental intake dietary supplementation of chenodeoxycholic acid supplementation of chenodeoxycholic acid chenodeoxycholic acid supplementation Addition of coenzyme Q10 to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 coenzyme Q10 supplemental intake dietary supplementation of coenzyme Q10 supplementation of coenzyme Q10 coenzyme Q10 supplementation Addition of glycine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of glycine glycine supplemental intake supplementation of glycine glycine supplementation Addition of N-acetyl-L-cysteine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 N-acetyl-L-cysteine supplemental intake dietary supplementation of N-acetyl-L-cysteine supplementation of N-acetyl-L-cysteine N-acetyl-L-cysteine supplementation Addition of ornithine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of ornithine ornithine supplemental intake supplementation of ornithine ornithine supplementation Addition of riboflavin to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of riboflavin riboflavin supplemental intake supplementation of riboflavin riboflavin supplementation Addition of vitamin B6 to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of vitamin B6 supplementation of vitamin B6 vitamin B6 supplemental intake vitamin B6 supplementation Addition of citrulline to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 citrulline supplemental intake dietary supplementation of citrulline supplementation of citrulline citrulline supplementation Addition of thiamine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of thiamine supplementation of thiamine thiamine supplemental intake thiamine supplementation Addition of amino acid to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 NCIT:C15509 amino acid supplemental intake dietary supplementation of amino acid supplementation of amino acid A concentrated dietary supplement for injection containing the essential amino acids leucine, isoleucine, lysine, valine, phenylalanine, histidine, threonine, methionine and tryptophan as well as the non-essential amino acids alanine, arginine, glycine, proline, serine and tyrosine, with potential anabolic and anti-catabolic activities. Upon dilution and intravenous infusion of the amino acid nutritional supplement, the amino acids serve as protein building blocks, promote protein synthesis in muscle cells and prevent protein breakdown. NCIT:C15509 amino acid supplementation Addition of L-serine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 L-serine supplemental intake dietary supplementation of L-serine supplementation of L-serine serine supplementation Addition of uridine to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of uridine supplementation of uridine uridine supplemental intake uridine supplementation Addition of medium-chain fatty acid to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of medium-chain fatty acid medium-chain fatty acid supplemental intake supplementation of medium-chain fatty acid medium-chain fatty acid supplementation Addition of essential fatty acid to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of essential fatty acid essential fatty acid supplemental intake supplementation of essential fatty acid essential fatty acid supplementation Addition of cholesterol to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 cholesterol supplemental intake dietary supplementation of cholesterol supplementation of cholesterol cholesterol supplementation Addition of elemental zinc to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of elemental zinc elemental zinc supplemental intake supplementation of elemental zinc elemental zinc supplementation Addition of hydroxocobalamin to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of hydroxocobalamin hydroxocobalamin supplemental intake supplementation of hydroxocobalamin hydroxocobalamin supplementation Addition of cyanocob(III)alamin to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 cyanocob(III)alamin supplemental intake dietary supplementation of cyanocob(III)alamin supplementation of cyanocob(III)alamin cyanocobalamin supplementation Addition of methylcobalamin to a the diet for complete nutrition support. 2019-11-13T04:45:00Z http://orcid.org/0000-0001-7941-2961 dietary supplementation of methylcobalamin methylcobalamin supplemental intake supplementation of methylcobalamin methylcobalamin supplementation The surgical transfer of a healthy bone marrow to a patient. 2019-07-11T09:00:01Z http://orcid.org/0000-0001-7941-2961 NCIT:C15194 bone marrow grafting transplantation of bone marrow bone marrow transplantation The surgical transfer of a healthy bone tissue to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of bone tissue bone grafting The surgical transfer of a healthy heart to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 NCIT:C15246 heart transplantation transplantation of heart cardiac transplantation The surgical transfer of a healthy umbilical cord blood to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 UCBT cord blood transplantation transplantation of umbilical cord blood umbilical cord blood transplantation The surgical transfer of a healthy cornea to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 NCIT:C50514 transplantation of cornea corneal transplantation The surgical transfer of a healthy dura mater to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 dura mater transplantation transplantation of dura mater dura mater graft The surgical transfer of a healthy intestine to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of intestine intestinal transplantation The surgical transfer of a healthy small intestine to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 small bowel transplantation transplantation of small intestine small intestine transplantation The surgical transfer of a healthy lung to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 NCIT:C15274 lung transplantation surgical procedure transplantation of lung lung transplantation The transfer of an organ, or organ subpart, from one body to another. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 NCIT:C122934 organ graft transplantation of organ organ transplantation The surgical transfer of a healthy ovary to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 ovary transplantation transplantation of ovary ovarian transplantation The surgical transfer of a healthy zone of skin to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 NCIT:C15325 skin transplantation transplantation of zone of skin skin grafting The surgical transfer of a healthy thymus to a patient. 2020-01-20T10:00:01Z http://orcid.org/0000-0001-7941-2961 transplantation of thymus thymic transplantation The surgical transfer of a healthy kidney to a patient. 2020-04-07T10:00:01Z http://orcid.org/0000-0001-7941-2961 NCIT:C15265 kidney grafting renal transplantation transplantation of kidney kidney transplantation A medical requirement or recommendation of avoiding the consumption of alcoholic beverage. 2019-11-18T11:00:00Z http://orcid.org/0000-0001-7941-2961 alcoholic beverage consumption avoidance avoid alcoholic beverage intake avoiding alcoholic beverage intake alcohol intake avoidance A medical requirement or recommendation of avoiding the consumption of broad bean (whole). 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid broad bean (whole) intake avoiding broad bean (whole) intake broad bean (whole) consumption avoidance fava bean avoidance fava bean consumption avoidance windsor bean intake avoidance fava bean intake avoidance A medical requirement or recommendation of avoiding the consumption of meat food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid meat food product intake avoiding meat food product intake meat food product consumption avoidance meat food product intake avoidance A medical requirement or recommendation of avoiding the consumption of nut food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid nut food product intake avoiding nut food product intake nut food product consumption avoidance nut food product intake avoidance A medical requirement or recommendation of avoiding the consumption of saffron food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid saffron food product intake avoiding saffron food product intake saffron food product consumption avoidance saffron food product intake avoidance A medical requirement or recommendation of avoiding the consumption of seafood product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid seafood product intake avoiding seafood product intake seafood product consumption avoidance seafood product intake avoidance A medical requirement or recommendation of avoiding the consumption of mussel food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid mussel food product intake avoiding mussel food product intake mussel food product consumption avoidance mussel food product intake avoidance A medical requirement or recommendation of avoiding the consumption of clove food product. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid clove food product intake avoiding clove food product intake clove food product consumption avoidance clove food product intake avoidance A medical requirement or recommendation of avoiding the consumption of dark chocolate. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid dark chocolate intake avoiding dark chocolate intake dark chocolate consumption avoidance dark chocolate intake avoidance A medical requirement or recommendation of avoiding the consumption of pumpkin seed (shell off). 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid pumpkin seed (shell off) intake avoiding pumpkin seed (shell off) intake pumpkin seed (shell off) consumption avoidance pumpkin seed intake avoidance A medical requirement or recommendation of avoiding the consumption of sesame seed. 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sesame seed intake avoiding sesame seed intake sesame seed consumption avoidance sesame seed intake avoidance A medical requirement or recommendation of avoiding the consumption of sunflower seed (whole kernel, raw). 2020-01-13T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sunflower seed (whole kernel, raw) intake avoiding sunflower seed (whole kernel, raw) intake sunflower seed (whole kernel, raw) consumption avoidance sunflower seed intake avoidance A medical requirement or recommendation of avoiding the consumption of liver (whole, raw). 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid liver (whole, raw) intake avoiding liver (whole, raw) intake liver (whole, raw) consumption avoidance liver intake avoidance A medical requirement or recommendation of avoiding the consumption of egg or egg component. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid egg or egg component intake avoiding egg or egg component intake egg or egg component consumption avoidance egg intake avoidance A medical requirement or recommendation of avoiding the consumption of kidney (whole, raw). 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid kidney (whole, raw) intake avoiding kidney (whole, raw) intake kidney (whole, raw) consumption avoidance kidney intake avoidance A medical requirement or recommendation of avoiding the consumption of peas (whole, rehydrated, canned). 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid peas (whole, rehydrated, canned) intake avoiding peas (whole, rehydrated, canned) intake peas (whole, rehydrated, canned) consumption avoidance pea intake avoidance A medical requirement or recommendation of avoiding the consumption of bean food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid bean food product intake avoiding bean food product intake bean food product consumption avoidance bean intake avoidance A medical requirement or recommendation of avoiding the consumption of peanut (whole). 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid peanut (whole) intake avoiding peanut (whole) intake peanut (whole) consumption avoidance peanut intake avoidance A medical requirement or recommendation of avoiding the consumption of soybean refined food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid soybean refined food product intake avoiding soybean refined food product intake soya intake avoiance soybean refined food product consumption avoidance soy intake avoidance A medical requirement or recommendation of avoiding the consumption of 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr). 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) consumption avoidance avoid 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) intake avoid brassicas intake avoiding 010 brassica (cole or cabbage) vegetables, head cabbage, flowerhead brassicas (vb) (ccpr) intake brassicas vegetable intake avoidance brassicas intake avoidance A medical requirement or recommendation of avoiding the consumption of brussels sprout vegetable food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid brussels sprout vegetable food product intake avoiding brussels sprout vegetable food product intake brussels sprout vegetable food product consumption avoidance brussels sprout intake avoidance A medical requirement or recommendation of avoiding the consumption of broccoli vegetable food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid broccoli vegetable food product intake avoiding broccoli vegetable food product intake broccoli vegetable food product consumption avoidance broccoli intake avoidance A medical requirement or recommendation of avoiding the consumption of cabbage vegetable food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid cabbage vegetable food product intake avoiding cabbage vegetable food product intake cabbage vegetable food product consumption avoidance cabbage intake avoidance A medical requirement or recommendation of avoiding the consumption of cauliflower vegetable food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid cauliflower vegetable food product intake avoiding cauliflower vegetable food product intake cauliflower vegetable food product consumption avoidance cauliflower intake avoidance A medical requirement or recommendation of avoiding the consumption of rapeseed food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid rapeseed food product intake avoiding rapeseed food product intake rapeseed food product consumption avoidance rapeseed intake avoidance A medical requirement or recommendation of avoiding the consumption of rapeseed oil. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid rapeseed oil intake avoiding rapeseed oil intake rapeseed oil consumption avoidance rapeseed oil intake avoidance A medical requirement or recommendation of avoiding the consumption of rapeseed meal. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid rapeseed meal intake avoiding rapeseed meal intake rapeseed meal consumption avoidance rapeseed flour intake avoidance A medical requirement or recommendation of avoiding the consumption of cephalopod. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid cephalopod intake avoiding cephalopod intake cephalopod consumption avoidance cephalopod intake avoidance A medical requirement or recommendation of avoiding the consumption of crustacean. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid crustacean intake avoiding crustacean intake crustacean consumption avoidance crustacean intake avoidance A medical requirement or recommendation of avoiding the consumption of beer. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid beer intake avoiding beer intake beer consumption avoidance beer intake avoidance A medical requirement or recommendation of avoiding the consumption of corn syrup (high fructose). 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid corn syrup (high fructose) intake avoiding corn syrup (high fructose) intake corn syrup (high fructose) consumption avoidance corn syrup (high fructose) intake avoidance A medical requirement or recommendation of avoiding the consumption of sorbitol syrup. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sorbitol syrup intake avoiding sorbitol syrup intake dietary sorbitol intake avoidance sorbitol intake avoidance sorbitol syrup consumption avoidance sorbitol syrup intake avoidance A medical requirement or recommendation of avoiding the consumption of human milk based food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid human milk based food product intake avoiding human milk based food product intake human milk based food product consumption avoidance human milk intake avoidance A medical requirement or recommendation of avoiding the consumption of cow milk based food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid cow milk based food product intake avoiding cow milk based food product intake bovine milk intake avoidance cow milk based food product consumption avoidance cow milk intake avoidance A medical requirement or recommendation of avoiding the consumption of fruit (whole, raw). 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid fruit (whole, raw) intake avoiding fruit (whole, raw) intake fruit (whole, raw) consumption avoidance fruit intake avoidance A medical requirement or recommendation of avoiding the consumption of hen egg (whole, shell off, raw). 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid hen egg (whole, shell off, raw) intake avoiding hen egg (whole, shell off, raw) intake hen egg (whole, shell off, raw) consumption avoidance raw egg intake avoidance A medical requirement or recommendation of avoiding the consumption of fruit juice food product. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid fruit juice food product intake avoiding fruit juice food product intake fruit juice food product consumption avoidance fruit juice intake avoidance A medical requirement or recommendation of avoiding the consumption of sugar cane juice (pure). 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sugar cane juice (pure) intake avoiding sugar cane juice (pure) intake sugar cane juice (pure) consumption avoidance cane juice intake avoidance A medical requirement or recommendation of avoiding the consumption of organ meat. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid organ meat intake avoiding organ meat intake organ meat consumption avoidance organ meat intake avoidance A medical requirement or recommendation of avoiding the consumption of isoleucine. 2020-05-12T09:00:01Z http://orcid.org/0000-0001-7941-2961 avoid isoleucine intake avoiding dietary isoleucine intake isoleucine consumption avoidance isoleucine restricted diet intake isoleucine restriction dietary isoleucine intake avoidance A medical requirement or recommendation of avoiding the consumption of arginine. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 arginine consumption avoidance arginine restricted diet intake arginine restriction avoid arginine intake avoiding dietary arginine intake dietary arginine intake avoidance A medical requirement or recommendation of avoiding the consumption of lysine. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid lysine intake avoiding dietary lysine intake lysine consumption avoidance lysine restricted diet intake lysine restriction dietary lysine intake avoidance A medical requirement or recommendation of avoiding the consumption of methionine. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid methionine intake avoiding dietary methionine intake methionine consumption avoidance methionine restricted diet intake methionine restriction dietary methionine intake avoidance A medical requirement or recommendation of avoiding the consumption of glycine. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid glycine intake avoiding dietary glycine intake glycine consumption avoidance glycine restricted diet intake glycine restriction dietary glycine intake avoidance A medical requirement or recommendation of avoiding the consumption of phenylalanine. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid phenylalanine intake avoiding dietary phenylalanine intake phenylalanine consumption avoidance phenylalanine restricted diet intake phenylalanine restriction dietary phenylalanine intake avoidance A medical requirement or recommendation of avoiding the consumption of tyrosine. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid tyrosine intake avoiding dietary tyrosine intake tyrosine consumption avoidance tyrosine restricted diet intake tyrosine restriction dietary tyrosine intake avoidance A medical requirement or recommendation of avoiding the consumption of sodium atom. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sodium atom intake avoiding dietary sodium atom intake sodium atom consumption avoidance sodium atom restricted diet intake sodium atom restriction sodium restriction dietary sodium intake avoidance A medical requirement or recommendation of avoiding the consumption of galactose. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid galactose intake avoiding dietary galactose intake galactose consumption avoidance galactose restricted diet intake galactose restriction dietary galactose intake avoidance A medical requirement or recommendation of avoiding the consumption of cholesterol. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid cholesterol intake avoiding dietary cholesterol intake cholesterol consumption avoidance cholesterol restricted diet intake cholesterol restriction cholesterol intake avoidance A medical requirement or recommendation of avoiding the consumption of cholesterol. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid cholesterol intake avoiding dietary cholesterol intake cholesterol consumption avoidance cholesterol restricted diet intake cholesterol restriction dietary cholesterol intake avoidance A medical requirement or recommendation of avoiding the consumption of iron atom. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid iron atom intake avoiding dietary iron atom intake dietary iron restriction iron atom consumption avoidance iron atom restricted diet intake iron atom restriction dietary iron intake avoidance A medical requirement or recommendation of avoiding the consumption of ascorbic acid. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 ascorbic acid consumption avoidance ascorbic acid restricted diet intake ascorbic acid restriction avoid ascorbic acid intake avoiding dietary ascorbic acid intake dietary ascorbic acid intake avoidance A medical requirement or recommendation of avoiding the consumption of branched-chain amino acid. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 BCAA-free diet recommendation avoid branched chain amino acids ingestion avoid branched-chain amino acid intake avoiding dietary branched-chain amino acid intake branched chain amino acid intake avoidance branched chain amino acid restriction branched-chain amino acid consumption avoidance branched-chain amino acid restricted diet intake branched-chain amino acid restriction low BCAA diet intake low BCAA diet recommendation dietary branched-chain amino acid intake avoidance A medical requirement or recommendation of avoiding the consumption of trimethylamine. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid trimethylamine intake avoiding dietary trimethylamine intake trimethylamine consumption avoidance trimethylamine restricted diet intake trimethylamine restriction dietary trimethylamine intake avoidance A medical requirement or recommendation of avoiding the consumption of choline. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid choline intake avoiding dietary choline intake choline consumption avoidance choline restricted diet intake choline restriction dietary choline intake avoidance A medical requirement or recommendation of avoiding the consumption of trimethylamine N-oxide. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid trimethylamine N-oxide intake avoiding dietary trimethylamine N-oxide intake trimethylamine N-oxide consumption avoidance trimethylamine N-oxide restricted diet intake trimethylamine N-oxide restriction dietary trimethylamine N-oxide intake avoidance A medical requirement or recommendation of avoiding the consumption of lecithin. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid lecithin intake avoiding dietary lecithin intake lecithin consumption avoidance lecithin restricted diet intake lecithin restriction dietary lecithin intake avoidance A medical requirement or recommendation of avoiding the consumption of sterol. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sterol intake avoiding dietary sterol intake sterol consumption avoidance sterol restricted diet intake sterol restriction dietary sterol intake avoidance A medical requirement or recommendation of avoiding the consumption of purine. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid purine intake avoiding dietary purine intake purine consumption avoidance purine restricted diet intake purine restriction dietary purine intake avoidance A medical requirement or recommendation of avoiding the consumption of fructose. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid fructose intake avoiding dietary fructose intake fructose consumption avoidance fructose restricted diet intake fructose restriction low fructose diet intake dietary fructose intake avoidance A medical requirement or recommendation of avoiding the consumption of lactose. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid lactose intake avoiding dietary lactose intake lactose consumption avoidance lactose restricted diet intake lactose restriction dietary lactose intake avoidance A medical requirement or recommendation of avoiding the consumption of leucine. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid leucine intake avoiding dietary leucine intake leucine consumption avoidance leucine restricted diet intake leucine restriction dietary leucine intake avoidance A medical requirement or recommendation of avoiding the consumption of oxalate. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid oxalate intake avoiding dietary oxalate intake oxalate consumption avoidance oxalate restricted diet intake oxalate restriction dietary oxalate intake avoidance A medical requirement or recommendation of avoiding the consumption of phosphate. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid phosphate intake avoiding dietary phosphate intake phosphate consumption avoidance phosphate restricted diet intake phosphate restriction dietary phosphate intake avoidance A medical requirement or recommendation of avoiding the consumption of saturated fatty acid. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid saturated fatty acid intake avoiding dietary saturated fatty acid intake saturated fatty acid consumption avoidance saturated fatty acid restricted diet intake saturated fatty acid restriction saturated fat intake avoidance A medical requirement or recommendation of avoiding the consumption of calcium atom. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid calcium atom intake avoiding dietary calcium atom intake calcium atom consumption avoidance calcium atom restricted diet intake calcium atom restriction dietary calcium avoidance A medical requirement or recommendation of avoiding the consumption of sucrose. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid sucrose intake avoiding dietary sucrose intake sucrose consumption avoidance sucrose restricted diet intake sucrose restriction dietary sucrose intake avoidance A medical requirement or recommendation of avoiding the consumption of triglyceride. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid triglyceride intake avoiding dietary triglyceride intake triglyceride consumption avoidance triglyceride restricted diet intake triglyceride restriction dietary triglyceride intake avoidance A medical requirement or recommendation of avoiding the consumption of riboflavin. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 B12 restriction avoid riboflavin intake avoiding dietary riboflavin intake riboflavin consumption avoidance riboflavin restricted diet intake riboflavin restriction vitamin B12 intake avoidance dietary riboflavin intake avoidance A medical requirement or recommendation of avoiding the consumption of phytanic acid. 2020-05-12T11:00:00Z http://orcid.org/0000-0001-7941-2961 avoid phytanic acid intake avoiding dietary phytanic acid intake phytanic acid consumption avoidance phytanic acid restricted diet intake phytanic acid restriction dietary phytanic acid intake avoidance A method of ultrasound imaging in which the ultrasound probe is pressed against the skin of the abdomen in order to create an image of the abdominal organs. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C71375 TUS abdomen diagnostic sonography abdomen medical ultrasound abdomen sonography abdomen ultrasound examination abdomen ultrasound imaging procedure abdomen ultrasound procedure diagnostic transabdominal ultrasound medical transabdominal ultrasound sonography of abdomen transabdominal sonography transabdominal ultrasound ultrasonography of abdomen transabdominal ultrasonography The use of ultrasound to produce images of structures in the body of uterus. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 body of uterus diagnostic sonography body of uterus medical ultrasound body of uterus sonography body of uterus ultrasound examination body of uterus ultrasound imaging procedure body of uterus ultrasound procedure sonography of body of uterus ultrasonography of body of uterus uterine ultrasonography The use of ultrasound to produce images of structures in the breast. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 breast diagnostic sonography breast medical ultrasound breast sonography breast ultrasound examination breast ultrasound imaging procedure breast ultrasound procedure sonography of breast ultrasonography of breast breast ultrasonography The use of ultrasound to produce images of structures in the heart. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 heart diagnostic sonography heart medical ultrasound heart sonography heart ultrasound examination heart ultrasound imaging procedure heart ultrasound procedure sonography of heart ultrasonography of heart echocardiography The use of ultrasound to produce images of structures in the liver. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2965 liver diagnostic sonography liver medical ultrasound liver sonography liver ultrasound examination liver ultrasound imaging procedure liver ultrasound procedure sonography of liver ultrasonography of liver liver ultrasonography The use of ultrasound to produce images of structures in the lung. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2969 lung diagnostic sonography lung medical ultrasound lung sonography lung ultrasound examination lung ultrasound imaging procedure lung ultrasound procedure sonography of lung ultrasonography of lung lung ultrasonography The use of ultrasound to produce images of structures in the lymph node. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2970 lymph node diagnostic sonography lymph node medical ultrasound lymph node sonography lymph node ultrasound examination lymph node ultrasound imaging procedure lymph node ultrasound procedure sonography of lymph node ultrasonography of lymph node lymph node ultrasonography The use of ultrasound to produce images of structures in the musculoskeletal system. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2975 musculoskeletal system diagnostic sonography musculoskeletal system medical ultrasound musculoskeletal system sonography musculoskeletal system ultrasound examination musculoskeletal system ultrasound imaging procedure musculoskeletal system ultrasound procedure sonography of musculoskeletal system ultrasonography of musculoskeletal system musculoskeletal ultrasonography The use of ultrasound to produce images of structures in the neck. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2979 neck diagnostic sonography neck medical ultrasound neck sonography neck ultrasound examination neck ultrasound imaging procedure neck ultrasound procedure sonography of neck ultrasonography of neck neck ultrasonography The use of ultrasound to produce images of structures in the pancreas. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2981 pancreas diagnostic sonography pancreas medical ultrasound pancreas sonography pancreas ultrasound examination pancreas ultrasound imaging procedure pancreas ultrasound procedure sonography of pancreas ultrasonography of pancreas pancreatic ultrasonography The use of ultrasound to produce images of structures in the rectum. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2987 rectum diagnostic sonography rectum medical ultrasound rectum sonography rectum ultrasound examination rectum ultrasound imaging procedure rectum ultrasound procedure sonography of rectum ultrasonography of rectum rectal ultrasonography The use of ultrasound to produce images of structures in the scrotum. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2990 scrotum diagnostic sonography scrotum medical ultrasound scrotum sonography scrotum ultrasound examination scrotum ultrasound imaging procedure scrotum ultrasound procedure sonography of scrotum ultrasonography of scrotum scrotal ultrasonography The use of ultrasound to produce images of structures in the spleen. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2994 sonography of spleen spleen diagnostic sonography spleen medical ultrasound spleen sonography spleen ultrasound examination spleen ultrasound imaging procedure spleen ultrasound procedure ultrasonography of spleen spleen ultrasonography The use of ultrasound to produce images of structures in the stomach. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2995 sonography of stomach stomach diagnostic sonography stomach medical ultrasound stomach sonography stomach ultrasound examination stomach ultrasound imaging procedure stomach ultrasound procedure ultrasonography of stomach stomach ultrasonography The use of ultrasound to produce images of structures in the thyroid gland. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3000 sonography of thyroid gland thyroid gland diagnostic sonography thyroid gland medical ultrasound thyroid gland sonography thyroid gland ultrasound examination thyroid gland ultrasound imaging procedure thyroid gland ultrasound procedure ultrasonography of thyroid gland thyroid ultrasonography The use of ultrasound to produce images of structures in the urinary bladder. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3008 sonography of urinary bladder ultrasonography of urinary bladder urinary bladder diagnostic sonography urinary bladder medical ultrasound urinary bladder sonography urinary bladder ultrasound examination urinary bladder ultrasound imaging procedure urinary bladder ultrasound procedure bladder ultrasonography The use of ultrasound to produce images of structures in the vagina. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 sonography of vagina ultrasonography of vagina vagina diagnostic sonography vagina medical ultrasound vagina sonography vagina ultrasound examination vagina ultrasound imaging procedure vagina ultrasound procedure vaginal ultrasonography The use of ultrasound to produce images of structures in the kidney. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 kidney diagnostic sonography kidney medical ultrasound kidney sonography kidney ultrasound examination kidney ultrasound imaging procedure kidney ultrasound procedure sonography of kidney ultrasonography of kidney renal ultrasonography The use of ultrasound to produce images of structures in the carotid artery segment. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 carotid artery segment diagnostic sonography carotid artery segment medical ultrasound carotid artery segment sonography carotid artery segment ultrasound examination carotid artery segment ultrasound imaging procedure carotid artery segment ultrasound procedure carotid ultrasound imaging sonography of carotid artery segment ultrasonography of carotid artery segment carotid ultrasonography The use of ultrasound to produce images of structures in the pelvic region of trunk. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 pelvic region of trunk diagnostic sonography pelvic region of trunk medical ultrasound pelvic region of trunk sonography pelvic region of trunk ultrasound examination pelvic region of trunk ultrasound imaging procedure pelvic region of trunk ultrasound procedure pelvic sonography pelvis sonography sonography of pelvic region of trunk ultrasonography of pelvic region of trunk pelvis ultrasonography The use of ultrasound to produce images of structures in the prostate gland. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 prostate gland diagnostic sonography prostate gland medical ultrasound prostate gland sonography prostate gland ultrasound examination prostate gland ultrasound imaging procedure prostate gland ultrasound procedure sonography of prostate gland ultrasonography of prostate gland prostate ultrasonography The use of ultrasound to produce images of structures in the testis. The use of ultrasound to produce images of structures in the venous blood vessel. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 sonography of testis sonography of venous blood vessel testis diagnostic sonography testis medical ultrasound testis sonography testis ultrasound examination testis ultrasound imaging procedure testis ultrasound procedure ultrasonography of testis ultrasonography of venous blood vessel venous blood vessel diagnostic sonography venous blood vessel medical ultrasound venous blood vessel sonography venous blood vessel ultrasound examination venous blood vessel ultrasound imaging procedure venous blood vessel ultrasound procedure venous sonography testicular ultrasonography venous ultrasonography The use of ultrasound to produce images of structures in the brain. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-3010 brain diagnostic sonography brain medical ultrasound brain sonography brain ultrasound examination brain ultrasound imaging procedure brain ultrasound procedure sonography of brain ultrasonography of brain neurosonology Collection biological material from within the rectum with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2961 anal swab swab collection of rectum rectal swab collection Collection biological material from within the vagina with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2961 swab collection of vagina vaginal swab collection Collection biological material from within the buccal mucosa with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2961 oral swab swab collection of buccal mucosa buccal swab collection Collection biological material from within the nasal turbinal with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2974 swab collection of nasal turbinal nasal turbinal swab collection Collection biological material from within the nasopharynx with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2978 swab collection of nasopharynx nasopharyngeal swab collection Collection biological material from within the nasal vestibule with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2978 swab collection of nasal vestibule nasal vestibule swab collection Collection biological material from within the zone of skin with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2978 swab collection of zone of skin skin swab collection Collection biological material from within the oropharynx with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2978 swab collection of oropharynx oropharyngeal swab collection Collection biological material from within the external naris with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2978 anterior naris swab swab collection of external naris anterior nares swab collection Collection biological material from within the throat with a cotton swab. 2020-03-27T20:39:14Z http://orcid.org/0000-0001-7941-2978 swab collection of throat throat swab collection The use of computed tomography to produce images of structures of the abdomen. 2020-03-31T20:39:14Z http://orcid.org/0000-0001-7941-2961 CAT scan of abdomen CT of abdomen abdomen CAT scan abdomen CT examination abdomen computed tomography abdomen computerized axial tomography abdominal CT The use of computed tomography to produce images of structures of the head. 2020-03-31T20:39:14Z http://orcid.org/0000-0001-7941-2961 CAT scan of head CT of head head CAT scan head CT examination head computed tomography head computerized axial tomography head CT The use of computed tomography to produce images of structures of the liver. 2020-03-31T20:39:14Z http://orcid.org/0000-0001-7941-2965 CAT scan of liver CT of liver liver CAT scan liver CT examination liver computed tomography liver computerized axial tomography liver CT The use of computed tomography to produce images of structures of the lung. 2020-03-31T20:39:14Z http://orcid.org/0000-0001-7941-2969 CAT scan of lung CT of lung lung CAT scan lung CT examination lung computed tomography lung computerized axial tomography lung CT The use of computed tomography to produce images of structures of the neck. 2020-03-31T20:39:14Z http://orcid.org/0000-0001-7941-2979 CAT scan of neck CT of neck neck CAT scan neck CT examination neck computed tomography neck computerized axial tomography neck CT The use of computed tomography to produce images of structures of the brain. 2020-03-31T20:39:14Z http://orcid.org/0000-0001-7941-3010 CAT scan of brain CT of brain brain CAT scan brain CT examination brain computed tomography brain computerized axial tomography brain CT The use of computed tomography to produce images of structures of the chest. 2020-03-31T20:39:14Z http://orcid.org/0000-0001-7941-3010 CAT scan of chest CT of chest chest CAT scan chest CT examination chest computed tomography chest computerized axial tomography chest CT The use of computed tomography to produce images of structures of the skull. 2020-03-31T20:39:14Z http://orcid.org/0000-0001-7941-3010 CAT scan of skull CT of skull skull CAT scan skull CT examination skull computed tomography skull computerized axial tomography skull CT The use of computed tomography to produce images of structures of the blood vasculature. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-3010 CAT scan of blood vasculature CT of blood vasculature blood vasculature CAT scan blood vasculature CT examination blood vasculature computed tomography blood vasculature computerized axial tomography CT angiogram The use of computed tomography to produce images of structures of the pulmonary vascular system. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-3010 CAT scan of pulmonary vascular system CT PE CT of pulmonary vascular system CT scan for pulmonary embolism pulmonary vascular system CAT scan pulmonary vascular system CT examination pulmonary vascular system computed tomography pulmonary vascular system computerized axial tomography CT pulmonary angiogram Avoid the administration or use of computed tomography procedure. 2020-03-30T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid computed tomography procedure avoiding computed tomography procedure avoid CT scans Avoid the administration or use of ketogenic diet intake. 2020-05-12T20:39:14Z http://orcid.org/0000-0001-7941-2961 avoid ketogenic diet intake avoiding ketogenic diet intake ketogenic diet intake avoidance Use of an imaging test that uses small amounts of radiation to produce pictures of abdomen. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C38102 abdomen X-ray procedure abdomen radiogram procedure abdominal X-ray procedure abdominal radiography radiograph of abdomen radiography of abdomen abdominal radiographic procedure Use of an imaging test that uses small amounts of radiation to produce pictures of head. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-2961 head X-ray procedure head radiogram procedure radiograph of head radiography of head head radiograph procedure Use of an imaging test that uses small amounts of radiation to produce pictures of liver. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-2961 liver X-ray procedure liver radiogram procedure radiograph of liver radiography of liver liver radiograph procedure Use of an imaging test that uses small amounts of radiation to produce pictures of lung. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-2961 lung X-ray procedure lung radiogram procedure radiograph of lung radiography of lung lung radiograph procedure Use of an imaging test that uses small amounts of radiation to produce pictures of neck. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-2961 neck X-ray procedure neck radiogram procedure radiograph of neck radiography of neck neck radiograph procedure Use of an imaging test that uses small amounts of radiation to produce pictures of chest. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C38103 chest X-ray procedure chest radiogram procedure radiograph of chest radiography of chest chest radiograph procedure The X-ray examination of the lower limbs of the body. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C20080 lower limb X-ray lower limb radiography lower limb segment X-ray procedure lower limb segment radiogram procedure radiograph of lower limb segment radiography of lower limb segment lower limb radiographic procedure The X-ray examination of the blood vessels or chambers of the heart. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C20080 angiography blood vasculature X-ray procedure blood vasculature radiogram procedure radiograph of blood vasculature radiography of blood vasculature angiography procedure An x-ray imaging technique that involves visualization of the pulmonary vasculature after fluoroscopy-guided catheter placement and injection of an iodinated contrast medium into the pulmonary circulation. 2020-04-07T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C154789 pulmonary vascular system X-ray procedure pulmonary vascular system radiogram procedure radiograph of pulmonary vascular system radiography of pulmonary vascular system pulmonary angiography procedure The radiographic examination of the tracheobronchial tree following the injection of a radiopaque material. 2020-04-27T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C38040 bronchographic image procedure bronchography radiograph of tracheobronchial tree radiography of tracheobronchial tree tracheobronchial tree X-ray procedure tracheobronchial tree radiogram procedure bronchography procedure The radiographic examination of the bile ducts after a contrast medium has been injected. 2020-04-27T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C61508 biliary tree X-ray procedure biliary tree radiogram procedure cholangiographic procedure cholangiography radiograph of biliary tree radiography of biliary tree cholangiography procedure A radiographic procedure to obtain an image of the urinary bladder by filling the bladder with contrast medium. 2020-04-27T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C38049 cystographic imaging procedure cystography radiograph of urinary bladder radiography of urinary bladder urinary bladder X-ray procedure urinary bladder radiogram procedure cystography procedure A type of radiography used specifically to examine breast tissue. The procedure utilizes a low-dose of x-rays or radiation to generate an image. A mammography exam or mammogram, is used as a screening tool to detect early breast cancer in women experiencing no symptoms and to detect and diagnose breast disease. 2020-04-27T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C16818 breast X-ray procedure breast radiogram procedure mammography radiograph of breast radiography of breast mammography procedure The radiographic examination of the spinal cord and nerve roots following the injection of a contrast medium into the spinal subarachnoid space. The X-rays taken may highlight conditions such as spinal tumors, spinal cord swelling and herniated discs. 2020-04-27T20:39:14Z http://orcid.org/0000-0001-7941-29610 NCIT:C20175 myelography radiograph of spinal cord radiography of spinal cord spinal cord X-ray procedure spinal cord radiogram procedure myelography procedure A radiologic test that involves the examination of the entire body in a single procedure. 2020-04-27T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C96640 multicellular organism X-ray procedure multicellular organism radiogram procedure radiograph of multicellular organism radiography of multicellular organism total body radiography whole body radiography total body radiography procedure A radiographic examination of the vagina using the intravaginal injection of contrast medium. 2020-04-27T20:39:14Z http://orcid.org/0000-0001-7941-2961 NCIT:C38096 radiograph of vagina radiography of vagina vagina X-ray procedure vagina radiogram procedure vaginography vaginography procedure The ketogenic diet is a high-fat, low-carbohydrate, adequate-protein diet that mimics a fasting state, resulting in the substitution of ketone bodies as a source of energy. The ketogenic diet can be used to reduce recurrent epileptic seizures in individuals with intractable epilepsy. Intractable epilepsy is defined as epilepsy that failed to respond to three or more antiepileptic drugs. keto diet intake classic ketogenic diet intake low glycemic index treatment medium-chain triglyceride(s) (MCT) ketogenic diet intake modified Atkins diet intake ketogenic diet intake The ketogenic diet is a high-fat, low-carbohydrate, adequate-protein diet that mimics a fasting state, resulting in the substitution of ketone bodies as a source of energy. The ketogenic diet can be used to reduce recurrent epileptic seizures in individuals with intractable epilepsy. Intractable epilepsy is defined as epilepsy that failed to respond to three or more antiepileptic drugs. PMID:23419562 PMID:27759811 PMID:28701250 Texture-modified foods and thickened drinks used to reduce the risks of choking and aspiration for individuals with oropharyngeal incoordination or dysphagia. dysphagia diet intake thickness modification of food and fluid for ingestion pureed food intake texture modified food intake thickened liquid intake texture modified diet intake Texture-modified foods and thickened drinks used to reduce the risks of choking and aspiration for individuals with oropharyngeal incoordination or dysphagia. PMID:27913916 PMID:28343526 obsolete phenylalanine restricted diet intake false Supplementation of uncooked cornstarch intended to prevent hepatomegaly and hypoglycemia, typically for individuals with irregular hepatic glycogen storage. Supplementation can include both regular cornstarch and extended release cornstarch. 2019-09-05T20:57:49Z administration of uncooked cornstarch uncooked cornstarch therapy uncooked cornstarch supplementation Supplementation of uncooked cornstarch intended to prevent hepatomegaly and hypoglycemia, typically for individuals with irregular hepatic glycogen storage. Supplementation can include both regular cornstarch and extended release cornstarch. PMID:2403059 PMID:25266922 PMID:26303612 Pathological structure or process mouse_pathology.ontology MPATH:0 pathological entity Pathological structure or process Pathbase: Curation Phenotypic observation of the presence or absence of a pathological entity. Luke Slater mouse_pathology.ontology MPATH:1000 pathological phenotype observation Phenotypic observation of the presence or absence of a pathological entity. UOB:LTS Lesions leading to or consequent on failure of, or atypical movement of, blood throughout the body. mouse_pathology.ontology MPATH:105 circulatory disorder Lesions leading to or consequent on failure of, or atypical movement of, blood throughout the body. Pathbase: Pathology Committee Abnormal release of whole blood or the cellular component from the circulation. mouse_pathology.ontology MPATH:119 hemorrhage and non-specified extravasation Abnormal release of whole blood or the cellular component from the circulation. Pathbase: Curation A pathological process of loss or degradation of function, or structural integrity, of a tissue, organ or cell. George Gkoutos mouse_pathology.ontology MPATH:14 process of degenerative change A pathological process of loss or degradation of function, or structural integrity, of a tissue, organ or cell. Pathbase: Pathology Committee The process, normal or abnormal, of damage repair or wound closure. George Gkoutos mouse_pathology.ontology MPATH:175 healing and repair process The process, normal or abnormal, of damage repair or wound closure. Pathbase: Pathology Committee Replacement of connective tissue by fibro-fatty deposits and scar tissue. George Gkoutos mouse_pathology.ontology MPATH:176 connective tissue replacement Replacement of connective tissue by fibro-fatty deposits and scar tissue. Pathbase: Curation Any pathological thickening or hardening of a tissue. George Gkoutos mouse_pathology.ontology Induration MPATH:184 sclerosis Any pathological thickening or hardening of a tissue. Pathbase: Curation Induration Pathbase: Curation Degenerative process characteristic of a particular tissue. mouse_pathology.ontology MPATH:25 tissue specific degenerative process Degenerative process characteristic of a particular tissue. Pathbase: Curation Abnormal accumulation of air in the interstitial connective tissue of a structure. Sensu Lung: Pulmonary emphysema; characterised by abnormal increase in the size of air (alveolar) spaces distal to the terminal bronchiole with degenerative changes in their walls and reduction in their number. mouse_pathology.ontology MPATH:31 emphysema Abnormal accumulation of air in the interstitial connective tissue of a structure. Sensu Lung: Pulmonary emphysema; characterised by abnormal increase in the size of air (alveolar) spaces distal to the terminal bronchiole with degenerative changes in their walls and reduction in their number. ISBN:0781727286 Developmental and structural abnormalities occurring during embryonic development or during adult life. mouse_pathology.ontology MPATH:55 developmental and structural abnormality Developmental and structural abnormalities occurring during embryonic development or during adult life. Pathbase: Pathology Committee Structural, physical or other general defect of prenatal development of the embryo and the placenta, or such as are acquired in the adult. mouse_pathology.ontology MPATH:56 developmental or adult structural defect Structural, physical or other general defect of prenatal development of the embryo and the placenta, or such as are acquired in the adult. Pathbase: Pathology Committee The organic response of tissues to external insult, injury or underlying genetic or epigenetic lesion. mouse_pathology.ontology MPATH:596 pathological process The organic response of tissues to external insult, injury or underlying genetic or epigenetic lesion. Pathbase: Pathology Committee Processes occurring during cell and tissue damage of either intrinsic or extrinsic etiology. mouse_pathology.ontology MPATH:597 cell and tissue damage process Processes occurring during cell and tissue damage of either intrinsic or extrinsic etiology. Pathbase: Pathology Committee Anatomically located instance of pathological response or entity. mouse_pathology.ontology MPATH:603 pathological anatomical entity Anatomically located instance of pathological response or entity. Pathbase: Pathology Committee Physical entity or structure associated with normal or abnormal tissue healing or repair following extrinsic or intrinsic damage. mouse_pathology.ontology MPATH:607 healing and repair structure Physical entity or structure associated with normal or abnormal tissue healing or repair following extrinsic or intrinsic damage. Pathbase: Pathology Committee A circumscribed collection of purulent exudate frequently associated with swelling and other signs of inflammation. mouse_pathology.ontology MPATH:608 Generally occur following damage or infection with subsequent inflammatory response. Result of the body`s defensive reaction to foreign material. abscess A circumscribed collection of purulent exudate frequently associated with swelling and other signs of inflammation. ISBN:0781727286 Formation of an epithelium bounded cavity not associated with neoplasia. mouse_pathology.ontology MPATH:62 cyst Formation of an epithelium bounded cavity not associated with neoplasia. Pathbase: Pathology Committee A blind ended outpouching through the wall of a tubular organ or bounded cavity. mouse_pathology.ontology MPATH:68 diverticulum A blind ended outpouching through the wall of a tubular organ or bounded cavity. Pathbase: Curation "Behavior related to the complex psychophysiological experience of an individual's state of mind as interacting with biochemical (internal) and environmental (external) influences." [wikipedia:Emotions] 2011-04-14T01:03:39Z George Gkoutos affective behaviour mood behavior_ontology emotional behavior Behavior directly related to the production of offspring [NBO:AC] 2011-04-14T01:03:39Z George Gkoutos reproduction reproductive behaviour behavior_ontology GO:0019098 reproductive behavior "Emotional behavior related to fear or anxiety." [NBO:GVG] 2011-04-14T01:03:39Z George Gkoutos fear/anxiety related behaviour behavior_ontology fear/anxiety related behavior "Behaviour related to the activity which primary purpose is the sexual reproduction." [NBO:GVG] 2011-04-14T01:03:39Z George Gkoutos behavior_ontology sexual actions sexual activity Male's insertion of sperm-transfer organ into the body of the female [NBO:SMAC] 2011-04-14T01:03:39Z George Gkoutos copulate behavior_ontology copulation "Emotional behavior related to excitement or restlessness." [NBO:GVG] 2011-03-31T12:22:11Z George Gkoutos behavior_ontology agitation behavior "The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610] 2011-04-05T09:53:10Z George Gkoutos NBO:0000000 behavior behaviour behavior_ontology GO:0007610 behavior process "Behavior related to how the body reacts to a stressor ( a stimulus that causes stress), real or imagined." [wikipedia:Stress_(biological)] 2011-04-08T01:52:36Z George Gkoutos behavior_ontology It refers to the consequence of the failure of an organism to respond adequately to mental, emotional or physical demands, whether actual or imagined. stress related behavior "Any process that modulates the frequency, rate or extent of behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [GO:0050795] George Gkoutos GO:0050795 regulation of behavior "Behavior related to the intake of substances." [NBOC:GVG] George Gkoutos ingest consumption behavior "Behavior related to the intake of addictive substances." [NBOC:GVG] George Gkoutos consumption of an addictive substance "Any process that modulates the frequency, rate or extent of consumption behavior, the specific actions or reactions of an organism in response to external or internal stimuli." [NBOC:GVG] George Gkoutos regulation of consumption behavior "Any process that modulates the frequency, rate or extent of consumption of an addictive substance, the specific actions or reactions of an organism in response to external or internal stimuli." [NBOC:GVG] George Gkoutos regulation of consumption of an addictive substance "Any process that modulates the frequency, rate or extent of sexual activity, the specific actions or reactions of an organism in response to external or internal stimuli." [NBOC:GVG] George Gkoutos regulation of sexual activity Consumption behavior that involves inhaling a material (such as finely ground tobacco leaves) through the nose. http://orcid.org/0000-0002-2908-3327 2019-09-06T10:51:02Z https://orcid.org/0000-0002-7356-1779 smoking behavior Any habitual use of the tobacco plant leaf and its products. 2020-01-27T20:46:57Z tobacco consumption 2020-01-27T21:03:19Z cannabis consumption Viruses Viruses Asteroideae Heliantheae Euteleostomi bony vertebrates bony vertebrates Euteleostomi Archelosauria Dipnotetrapodomorpha Boreoeutheria Mesangiospermae Petrosaviidae Pentapetalae Pooideae Panicoideae PACMAD clade Triticeae Andropogoneae Galloanserae Phaseoleae Fabeae Hordeinae Bacteria eubacteria Bacteria Homininae Archaea Archaea NPAAA clade Pterocarpus clade 50 kb inversion clade Hologalegina IRL clade indigoferoid/millettioid clade iris family Iridaceae Eukaryota eucaryotes eukaryotes eucaryotes eukaryotes ncbi_taxonomy euk- NCBITaxon:2759 Eukaryota euk- PRO:DAN Bovinae Laurasiatheria Euarchontoglires Euarchontoglires Simiiformes Tetrapoda tetrapods tetrapods Tetrapoda Amniota amniotes amniotes Amniota Theria Theria <mammals> diapsids Sauria Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants Viridiplantae Opisthokonta ncbi_taxonomy Fungi/Metazoa group NCBITaxon:33154 Opisthokonta ncbi_taxonomy metazoan- NCBITaxon:33208 Metazoa metazoan- PRO:DAN Bilateria Bilateria deuterostomes Deuterostomia angiosperms flowering plants Magnoliophyta Magnoliopsida Pecora BEP clade BOP clade cucumber family Cucurbitaceae marrows pumpkins squashes Cucurbita http://langual.org DPNL 2003:9052 GRIN:12606 ITIS:22373 PLANTS:CUPE Cucurbita pepo L. Cucurbita pepo Brassicales mustard family Brassicaceae Brassica Kale or borecole is a form of cabbage (*Brassica oleracea* Acephala Group), green or purple, in which the central leaves do not form a head. Damion Dooley http://langual.org DPNL 2003:8103 DPNL 2003:8105 DPNL 2003:8110 DPNL 2003:8113 DPNL 2003:8114 DPNL 2003:8115 GRIN:311416 GRIN:319629 GRIN:319632 GRIN:7668 GRIN:7670 GRIN:7672 ITIS:23062 MANSFELD:23907 http://eol.org/pages/583899 Brassica oleracea L. wild cabbage Brassica oleracea L. var. conica DC. borecole brassica oleracea convar. capitate var. conica "It is considered to be closer to wild cabbage than most domesticated forms. The species *Brassica oleracea* contains a wide array of vegetables including broccoli, cauliflower, collard greens, and brussels sprouts. The cultivar group Acephala also includes spring greens and collard greens, which are extremely similar genetically." - Wikipedia Brassica oleracea cauliflower Brassica oleracea var. botrytis pea family Fabaceae Indian corn Zea mays subsp. sacharata Zea mays var. sacharata corn maize Zea mays subsp. mays Papilionoideae peanut plant http://langual.org DPNL 2003:7636 GRIN:3785 ITIS:26463 MANSFELD:29861 PLANTS:ARHY http://eol.org/pages/4277 http://www.langual.org/langual_thesaurus.asp?termid=B1337 goober ground-nut peanut Arachis hypogaea L. arachis hypogaea earthnut groundnut Arachis hypogaea The soybean or soya bean (Glycine max) is a species of legume native to East Asia, widely grown for its edible bean, which has numerous uses. Traditional unfermented food uses of soybeans include soy milk, from which tofu and tofu skin are made. Fermented soy foods include soy sauce, fermented bean paste, nattō, and tempeh. soybean plant https://en.wikipedia.org/wiki/Soybean http://langual.org soya bean soybean DPNL 2003:10065 GRIN:17711 ITIS:26716 MANSFELD:27017 PLANTS:GLMA4 http://eol.org/pages/4277 http://www.langual.org/langual_thesaurus.asp?termid=B1452 glycine max soybean soybeans Glycine max (L.) Merr. Glycine max Poales Vicia broad bean faba bean fava bean Vicia faba Mammalia mammals mammals Mammalia daisy family Asteraceae sunflowers Helianthus sunflower plant http://langual.org DPNL 2003:10207 GRIN:27923 ITIS:36616 MANSFELD:32888 PLANTS:HEAN3 http://eol.org/pages/468106 http://www.langual.org/langual_thesaurus.asp?termid=B1547 common sunflower Helianthus annuus L. giant greystripe helianthus annuus Helianthus annuus monocots monocotyledons Liliopsida grass family Poaceae http://langual.org DPNL 2003:10323 DPNL 2003:10324 DPNL 2003:10325 GRIN:19333 GRIN:317403 ITIS:40874 MANSFELD:37920 PLANTS:HOVU http://eol.org/pages/1114455 barley Hordeum vulgare L. Hordeum vulgare L. convar. vulgare hordeum vulgare subsp. vulgare Hordeum vulgare maize FoodOn Note: the NCBITaxon exact synonym "maize" is more appropriate for "Zea mays subsp. mays" Zea mays commelinids vascular plants Tracheophyta seed plants Spermatophyta Asteridae asterids rosids Fabales Asparagales chordates Chordata Vertebrata <vertebrates> Vertebrata vertebrates Vertebrata vertebrates Vertebrata <vertebrates> Gnathostomata jawed vertebrates Gnathostomata <vertebrates> euphyllophytes Euphyllophyta saffron plant http://langual.org GRIN:12265 MANSFELD:14971 http://www.langual.org/langual_thesaurus.asp?termid=B1459 saffron crocus Crocus sativus L. crocus sativus Crocus sativus Archosauria birds avian Aves Neognathae landfowls Galliformes turkeys Phasianidae Gallus domesticus bantam chicken chickens Gallus gallus Phasianinae Heliantheae alliance whales, hippos, ruminants, pigs, camels etc. Artiodactyla fabids malvids campanulids eutherian mammals placental mammals placentals Eutheria primate Primates Catarrhini Homo sapiens human human as milk source human being man http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=B1087 human man Homo sapiens Brassiceae Bovidae oxen, cattle Bos bovine cattle cow dairy cow domestic cattle domestic cow Bos taurus A group of organic food substances found in animals and plants in small quantities. They must be supplied in diet or dietary supplement and are essential for normal metabolism. Vitamin planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process regulator role Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel regulator OBI regulator role regulatory role Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. GROUP: Role branch OBI, CDISC govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent regulatory role material supplier role Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel material provider role supplier material supplier role classified data set A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels classified data set processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush reagent PERSON:Matthew Brush Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent role material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization analyte measurement objective The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant PERSON: Bjoern Peters PPPB branch analyte measurement objective assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective analyte assay example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Alan Ruttenberg Bjoern Peters Helen Parkinson Philippe Rocca-Serra Alan Ruttenberg Bjoern Peters Helen Parkinson OBI Planned process branch Philippe Rocca-Serra analyte assay regulatory agency The US Environmental Protection Agency A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. GROUP: OBI Biomaterial Branch WEB: en.wikipedia.org/wiki/Regulator regulatory agency material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective manufacturing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective manufacturer role With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role clustered data set A clustered data set is the output of a K means clustering data transformation A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead clustered data set specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process enzyme-linked immunosorbent assay 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody. An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. IEDB ELISA IEDB enzyme-linked immunosorbent assay class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone supervised classification data transformation PERSON: James Malone class prediction data transformation specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective support vector machine A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. James Malone Ryan Brinkman SVM PERSON: Ryan Brinkman support vector machine decision tree induction objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone PERSON: James Malone decision tree building data transformation GenePattern software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ GenePattern software peak matching Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold James Malone Ryan Brinkman PERSON: Ryan Brinkman peak matching k-nearest neighbors A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. James Malone k-NN PERSON: James Malone k-nearest neighbors CART A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART statistical model validation Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation manufacturer A person or organization that has a manufacturer role manufacturer service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster questionnaire reagent A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. PERSON:Matthew Brush PERSON:Matthew Brush (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens histologic grade according to AJCC 7th edition G4: Undifferentiated G1:Well differentiated A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade according to AJCC 7th edition histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI NCI BBRB histologic grade according to the Fuhrman Nuclear Grading System histologic grade for ovarian tumor A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to a two-tier grading system histologic grade for ovarian tumor according to the World Health Organization A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to the World Health Organization pathologic primary tumor stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for colon and rectum according to AJCC 7th edition pathologic primary tumor stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for lung according to AJCC 7th edition pathologic primary tumor stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for kidney according to AJCC 7th edition pathologic primary tumor stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for ovary according to AJCC 7th edition pathologic lymph node stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for colon and rectum according to AJCC 7th edition pathologic lymph node stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for lung according to AJCC 7th edition pathologic lymph node stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for kidney according to AJCC 7th edition pathologic lymph node stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for ovary according to AJCC 7th edition pathologic distant metastases stage for colon according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for colon according to AJCC 7th edition pathologic distant metastases stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for lung according to AJCC 7th edition pathologic distant metastases stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for kidney according to AJCC 7th edition pathologic distant metastases stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for ovary according to AJCC 7th edition clinical tumor stage group according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB clinical tumor stage group according to AJCC 7th edition International Federation of Gynecology and Obstetrics cervical cancer stage value specification A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics cervical cancer stage value specification International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics ovarian cancer stage value specification performance status value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status NCI BBRB performance status value specification Eastern Cooperative Oncology Group score value specification A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI NCI BBRB Eastern Cooperative Oncology Group score value specification Karnofsky score vaue specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI NCI BBRB Karnofsky score vaue specification swab specimen A specimen that is stored on a swab as the output of a collecting specimen with swab process. Chris Stoeckert OBIB/OBI https://github.com/obi-ontology/obi/issues/910 OBIB swab specimen collecting specimen with swab A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 OBIB collecting specimen with swab breast swab specimen A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert Chris Stoeckert, OBIB breast swab specimen nasopharyngeal swab specimen A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert Chris Stoeckert, OBIB nasopharyngeal swab specimen oral swab specimen A specimen that is collected with a swab from the inside surface of a mouth. Chris Stoeckert Chris Stoeckert, OBIB oral swab specimen oropharyngeal swab specimen A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert Chris Stoeckert, OBIB oropharyngeal swab specimen rectal swab specimen A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert Chris Stoeckert, OBIB rectal swab specimen tongue swab specimen A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert Chris Stoeckert, OBIB tongue swab specimen vagina swab specimen A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert Chris Stoeckert, OBIB vagina swab specimen organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism obi OBI:0100026 organism organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation leave one out cross validation method The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368 is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson leave one out cross validation method k-means clustering A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). Elisabetta Manduchi James Malone Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/K-means k-means clustering hierarchical clustering A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). James Malone WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering hierarchical clustering dimensionality reduction A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction principal components analysis dimensionality reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. Elisabetta Manduchi James Malone Melanie Courtot Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot principal components analysis dimensionality reduction data visualization Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data visualization data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. James Malone PERSON: James Malone partitioning data transformation partitioning objective A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi partitioning objective class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone clustering data transformation unsupervised classification data transformation PERSON: James Malone class discovery data transformation class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery objective class prediction objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. James Malone classification objective supervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class prediction objective cross validation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. James Malone rotation estimation objective WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective clustered data visualization A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. James Malone clustered data visualization adaptive immune receptor is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. IEDB IEDB adaptive immune receptor A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG A quality of inhering in a bearer by virtue of the bearer's disposition to move freely. quality PATO:0000004 Should be defined using translocation. mobility A quality of inhering in a bearer by virtue of the bearer's disposition to move freely. PATOC:GVG A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATO:0002015 composed of compositionality content structure, composition quality PATO:0000025 For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATOC:GVG A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0001647 relational shape quality quality PATO:0000052 Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. shape A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's occurrence. PATO:0000156 PATO:0000158 temporal incidence quality PATO:0000057 occurrence A quality of a single process inhering in a bearer by virtue of the bearer's occurrence. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATO:0000132 PATO:0001565 distribution quality pattern PATO:0000060 spatial pattern A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATOC:GVG quality PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 deviation (from_normal) deviation(from_normal) A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATOC:GVG The number of entities of this type that are part of the whole organism. PATO:0000053 PATO:0000071 PATO:0001169 PATO:0001226 presence or absence in organism quantitative quality count in organism number presence PATO:0000070 This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. amount The number of entities of this type that are part of the whole organism. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. quality PATO:0000117 size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. WordNet:WordNet A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. quality PATO:0000119 height A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. PATOC:GVG A 1-D extent quality which is equal to the distance between two points. quality PATO:0000122 length A 1-D extent quality which is equal to the distance between two points. PATOC:GVG A physical quality inhering in a bearer that has mass near a gravitational body. quality PATO:0000128 weight A physical quality inhering in a bearer that has mass near a gravitational body. Wikipedia:http://en.wikipedia.org/wiki/Weight A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent. quality PATO:0000136 closure A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent. PATOC:CJM PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATO:0001032 PATO:0001631 location placement relational spatial quality quality PATO:0000140 position A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0001452 conformation relational structural quality quality PATO:0000141 structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATOC:GVG conformation VT:1000738 A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. quality PATO:0000161 rate A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. PATOC:melissa behavioral quality An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. behavioral quality A mobility quality of inhering in a bearer by virtue of the bearer's disposition to move freely. quality PATO:0000299 mobile A mobility quality of inhering in a bearer by virtue of the bearer's disposition to move freely. PATOC:GVG A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency. quality PATO:0000330 irregular spatial pattern A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency. PATOC:GVG A branchiness quality inhering in a bearer by virtue of the bearer's having branches. ramified ramiform quality PATO:0000402 branched A branchiness quality inhering in a bearer by virtue of the bearer's having branches. WordNet:WordNet A concave quality inhering in a bearer by virtue of the bearer's resembling a groove or fissure. quality PATO:0000403 cleft A concave quality inhering in a bearer by virtue of the bearer's resembling a groove or fissure. WordNet:WordNet A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. quality aberrant atypia atypical defective PATO:0000460 abnormal A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. quality average PATO:0000461 normal A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. PATOC:GVG A quality denoting the lack of an entity. PATO:0001996 absence absent from organism quality PATO:0000462 See documentation here: http://code.google.com/p/phenotype-ontologies/wiki/ModelingOfAbsence absent A quality denoting the lack of an entity. thefreedictionary.:thefreedictionary. A quality inhering in a bearer by virtue of the bearer's existence. quality present in organism PATO:0000467 present A quality inhering in a bearer by virtue of the bearer's existence. PATOC:GVG An amount which is relatively high. PATO:0000420 PATO:0000650 increased number present in greater numbers in organism supernumerary quality accessory increased PATO:0000470 increased amount An amount which is relatively high. PATOC:GVG A duration quality of a process which is relatively high. PATO:0000715 high time increased period increased time quality chronic prolonged period slow time PATO:0000498 increased duration A duration quality of a process which is relatively high. PATOC:GVG A duration quality of a process which is relatively low. PATO:0000716 decreased period decreased time low period shortened period quality fast time PATO:0000499 decreased duration A duration quality of a process which is relatively low. PATOC:GVG A quality of a process which starts later than the natural start time or the reference process. quality late PATO:0000502 delayed A quality of a process which starts later than the natural start time or the reference process. PATOC:LC A height which is relatively low. quality short PATO:0000569 decreased height A height which is relatively low. PATOC:GVG A height which is relatively high. quality tall PATO:0000570 increased height A height which is relatively high. PATOC:GVG A length quality which is relatively large. long quality PATO:0000573 increased length A length quality which is relatively large. PATOC:GVG A length quality which is relatively small. short quality shortened stubby PATO:0000574 decreased length A length quality which is relatively small. PATOC:GVG A weight which is relatively high. heavy high weight quality PATO:0000582 increased weight A weight which is relatively high. PATOC:GVG A weight which is relatively low. light weight low weight quality PATO:0000583 decreased weight A weight which is relatively low. PATOC:GVG An increased size quality inhering in a bearer by virtue of the bearer's exhibiting enlargement of a cell or constituent group of cells (for example, organ). hypertrophy quality PATO:0000584 hypertrophic An increased size quality inhering in a bearer by virtue of the bearer's exhibiting enlargement of a cell or constituent group of cells (for example, organ). PATOC:MAH A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced size of a cell or constituent group of cells (for example, organ). PATO:0000412 shrunken quality PATO:0000585 hypotrophic A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced size of a cell or constituent group of cells (for example, organ). PATOC:MAH A size quality which is relatively high. PATO:0001202 quality big enlarged expanded great large PATO:0000586 increased size A size quality which is relatively high. PATOC:GVG A size quality which is relatively low. hypoplasia underdeveloped quality reduced small tiny PATO:0000587 decreased size A size quality which is relatively low. PATOC:GVG A volume which is relatively high. high volume quality large volume PATO:0000595 increased volume A volume which is relatively high. PATOC:GVG A volume which is relatively low. low volume quality small volume PATO:0000596 decreased volume A volume which is relatively low. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's affording not completed blocked passage or view. quality PATO:0000609 closure incomplete A morphological quality inhering in a bearer by virtue of the bearer's affording not completed blocked passage or view. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view. quality PATO:0000610 open A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view. answers.com:answers.com A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location. focal localised quality PATO:0000627 localized A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location. WordNet:WordNet A structural quality inhering in a bearer by virtue of the bearer's exhibiting an alteration in size, shape or organization of its constituent cells. dysplasia quality PATO:0000640 dysplastic A structural quality inhering in a bearer by virtue of the bearer's exhibiting an alteration in size, shape or organization of its constituent cells. PATOC:MAH A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced number of cells within an organ or tissue. PATO:0000942 hypoplasia quality underdeveloped PATO:0000645 hypoplastic A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced number of cells within an organ or tissue. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's being distorted during formation. malformation quality PATO:0000646 malformed A morphological quality inhering in a bearer by virtue of the bearer's being distorted during formation. PATOC:MAH A rate which is relatively low. slow rate quality PATO:0000911 decreased rate A rate which is relatively low. PATO:GVG A rate which is relatively high. fast rate high rate quality PATO:0000912 increased rate A rate which is relatively high. PATO:GVG A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. quality PATO:0000918 volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. PATOC:GVG A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality density PATO:0001019 mass density A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. WordNet:WordNet A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. quality PATO:0001025 pressure A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. force amplitude quality PATO:0001035 force A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. thesaurus.maths:thesaurus.maths A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus. resistance quality PATO:0001046 resistance to A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus. PATOC:GVG A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. quality PATO:0001164 dense A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. PATOC:GVG A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus. resistant quality PATO:0001178 resistant to A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being located more centrally than another entity. quality PATO:0001195 proximal to A spatial quality inhering in a bearer by virtue of the bearer's being located more centrally than another entity. PATOC:nw A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in an process. PATOC:GVG physical object quality A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATO:0000081 period quality time PATO:0001309 duration A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATOC:mellybelly A monadic quality of continuant that exists at the cellular level of organisation. quality PATO:0001396 cellular quality A monadic quality of continuant that exists at the cellular level of organisation. PATOC:GVG A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. quality PATO:0001404 nucleate quality A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. quality PATO:0001405 anucleate A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. quality PATO:0001406 binucleate A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. quality PATO:0001407 mononucleate A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. Biology-online:Biology-online A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311). calcareous calcification quality PATO:0001447 calcified A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311). thefreedictionary.com:thefreedictionary.com A quality inhering in a bearer by virtue of the bearer's being present in two copies. doubled quality PATO:0001473 duplicated A quality inhering in a bearer by virtue of the bearer's being present in two copies. Dictionary.com:Dictionary.com A position which is relatively high. quality high position PATO:0001475 increased position A position which is relatively high. PATOC:GVG A positional which is relatively low. quality low position PATO:0001476 decreased position A positional which is relatively low. PATOC:GVG A quality of a single physical entity that arises by virtue of whether the bearer exhibits the ability to perform a regular function(s). quality PATO:0001509 functionality A quality of a single physical entity that arises by virtue of whether the bearer exhibits the ability to perform a regular function(s). PATOC:MAH A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. liquidity quality PATO:0001548 quality of a liquid A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. url:http://www.chemistry-dictionary.com/definition/liquid.php The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. OBO_REL:has_part extra or missing physical or functional parts has or lacks parts of type mereological quality number of quality cardinality number PATO:0001555 has number of The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. PATOC:CJM A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity. quality PATO:0001558 lacking processual parts A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity. PATOC:GVG A functionality quality which is held by the bearer when the latter is able to perform additional or different function(s). having supernumerary functions quality PATO:0001559 having extra function A functionality quality which is held by the bearer when the latter is able to perform additional or different function(s). PATO:MAH A quality of a process inhering in a bearer by virtue of the bearer's processual parts. quality PATO:0001564 extra or missing processual parts A quality of a process inhering in a bearer by virtue of the bearer's processual parts. PATOC:GVG A pressure which is relatively low. low pressure quality PATO:0001575 decreased pressure A pressure which is relatively low. PATO:GVG A pressure which is relatively high. high pressure quality PATO:0001576 increased pressure A pressure which is relatively high. PATO:GVG A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form. quality disfigured distorted PATO:0001617 deformed A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form. thefreedictionary.com:thefreedictionary.com An 1-D extent quality which is equal to the length of the closed curve of a circle. quality PATO:0001648 circumference An 1-D extent quality which is equal to the length of the closed curve of a circle. WordNet:WordNet A resistance to a stimulus which is relatively high. high resistance to increased resistance quality PATO:0001650 increased resistance to A resistance to a stimulus which is relatively high. PATOC:GVG A resistance to a stimulus which is relatively low. decreased resistance low resistance to quality PATO:0001651 decreased resistance to A resistance to a stimulus which is relatively low. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. 1-D size quality PATO:0001708 1-D extent A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. 3D size quality PATO:0001710 3-D extent A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. PATOC:GVG An 1-D extent quality inhering in two-dimensional bearer by virtue of being equal to the distance around it. quality PATO:0001711 perimeter An 1-D extent quality inhering in two-dimensional bearer by virtue of being equal to the distance around it. Wikipedia:http://en.wikipedia.org/wiki/Perimeter A perimeter which is relatively high. quality PATO:0001712 increased perimeter A perimeter which is relatively high. PATOC:GVG A perimeter which is relatively low. quality PATO:0001713 decreased perimeter A perimeter which is relatively low. PATOC:GVG A density which is higher relative to the normal or average. high density quality PATO:0001788 increased mass density A density which is higher relative to the normal or average. PATOC:GVG A density which is lower relative to the normal or average. low density quality PATO:0001790 decreased mass density A density which is lower relative to the normal or average. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's increasing over time. quality PATO:0001818 progressive A quality of a single process inhering in a bearer by virtue of the bearer's increasing over time. PATOC:GVG A shape quality in a bearer by virtue of the bearer's curving inward. quality PATO:0001857 concave A shape quality in a bearer by virtue of the bearer's curving inward. WordNet:WordNet A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. quality PATO:0001863 chronic A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. PATOC:cjm A quality inhering in a bearer by virtue of the bearer's being abnormal and having a destructive effect on living tissue. quality PATO:0001869 pathological A quality inhering in a bearer by virtue of the bearer's being abnormal and having a destructive effect on living tissue. PATOC:cjm A shape quality inhering in a bearer by virtue of the bearer's having three angles. deltoid quality delta shaped triangle triangle-shaped PATO:0001875 triangular A shape quality inhering in a bearer by virtue of the bearer's having three angles. wordreference:wordreference A circumference which is relatively high. quality PATO:0001898 increased circumference A circumference which is relatively high. PATOC:GVG A circumference which is relatively low. quality PATO:0001899 decreased circumference A circumference which is relatively low. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. quality PATO:0001908 multinucleate A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. PATOC:GVG An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. quality PATO:0001992 cellularity An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. PATOC:GVG A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. quality PATO:0001993 multicellular A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. PATOC:GVG organismal quality A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality A quality that inheres in an entire organism or part of an organism. PATOC:CJM An amount which is relatively low. PATO:0000419 PATO:0000468 decreased number present in fewer numbers in organism quality decreased reduced subnumerary PATO:0001997 decreased amount An amount which is relatively low. PATOC:GVG The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type. loss of quality PATO:0001999 lacks parts or has fewer parts of type The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type. PATOC:CJM A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity. PATO:0001557 OBO_REL:lacks_part lacks all physical parts of type quality PATO:0002000 Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2. lacks all parts of type A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity. PATOC:CJM The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. PATO:0001569 decreased number of has decreased number of has fewer physical parts of type quality PATO:0002001 Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type. has fewer parts of type The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. PATOC:CJM The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. PATO:0001560 has extra parts of has increased number of having extra physical parts having supernumerary physical parts increased number of quality PATO:0002002 In polydactyly, the bearer of the quality is the hand, and the entity type being counted is 'finger'. In EQ syntax, E=hand, Q=<this> E2=finger. has extra parts of type The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. PATOC:CJM Surface shape that refers to the inward or outward curvature of the surface. quality PATO:0002005 concavity Surface shape that refers to the inward or outward curvature of the surface. PATOC:MAH A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. quality 2-D projection cross-sectional PATO:0002006 2-D shape A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. PATOC:CJM A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity. quality PATO:0002009 branchiness A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity. PATOC:MAH An occurrence which is relatively high. George Gkoutos 2009-03-26T11:10:11Z increased incidence quality PATO:0002051 increased occurrence An occurrence which is relatively high. PATOC:GVG An occurrence which is relatively low. George Gkoutos 2009-03-26T11:12:35Z decreased incidence quality PATO:0002052 decreased occurrence An occurrence which is relatively low. PATOC:GVG george 2009-06-05T09:16:46Z quality PATO:0002062 physical quality of a process Having extra or fewer parts. George Gkoutos 2009-09-21T10:41:58Z quality PATO:0002083 altered number of Having extra or fewer parts. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. george 2009-10-06T04:37:14Z quality PATO:0002124 laminar A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's changed direction of position towards another entity. George Gkoutos 2010-02-25T09:14:42Z quality PATO:0002175 deviation A spatial quality inhering in a bearer by virtue of the bearer's changed direction of position towards another entity. PATO:GVG A deviation quality inhering in a bearer by virtue of the bearer's changed direction of position towards the side. George Gkoutos 2010-02-25T09:16:04Z quality PATO:0002176 deviation towards the lateral side A deviation quality inhering in a bearer by virtue of the bearer's changed direction of position towards the side. PATOC:GVG A quality inhering in a bearer by virtue of its constitution. George Gkoutos 2010-03-15T04:35:27Z quality PATO:0002198 quality of a substance A quality inhering in a bearer by virtue of its constitution. PATOC:GVG handedness A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. handedness left handedness Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. left handedness right handedness Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. right handedness ambidextrous handedness Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. ambidextrous handedness A force which relative high. george 2010-08-04T11:12:20Z increased force amplitude quality PATO:0002245 increased force A force which relative high. PATOC:GVG A force which is relative low. george 2010-08-04T11:13:13Z decreased force amplitude quality PATO:0002246 decreased force A force which is relative low. PATOC:GVG A mobility which is relative high. george 2011-03-09T09:16:03Z quality PATO:0002282 increased mobility A mobility which is relative high. PATO:GVG A mobility which is relative low. george 2011-03-09T09:16:47Z quality PATO:0002283 decreased mobility A mobility which is relative low. PATOC:GVG George Gkoutos 2011-04-18T05:11:33Z quality PATO:0002290 aplastic/hypoplastic A quality that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:39:43Z quality PATO:0002300 increased quality A quality that has a value that is increased compared to normal or average. PATOC:GVG A quality that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:40:15Z quality PATO:0002301 decreased quality A quality that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:50:59Z quality PATO:0002302 decreased process quality A quality of a process that has a value that is decreased compared to normal or average. PATOC:GVG A quality of an object that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:51:54Z quality PATO:0002303 decreased object quality A quality of an object that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:53:08Z quality PATO:0002304 increased process quality A quality of a process that has a value that is increased compared to normal or average. PATOC:GVG A quality of an object that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:54:01Z quality PATO:0002305 increased object quality A quality of an object that has a value that is increased compared to normal or average. PATOC:GVG A temporal distribution pattern of process occurrences within a regulation/reference process. George Gkoutos 2011-11-22T01:12:28Z quality PATO:0002323 temporal distribution quality A temporal distribution pattern of process occurrences within a regulation/reference process. PATOC:LC The temporal relation between the start of the process with respect to a reference process. George Gkoutos 2011-11-23T11:47:34Z quality initiation PATO:0002325 onset quality The temporal relation between the start of the process with respect to a reference process. PATOC:LC A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. gkoutos 2013-10-21T05:44:34Z quality PATO:0002505 nucleated A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. PATOC:GVG A plant structure (PO:0005679) which is a whole organism. genet (broad) ramet (broad) PO_GIT:538 PO_GIT:69 planta entera (Spanish, exact) 植物体全体 (Japanese, exact) bush (narrow) frutex (narrow) frutices (narrow) gametophyte (narrow) herb (narrow) liana (narrow) prothalli (narrow) prothallium (narrow) prothallus (narrow) seedling (narrow) shrub (narrow) sporophyte (narrow) suffrutex (narrow) suffrutices (narrow) tree (narrow) vine (narrow) woody clump (narrow) plant_anatomy clonal colony (related) colony (related) PO:0000003 Examples include plant embryo (PO:0009009), megagametophyte (PO:0025279) and microgametophyte (PO:0025280). whole plant A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062), or a single carpel (PO:0009030), and at maturity may have as parts one or more seeds (PO:0009010). PO:0020067 PO:0020068 PO:0020069 PO:0020070 PO:0020071 PO:0020072 PO:0020073 PO:0020074 PO:0020076 PO:0020077 PO:0020078 PO:0020079 PO:0020080 PO:0020082 PO:0020083 PO:0020087 PO:0020107 aggregate fruit (broad) compound fruit (broad) dehiscent fruit (broad) diaspore (broad) indehiscent fruit (broad) multiple fruit (broad) propagule (broad) PO_GIT:76 frucht (exact, German) fruto (exact, Spanish) 果実 (exact, Japanese) coenocarp (narrow) syncarp (narrow) plant_anatomy PO:0009001 A fruit (PO:0009001) may contain additional plant structures (PO:0009011) that were part of a flower (PO:0009046) and mature along with the gynoecium, such as a receptacle (PO:0009064). A fruit may develop without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions and may not always contain seeds (PO:0009010). When annotating to fruit (PO:0009001) that are referred to as ‘aggregate’, ‘multiple’, or ‘compound’, please annotate directly to the appropriate plant structure, such as receptacle, hypanthium (PO:0009065) or infructescence (PO:0006342). Fruits only occur in angiosperms. fruit https://en.wikipedia.org/wiki/Fruit_anatomy A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. organ (broad) PO_GIT:55 &#243rgano vegetal (Spanish, exact) 植物 器官 (Japanese, exact) plant_anatomy compound plant organ (related) simple plant organ (related) PO:0009008 Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual plant cells (PO:0009002) that are not part of a portion of plant tissue (e.g., idioblasts, PO:0000283). A plant organ may have one or more different plant organs as parts, such as a sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel (PO:0009030) that may have as part a plant ovule (PO:0020003). plant organ A whole plant (PO:0000003) that participates in the plant embryo stage (PO:0007631). plant embryo A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088). diaspore (broad) PO_GIT:405 semilla (Spanish, exact) 種子 (Japanese, exact) pyrene (narrow) plant_anatomy PO:0009010 A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms). seed A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. PO_GIT:57 estructura vegetal (Spanish, exact) 植物 構造 (Japanese, exact) plant_anatomy PO:0009011 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. plant structure A collective phyllome structure (PO:0025023) composed all of the carpels (PO:0009030) in a flower (PO:0009046). gynoecium A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006). plant ovule A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007). rwalls 2010-02-09T04:12:11Z PO_GIT:63 estructura vegetal colectiva de &#243rgano (Spanish, exact) 集合植物器官構造 (Japanese, exact) plant_anatomy PO:0025007 Organs can be of the same type or different types. Examples include flower (PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs, but no complete plant organs. This was formerly named collective plant structure. collective plant organ structure A collective plant organ structure (PO:0025007) that consists of two or more phyllomes (PO:0006001) originating from the same node or from one or more adjacent nodes with compressed shoot internodes (PO:0005005). Laurel_Cooper 2010-04-28T11:04:34Z PO:0008033 cycle (broad) verticil (broad) PO_GIT:90 PO_GIT:99 estructura colectiva del filoma (Spanish, exact) 葉的器官が集まった構造 (Japanese, exact) floral whorl (narrow) whorl (narrow) plant_anatomy phyllome whorl (related) PO:0025023 collective phyllome structure A plant structure (PO:0009011) that is part of an plant embryo (PO:0009009). rwalls 2010-11-05T01:36:24Z PO_GIT:245 PO_GIT:339 embryonic plant structure (exact) estructura vegetal embri&#243nica (Spanish, exact) 胚性植物構造 (Japanese, exact) plant_anatomy PO:0025099 Includes plant structures that only occur in embryos (such as suspensor) as well as plant structures that are part of an embryo when a plant is in the embryonic phase (such as embryonic radicle). embryo plant structure A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. Laurel_Cooper 2012-06-11T14:57:00Z PO_GIT:480 estructura vegetal con m&#250ltiples tejidos (Spanish, exact) 複数の組織からなる植物構造 (Japanese, exact) plant_anatomy PO:0025496 Most multi-tissue plant structures have at least a small connection to other plant structures via a fiat boundary, such as where a leaf (PO:0025034) connects to a shoot axis (PO:0025029), a petal (PO:0009032) connects to a receptacle (PO:0009064), or a branch (PO:0025073) connects to a stem (PO:0009047). Refers to CARO:0000055 multi-tissue structure, def'n: Anatomical structure that has as parts two or more portions of tissue of at least two different types, and which through specific morphogenetic processes, form a single distinct structural unit demarcated by bona-fide boundries from other structural units of differnt types. multi-tissue plant structure A plant structure (PO:0009011) that is a proper part of a whole plant (PO:0000003) and includes two or more adjacent plant organs (PO:0009008) or adjacent cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007). Laurel_Cooper 2012-06-11T15:09:20Z PO_GIT:479 estructura vegetal colectiva (Spanish, exact) 集合的植物構造 (Japanese, exact) plant_anatomy PO:0025497 This is a parent term to describe both collective organ part structure (PO:0025269) (e.g. septum), as well as collective plant organ structure (PO:0025007) (which was formerly named collective plant structure), for example shoot system (PO:0009006). collective plant structure protein antithrombin III is a protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall http://www.jbiomedsem.com/content/4/1/43 system An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. uberon UBERON:0000000 processual entity An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. span:ProcessualEntity uterine cervix Lower, narrow portion of the uterus where it joins with the top end of the vagina. The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] cervical cervix BTO:0001421 BTO:0002249 CALOHA:TS-0134 EFO:0000979 EMAPA:29927 EV:0100114 FMA:17740 GAID:376 MA:0000392 MAT:0000292 MESH:D002584 NCIT:C12311 OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA UMLS:C0007874 VHOG:0001359 galen:CervixUteri canalis cervicis uteri caudal segment of uterus cervical canal of uterus cervix uteri neck of uterus uterine cervix uberon cervical canal cervix of uterus UBERON:0000002 uterine cervix Lower, narrow portion of the uterus where it joins with the top end of the vagina. The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] 2012-09-17 VHOG:0001359 VHOG The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] 2012-09-17 VHOG:0001359 VHOG DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004) cervix EFO:0000979 UMLS:C0007874 ncithesaurus:Cervix canalis cervicis uteri FMA:17740 FMA:TA cervical canal of uterus FMA:17740 cervix uteri EMAPA:29927 neck of uterus FMA:17740 uterine cervix FMA:17740 cervical canal FMA:17740 cervix of uterus BTO:0001421 Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH]. One of paired external openings of the nasal chamber.[AAO] Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure AAO:0000311 EHDAA2:0001225 EHDAA:9083 EMAPA:17847 MA:0000282 VHOG:0000663 galen:Naris uberon UBERON:0000003 naris ZFA Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH]. One of paired external openings of the nasal chamber.[AAO] 2012-06-20 AAO:0000311 AAO AAO:EJS Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] 2012-09-17 VHOG:0000663 VHOG DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004) we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure FMA The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. the organ that is specialized for smell and is part of the respiratory system the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359] BTO:0000840 CALOHA:TS-2037 EHDAA2:0001274 EHDAA:1502 EMAPA:16542 EV:0100037 EV:0100370 FMA:46472 GAID:77 MA:0000281 MAT:0000139 MESH:D009666 MIAA:0000139 NCIT:C12756 OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA TAO:0000047 UMLS:C0028429 ZFA:0000047 galen:Nose nasal sac nose peripheral olfactory organ uberon nasus olfactory apparatus proboscis UBERON:0000004 nose http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg FMA ZFA-def ZFA The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. UBERON:cjm Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. ZFA:0000047 a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. the organ that is specialized for smell and is part of the respiratory system MP:0002233 UMLS:C0028429 ncithesaurus:Nose nasal sac ZFA:0000047 nose MA:0000281 peripheral olfactory organ ZFA:0000047 nasus olfactory apparatus UBERON:cjm FBbt:00005157 chemosensory sensory organ uberon UBERON:0000005 chemosensory organ chemosensory sensory organ FBbt:00005157 the clusters of hormone-producing cells that are scattered throughout the pancreas Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG] A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986) AAO:0010406 BTO:0000991 CALOHA:TS-0741 EFO:0000856 EMAPA:32927 EV:0100130 FMA:16016 GAID:324 MA:0000127 MAT:0000076 MESH:D007515 MIAA:0000076 NCIT:C12608 UMLS:C0022131 VHOG:0000646 XAO:0000159 pancreatic insula pancreatic islet uberon island of Langerhans island of pancreas islets of Langerhans UBERON:0000006 islet of Langerhans http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png the clusters of hormone-producing cells that are scattered throughout the pancreas MA:0000127 MESH:A03.734.414 MP:0005215 Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] 2012-06-20 AAO:0010406 AAO AAO:BJB Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG] 2012-09-17 VHOG:0000646 VHOG PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995) A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986) UMLS:C0022131 ncithesaurus:Islet_of_Langerhans island of Langerhans BTO:0000991 island of pancreas BTO:0000991 pituitary gland The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO] An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9] Hp AAO:0010536 BAMS:PIT BAMS:Pit BIRNLEX:1353 BM:Die-Hy-HY BTO:0001073 CALOHA:TS-0798 DHBA:10505 EFO:0000857 EHDAA2:0001471 EHDAA:2183 EHDAA:4477 EMAPA:35998 EV:0100132 FMA:13889 GAID:457 HBA:4634 MA:0000176 MAT:0000077 MESH:D010902 MIAA:0000077 NCIT:C12399 OpenCyc:Mx4rv6NQYJwpEbGdrcN5Y29ycA TAO:0000118 UMLS:C0032005 VHOG:0000143 XAO:0000017 ZFA:0000118 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=399 glandula pituitaria pituitary pituitary body uberon hypophysis hypophysis cerebri UBERON:0000007 Terminology note: hypophysis and pituitary gland are often used informally as synonyms, but the hypophysis also includes the small infundibular or pituitary stalk[Neumann 2020] pituitary gland http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png BGEE:ANN The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. ZFIN:curator An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO] 2012-06-20 AAO:0010536 AAO AAO:BJB An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO] 2012-08-14 TAO:0000118 TAO ZFIN:curator It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000143 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 Hp BIRNLEX:1353 NIFSTD:NeuroNames_abbrevSource UMLS:C0032005 BIRNLEX:1353 UMLS:C0032005 ncithesaurus:Pituitary_Gland http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=399 BIRNLEX:1353 glandula pituitaria pituitary BTO:0001073 pituitary body BTO:0001073 hypophysis ZFA:0000118 hypophysis cerebri MA:0000176 A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. submucosal BTO:0002107 FMA:85391 FMA:85392 NCIT:C13167 UMLS:C0225344 organ submucosa region of submucosa submucosa of organ submucosa of region of organ uberon submucous layer tela submucosa tunica submucosa UBERON:0000009 submucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. UMLS:C0225344 ncithesaurus:Submucosa organ submucosa FMA:85391 region of submucosa FMA:85392 submucosa of organ FMA:85391 submucosa of region of organ FMA:85392 submucous layer BTO:0002107 tela submucosa BTO:0002107 A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] PNS AAO:0000429 BAMS:PNS BILA:0000081 BIRNLEX:1111 BTO:0001028 CALOHA:TS-0808 EFO:0000891 EHDAA2:0001445 EHDAA:2893 EMAPA:16665 EV:0100335 FBbt:00005098 FMA:9903 GAID:715 MA:0000218 MAT:0000338 MESH:D017933 MIAA:0000338 NCIT:C12465 TAO:0000142 UMLS:C0206417 UMLS:C1305921 VHOG:0000399 XAO:0000178 ZFA:0000142 pars peripherica systema nervosum periphericum uberon UBERON:0000010 peripheral nervous system http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png cjm A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. GO:0007422 Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000142 TAO ZFIN:curator Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] 2012-06-20 AAO:0000429 AAO AAO:BJB The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] 2012-09-17 VHOG:0000399 VHOG DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006) PNS UMLS:C0206417 BIRNLEX:1111 UMLS:C0206417 ncithesaurus:Peripheral_Nervous_System UMLS:C1305921 BIRNLEX:1111 pars peripherica FMA:9903 FMA:TA systema nervosum periphericum FMA:9903 FMA:TA The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO]. Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO] In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG] AAO:0010488 BIRNLEX:2517 BTO:0001833 CALOHA:TS-2094 EFO:0000894 EHDA:10096 EHDAA2:0001402 EHDAA:4655 EMAPA:17270 FMA:9907 GAID:708 MA:0000223 MAT:0000101 MESH:D010275 MIAA:0000101 NCIT:C12764 TAO:0001575 UMLS:C0030510 UMLS:C1305770 VHOG:0000755 ZFA:0001575 PNS - parasympathetic parasympathetic part of autonomic division of nervous system pars parasympathica divisionis autonomici systematis nervosi uberon pars parasympathica divisionis autonomici systematis nervosi UBERON:0000011 parasympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png cjm FMA MA WP ZFA-modified-from-isa The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO]. GO:0048486 Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO] 2012-06-20 AAO:0010488 AAO AAO:BJB In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000755 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998) UMLS:C0030510 BIRNLEX:2517 UMLS:C0030510 ncithesaurus:Parasympathetic_Nervous_System UMLS:C1305770 BIRNLEX:2517 pars parasympathica divisionis autonomici systematis nervosi FMA:9907 FMA:TA pars parasympathica divisionis autonomici systematis nervosi Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. EFO:0000892 FMA:9904 MA:0002850 MAT:0000099 MIAA:0000099 NLXANAT:100301 PNS - somatic somatic nervous system, somatic division somatic part of peripheral nervous system somatic peripheral nervous system uberon UBERON:0000012 somatic nervous system cjm Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. NLXANAT:100301 somatic nervous system, somatic division NLXANAT:100301 somatic part of peripheral nervous system UBERON:cjm somatic peripheral nervous system NLXANAT:100301 The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest) AAO:0010487 BIRNLEX:2516 BTO:0001832 CALOHA:TS-2050 EFO:0000893 EHDAA2:0001971 EHDAA:3769 EMAPA:16985 FMA:9906 GAID:710 MA:0000225 MESH:D013564 MIAA:0000100 NCIT:C12795 TAO:0001576 UMLS:C0039044 UMLS:C1269646 VHOG:0000384 ZFA:0001576 pars sympathica divisionis autonomici systematis nervosi sympathetic nervous system sympathetic part of autonomic division of nervous system uberon pars sympathica divisionis autonomici systematis nervosi UBERON:0000013 sympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png cjm FMA MA ZFA-modified-from-isa The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. GO:0048485 Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] 2012-06-20 AAO:0010487 AAO AAO:BJB The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000384 VHOG The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] 2012-09-17 VHOG:0000384 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463 UMLS:C0039044 BIRNLEX:2516 UMLS:C0039044 ncithesaurus:Sympathetic_Nervous_System UMLS:C1269646 BIRNLEX:2516 pars sympathica divisionis autonomici systematis nervosi FMA:9906 FMA:TA pars sympathica divisionis autonomici systematis nervosi Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive EHDAA2:0001844 EHDAA:6530 EMAPA:17525 EV:0100152 FMA:86166 GAID:933 MA:0000151 MAT:0000284 MESH:D012867 MIAA:0000284 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA VHOG:0000860 portion of skin region of skin skin skin region skin zone uberon UBERON:0000014 zone of skin http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg FMA Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] 2012-09-17 VHOG:0000860 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) skin MA:0000151 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. AEO:0000192 CARO:0000010 FMA:50705 anatomical boundary uberon UBERON:0000015 Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. non-material anatomical boundary CARO A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CARO:0000010 anatomical boundary CARO:0000010 The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. create a separate class for distributed pancreas, eg cyclostomes? The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG] The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys BTO:0000650 CALOHA:TS-1302 EFO:0002542 EMAPA:35305 EV:0100129 FMA:16018 MA:0001582 NCIT:C32509 TAO:0001260 VHOG:0000049 ZFA:0001260 endocrine pancreas pars endocrina pancreatis uberon endocrine part of pancreas islets of Langerhans part of pancreas UBERON:0000016 endocrine pancreas ZFA AAO FMA XAO The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. GO:GO The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG] 2012-09-17 VHOG:0000049 VHOG The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO] 2012-08-14 TAO:0001260 TAO ZFIN:curator In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] 2012-09-17 VHOG:0000049 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys endocrine part of pancreas BTO:0000650 The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] AAO:0010407 BTO:0000434 CALOHA:TS-1241 EMAPA:35328 EV:0100093 FMA:16017 MA:0002415 NCIT:C32546 TAO:0001249 UMLS:C0553695 VHOG:0000048 XAO:0000137 ZFA:0001249 exocrine pancreas pars exocrina pancreatis uberon exocrine component of pancreas exocrine part of pancreas UBERON:0000017 exocrine pancreas The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. GOC:GO The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] 2012-08-14 TAO:0001249 TAO ZFIN:curator The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG] 2012-09-17 VHOG:0000048 VHOG In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] 2012-09-17 VHOG:0000048 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) UMLS:C0553695 ncithesaurus:Exocrine_Pancreas exocrine part of pancreas BTO:0000434 An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. A cavitated compound organ that transduces light waves into neural signals.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this eye AAO:0010340 BIRNLEX:1169 BTO:0004688 EHDAA2:0000484 EHDAA:936 EMAPA:16198 FMA:54448 MA:0000261 NCIT:C12401 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA TAO:0000107 UMLS:C0015392 UMLS:C1280202 VHOG:0000275 XAO:0000179 ZFA:0000107 regio orbitalis vertebrate eye uberon camera-type eye plus associated structures eyes orbital part of face orbital region UBERON:0000019 camera-type eye definitional An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. GO:0043010 A cavitated compound organ that transduces light waves into neural signals.[TAO] 2012-08-14 TAO:0000107 TAO TAO:wd The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000275 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this FMA eye FMA:54448 UMLS:C0015392 BIRNLEX:1169 UMLS:C0015392 ncithesaurus:Eye UMLS:C1280202 BIRNLEX:1169 regio orbitalis FMA:54448 FMA:TA eyes TAO:0000107 orbital part of face FMA:54448 orbital region FMA:54448 An organ that is capable of transducing sensory stimulus to the nervous system. AEO:0000094 BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 NCIT:C33224 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensory organ sensory organ system organ sensory system organ sensillum uberon Sinnesorgan sensor UBERON:0000020 sense organ http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png An organ that is capable of transducing sensory stimulus to the nervous system. UMLS:C0935626 ncithesaurus:Organ_of_the_Special_Sense organ of sense organ system OBOL:accepted organ of sensory organ system OBOL:accepted organ of sensory system OBOL:accepted sense organ system organ OBOL:automatic sensory organ system organ OBOL:automatic sensory system organ OBOL:accepted sensillum WBbt:0006929 Sinnesorgan BTO:0000202 Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here. CALOHA:TS-0051 FMA:71012 skin appendage epidermal appendage uberon epidermal growth UBERON:0000021 cutaneous appendage Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. skin appendage FMA:71012 Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) tubular galen:Tube anatomical tube duct uberon UBERON:0000025 tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. Major subdivision of an organism that protrudes from the body[DOS, CARO]. An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. appendicular this is currently a subtype of organism subdivision - which would exclude feathers AEO:0000193 BILA:0000018 BTO:0001492 CARO:0010003 EFO:0000799 EHDAA2:0003193 EMAPA:37283 EV:0100155 FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 MIAA:0000023 NCIT:C61460 OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA UMLS:C0598782 VSAO:0000075 XAO:0000218 uberon appendages extremitaet extremity limbs/digits/tail UBERON:0000026 appendage Major subdivision of an organism that protrudes from the body[DOS, CARO]. CARO:DOS An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. BILA:0000018 Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. GO:0048736 EMAPA:37283 MA:th UMLS:C0598782 ncithesaurus:Appendage appendages XAO:0000218 extremitaet BTO:0001492 limbs/digits/tail MP:0000001 lymph node Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] BTO:0000784 CALOHA:TS-0579 EFO:0000872 EMAPA:35523 EV:0100050 FMA:5034 GAID:947 MA:0000139 MAT:0000442 MESH:D008198 NCIT:C12745 NCIT:C33027 OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA TAO_RETIRED:0005318 UMLS:C0024204 VHOG:0001273 ZFA_RETIRED:0005318 galen:Lymphnode uberon lymph gland nodus lymphaticus UBERON:0000029 lymph node https://github.com/obophenotype/uberon/issues/650 http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. BTO:0000784 Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] 2012-09-17 VHOG:0001273 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630 UMLS:C0024204 ncithesaurus:Lymph_Node lymph gland VHOG:0001273 nodus lymphaticus A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. BTO:0002330 FMA:62517 NCIT:C32918 UMLS:C1179187 lamina propria mucosa lamina propria mucosae uberon tunica propria UBERON:0000030 lamina propria GI:Organization.svg A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. UMLS:C1179187 ncithesaurus:Lamina_Propria tunica propria BTO:0002330 A lamina propria that is part of a respiratory airway. EMAPA:35877 FMA:265157 MA:0001858 NCIT:C49305 UMLS:C1710457 lamina propria mucosa of trachea lamina propria mucosa of windpipe lamina propria mucosae of trachea lamina propria mucosae of windpipe lamina propria of windpipe trachea lamina propria trachea lamina propria mucosa trachea lamina propria mucosae tracheal lamina propria windpipe lamina propria windpipe lamina propria mucosa windpipe lamina propria mucosae uberon UBERON:0000031 lamina propria of trachea true A lamina propria that is part of a respiratory airway. OBOL:automatic UMLS:C1710457 ncithesaurus:Trachea_Lamina_Propria lamina propria mucosa of trachea OBOL:automatic lamina propria mucosa of windpipe OBOL:automatic lamina propria mucosae of trachea OBOL:automatic lamina propria mucosae of windpipe OBOL:automatic lamina propria of windpipe OBOL:automatic trachea lamina propria mucosa OBOL:automatic trachea lamina propria mucosae OBOL:automatic windpipe lamina propria OBOL:automatic windpipe lamina propria mucosa OBOL:automatic windpipe lamina propria mucosae OBOL:automatic The head is the anterior-most division of the body [GO]. Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] AAO:0010335 AEO:0000106 BILA:0000115 BIRNLEX:1230 BTO:0000282 CALOHA:TS-0436 EFO:0000964 EHDAA2:0003106 EMAPA:31858 FBbt:00000004 FMA:7154 GAID:61 HAO:0000397 MA:0000023 MAT:0000294 MESH:D006257 MIAA:0000294 NCIT:C12419 OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA SPD:0000016 TAO:0001114 TGMA:0000002 UMLS:C0018670 VHOG:0001644 WBbt:0005739 XAO:0003024 ZFA:0001114 galen:Head head (volume) adult head uberon cephalic area UBERON:0000033 head The head is the anterior-most division of the body [GO]. GO:0060322 Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] 2012-06-20 AAO:0010335 AAO AAO:BJB Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] 2012-08-14 TAO:0001114 TAO ZFIN:curator Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] 2012-09-17 VHOG:0001644 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 UMLS:C0018670 BIRNLEX:1230 UMLS:C0018670 ncithesaurus:Head head (volume) FMA:7154 cephalic area SPD:0000016 multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA:9581 GAID:19 MESH:D012704 NCIT:C13169 TAO:0005425 UMLS:C0036760 ZFA:0005425 tunica serosa wall of serous sac uberon serosa UBERON:0000042 serous membrane http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] 2012-08-14 TAO:0005425 TAO a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA UMLS:C0036760 ncithesaurus:Serosa tunica serosa FMA:9581 wall of serous sac FMA:9581 serosa Dense regular connective tissue that connects muscle to bone[VSAO]. Dense regular connective tissue that connects muscle to bone.[VSAO] Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis AEO:0000091 BTO:0001356 CALOHA:TS-1021 EHDAA2:0003091 EMAPA:35854 EV:0100149 FMA:9721 GAID:276 MA:0000115 MESH:D013710 NCIT:C13045 OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA UMLS:C0039508 VHOG:0001286 VSAO:0000073 XAO:0000173 ZFA:0005647 galen:Tendon uberon sinew tendo UBERON:0000043 tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg VSAO OG Dense regular connective tissue that connects muscle to bone[VSAO]. GO_REF:0000034 VSAO:0000073 Dense regular connective tissue that connects muscle to bone.[VSAO] 2012-08-14 VSAO:0000073 VSAO PSPUB:0000170 Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] 2012-09-17 VHOG:0001286 VHOG DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002) in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis FMA UMLS:C0039508 ncithesaurus:Tendon sinew tendo A biological tissue mass, most commonly a mass of nerve cell bodies. TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] ganglionic AAO:0010426 AEO:0000135 BAMS:G BTO:0000497 CALOHA:TS-0397 EFO:0000899 EHDAA2:0003135 EHDAA:2897 EHDAA:4662 EHDAA:5621 EHDAA:918 EMAPA:32846 EV:0100372 FBbt:00005137 FMA:5884 MA:0002406 MAT:0000207 MAT:0000343 MESH:D005724 MIAA:0000207 MIAA:0000343 NCIT:C12719 NLXANAT:100302 TAO:0000190 TGMA:0001016 UMLS:C0017067 VHOG:0000156 WBbt:0005189 XAO:0000209 ZFA:0000190 uberon ganglia neural ganglion UBERON:0000045 ganglion EHDAA2 Bgee:AN A biological tissue mass, most commonly a mass of nerve cell bodies. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] 2012-06-20 AAO:0010426 AAO AAO:EJS Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000190 TAO ZFIN:curator Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. NLXANAT:100302 Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000156 VHOG DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005) UMLS:C0017067 ncithesaurus:Ganglion neural ganglion BTO:0000497 An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. TGMA:0000729 uberon UBERON:0000047 simple eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. A tubular structure that contains, conveys body fluid, such as blood or lymph. uberon UBERON:0000055 vessel A tubular structure that contains, conveys body fluid, such as blood or lymph. Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] ureteral ureteric in humans, consists of adventitial, muscular and mucoa layers AAO:0010254 BTO:0001409 CALOHA:TS-1084 EFO:0000930 EHDAA2:0002139 EHDAA:9341 EMAPA:17950 EV:0100097 FMA:9704 GAID:438 MA:0000378 MAT:0000120 MESH:D014513 MIAA:0000120 NCIT:C12416 OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA UMLS:C0041951 VHOG:0000605 XAO:0000144 galen:Ureter uberon metanephric duct UBERON:0000056 ureter Urinary:system.svg GO Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. GO:0090189 Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] 2012-06-20 AAO:0010254 AAO AAO:BJB The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000605 VHOG The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] 2012-09-17 VHOG:0000605 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C0041951 ncithesaurus:Ureter metanephric duct ISBN:0073040584 VHOG:0000605 urethra the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening urethral In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. BTO:0001426 CALOHA:TS-1132 EFO:0000931 EMAPA:30901 EV:0100099 FMA:19667 GAID:390 MA:0000379 MAT:0000121 MESH:D014521 MIAA:0000121 NCIT:C12417 OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA UMLS:C0041967 VHOG:0001264 XAO:0000153 galen:Urethra uberon UBERON:0000057 urethra Female:anatomy.png pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra Wikipedia Wikipedia the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening MGI:anna MP:0000537 UMLS:C0041967 ncithesaurus:Urethra A tubular structure that transports secreted or excreted substances. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 FBbt:00100314 FMA:30320 NCIT:C12948 TAO:0005171 UMLS:C0687028 XAO:0004000 ZFA:0005171 galen:Duct anatomical duct exocrine duct exocrine gland duct uberon ducts UBERON:0000058 duct A tubular structure that transports secreted or excreted substances. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. ZFA:0005171 UMLS:C0687028 ncithesaurus:Duct ducts XAO:0004000 A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 MA:0000333 MESH:A03.492.411.495 MIAA:0000046 NCIT:C12379 OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA UMLS:C0021851 VHOG:0000054 XAO:0000131 galen:LargeIntestine uberon intestinum crassum UBERON:0000059 large intestine cjm A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. ISBN:0073040584 Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000054 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 UMLS:C0021851 ncithesaurus:Large_Intestine intestinum crassum BTO:0000706 Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. in FMA, serosa is a wall UBERON:0009915 wall EMAPA:25036 FMA:82482 galen:Wall wall of organ uberon organ wall UBERON:0000060 anatomical wall Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 in FMA, serosa is a wall FMA wall of organ FMA:82482 organ wall FMA:82482 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 connected biological structure CARO:0000003 Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA UMLS:C0178784 WBbt:0003760 uberon anatomical unit body organ element UBERON:0000062 organ Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GO:0048513 UMLS:C0178784 ncithesaurus:Organ element A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary organ segment segment of organ UBERON:0000063 organ subunit A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. FMA:86140 3 Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 1 organ region with fixed fiat boundary FMA:86140 organ segment FMA:86140 segment of organ FMA:86140 A multicellular structure that is a part of an organ. currently defined in a very broad sense, may be replaced by more specific classes in the future AAO:0011124 BIRNLEX:16 EFO:0000635 FMA:82472 cardinal organ part uberon regional part of organ UBERON:0000064 organ part A multicellular structure that is a part of an organ. cardinal organ part FMA:82472 regional part of organ BIRNLEX:16 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts EHDAA2:0001606 EHDAA:1568 EHDAA:2219 EMAPA:16737 FMA:265130 OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA VHOG:0000393 uberon UBERON:0000065 respiratory tract NCBIBook:NBK10107 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. adult stage BTO:0001043 BilaDO:0000004 EFO:0001272 FBdv:00005369 WBls:0000041 XtroDO:0000084 fully formed animal stage juvenile-adult stage uberon UBERON:0000066 fully formed stage https://github.com/obophenotype/uberon/issues/566 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. A life cycle stage that starts with fertilization and ends with the fully formed embryo. BilaDO:0000002 EV:0300001 FBdv:00005289 FMA:72652 HsapDv:0000002 MmusDv:0000002 OGES:000000 OGES:000022 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryonic stage uberon embryogenesis UBERON:0000068 embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. End of the life of an organism. ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon death UBERON:0000071 death stage End of the life of an organism. XAO:0000437 ncit:Death is an outcome ncit An section of a respiratory tract. MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole EMAPA:16737 FMA:45660 MA:0000434 uberon respiratory tract subdivision of respiratory tract UBERON:0000072 proximo-distal subdivision of respiratory tract An section of a respiratory tract. MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole MA respiratory tract MA:0000434 Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. Melissa Haendel 2009-06-18T09:00:04Z BIRNLEX:1157 NCIT:C13040 UMLS:C1518256 part of nervous system uberon UBERON:0000073 regional part of nervous system Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. BIRNLEX:1157 UMLS:C1518256 ncithesaurus:Nervous_System_Part part of nervous system BIRNLEX:1157 Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERON:0010322 FMA:85544 NCIT:C34076 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system subdivision uberon skeletal system part UBERON:0000075 subdivision of skeletal system cjm Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERONREF:0000003 UMLS:C1519343 ncithesaurus:Skeletal_System_Part skeletal system subdivision FMA:85544 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis EHDAA2:0001968 EHDAA:1494 EHDAA:350 EHDAA:4784 EHDAA:4790 EHDAA:4796 EHDAA:7860 EMAPA:16096 FMA:87656 NCIT:C34309 UMLS:C1515087 surface (external) ectoderm surface ectoderm uberon UBERON:0000076 external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png EHDAA2 EHDAA2 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. MGI:anna MP:0012532 UMLS:C1515087 ncithesaurus:Surface_Ectoderm surface ectoderm MP:0012532 An anatomical structure that develops from the endoderm and the mesoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000077 mixed endoderm/mesoderm-derived structure An anatomical structure that develops from the endoderm and the mesoderm. An anatomical structure that develops from the ectoderm, mesoderm and endoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000078 mixed ectoderm/mesoderm/endoderm-derived structure An anatomical structure that develops from the ectoderm, mesoderm and endoderm. The organs associated with producing offspring in the gender that produces spermatozoa. By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] BTO:0000082 CALOHA:TS-1310 EFO:0000970 EHDAA2:0001054 EHDAA:8136 EMAPA:17968 EV:0100101 FBbt:00004927 FMA:45664 GAID:386 HAO:0000505 MA:0000396 MESH:D005837 NCIT:C12722 OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA TGMA:0000634 UMLS:C0017422 UMLS:C1963704 VHOG:0000725 WBbt:0008423 XAO:0000155 genitalia of male organism male genital system male genitalia male genitals male organism genitalia male organism reproductive system reproductive system of male organism uberon male genital organ male genital tract male reproductive tract systema genitale masculinum UBERON:0000079 male reproductive system The organs associated with producing offspring in the gender that produces spermatozoa. MP:0001145 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000725 VHOG ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43 UMLS:C0017422 ncithesaurus:Male_Genitalia UMLS:C1963704 ncithesaurus:Male_Reproductive_System genitalia of male organism OBOL:automatic male genital system FMA:45664 male organism genitalia OBOL:automatic male organism reproductive system OBOL:automatic reproductive system of male organism OBOL:automatic male genital organ BTO:0000082 male reproductive tract MA:0000396 systema genitale masculinum BTO:0000082 The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] mesonephric In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified] AAO:0010384 BTO:0001542 CALOHA:TS-0624 EFO:0000928 EHDAA2:0001130 EHDAA:1581 EHDAA:5903 EMAPA:16744 FMA:72171 GAID:1308 MESH:D001755 NCIT:C26467 TAO:0000529 UMLS:C0025492 VHOG:0000038 XAO:0000141 ZFA:0000529 Wolffian body mesonephric kidney mesonephroi uberon amphibian adult kidney corpus Wolffi middle kidney opisthonephros opisto nephros opistonephros UBERON:0000080 mesonephros http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. GO:0001823 A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] 2012-09-17 VHOG:0000038 VHOG Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] 2012-06-20 AAO:0010384 AAO AAO:BJB As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] 2012-09-17 VHOG:0000038 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 UMLS:C0025492 ncithesaurus:Mesonephros Wolffian body BTO:0001542 GOC:yaf MESH:A16.254.500 mesonephric kidney XAO:0000141 mesonephroi amphibian adult kidney XAO:0000141 corpus Wolffi BTO:0001542 middle kidney BTO:0001542 opisthonephros VHOG:0000038 XAO:0000141 opistonephros In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO] TODO check developmental relationships A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] metanephric During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis BTO:0001543 EHDAA2:0001137 EHDAA:3089 EHDAA:5911 EMAPA:17373 EMAPA_RETIRED:17207 FMA:72172 NCIT:C34209 UMLS:C0231049 VHOG:0000039 metanephron uberon definite kidney definitive kidney hind kidney metanephric kidney UBERON:0000081 metanephros definitional GO ISBN:9780878932504 In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO] GO:0001656 A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] 2012-09-17 VHOG:0000039 VHOG The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] 2012-09-17 VHOG:0000039 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C0231049 ncithesaurus:Metanephros metanephron BTO:0001543 definite kidney BTO:0001543 definitive kidney BTO:0001543 hind kidney BTO:0001543 metanephric kidney VHOG:0000039 A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. TODO check Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] AAO:0010389 EHDAA2:0001134 EMAPA:16747 VHOG:0000500 XAO:0000148 uberon renal tubules tubuli mesonephrici UBERON:0000083 mesonephric tubule A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] 2012-09-17 VHOG:0000500 VHOG As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000500 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 renal tubules VHOG:0000500 tubuli mesonephrici An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP] Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] BTO:0001646 EHDAA2:0002140 EHDAA:3091 EHDAA:5917 EMAPA:17209 NCIT:C34207 UMLS:C1284058 VHOG:0000541 uberon diverticulum diverticulum metanephricum gemma ureterica metanephric bud metanephric diverticulum ureteric ampulla ureteric diverticulum UBERON:0000084 ureteric bud EHDAA2 EHDAA2 ISBN:9780878932504 An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP] MP:0010979 Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] 2012-09-17 VHOG:0000541 VHOG Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. VHOG:0000541 The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] 2012-09-17 VHOG:0000541 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C1284058 ncithesaurus:Metanephric_Diverticulum diverticulum BTO:0001646 diverticulum metanephricum gemma ureterica metanephric bud BTO:0001646 metanephric diverticulum ureteric diverticulum VHOG:0000541 A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum. EHDAA2 has embryo starting later BTO:0001508 EHDAA2:0000005 FMA:292334 GAID:1295 MESH:A16.254.270.550 NCIT:C34212 UMLS:C0026573 uberon morula (2-16 cells) UBERON:0000085 morula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png EHDAA2 A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum. MP:0012130 EHDAA2 has embryo starting later EHDAA2 UMLS:C0026573 ncithesaurus:Morula morula (2-16 cells) EHDAA2:0000005 A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes. Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG] zona pellucida - vitelline membrane BTO:0003135 EHDAA2:0002220 EHDAA:31 EHDAA:62 EMAPA:16035 FMA:18674 GAID:410 MA:0001715 MESH:D015044 NCIT:C33896 TAO:0001111 UMLS:C0043519 VHOG:0000720 ZFA:0001111 uberon oolemma pellucid zone striated membrane vitelline envelope vitelline membrane zona radiata zona striata UBERON:0000086 zona pellucida http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes. Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG] 2012-09-17 VHOG:0000720 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159 zona pellucida - vitelline membrane VHOG:0000720 UMLS:C0043519 ncithesaurus:Zona_Pellucida oolemma BTO:0003135 pellucid zone BTO:0003135 striated membrane BTO:0003135 zona radiata BTO:0003135 zona striata BTO:0003135 A mass of cells that develop into the body of the embryo and some extraembryonic tissues A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG] A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG] This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass] EFO:0000547 EHDAA2:0000830 EHDAA:40 EMAPA:16041 FMA:86557 NCIT:C13740 UMLS:C1283994 VHOG:0000742 uberon ICM early embryoblast embryoblast embryoblastus; massa cellularis interna; pluriblastus senior pluriblast UBERON:0000087 inner cell mass Blastocyst:English.svg Wikipedia Wikipedia A mass of cells that develop into the body of the embryo and some extraembryonic tissues ISBN:0-683-40008-8 MGI:pvb A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG] 2012-09-17 VHOG:0000742 VHOG A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG] 2012-09-17 VHOG:0000742 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144 UMLS:C1283994 ncithesaurus:Inner_Cell_Mass ICM VHOG:0000742 early embryoblast FMA:86557 embryoblastus; massa cellularis interna; pluriblastus senior the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP] trophoblastic The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta BTO:0001079 CALOHA:TS-1070 EV:0100120 FMA:83029 GAID:1152 MESH:A11.936 NCIT:C93292 UMLS:C0041178 trophoblast layer uberon massa cellularis externa trophoblastus trophoderm UBERON:0000088 Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg. [Wikipedia:Trophoblast] trophoblast Blastocyst:English.svg MP-def the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta ISBN:0-683-40008-8 MP:0005031 the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP] 2012-08-23 MP:0005031 trophoblast layer MP ISBN:0-683-40008-8 The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta UMLS:C0041178 ncithesaurus:Trophoblast trophoblast layer MP:0005031 massa cellularis externa trophoblastus trophoderm BTO:0001079 A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. embryonic disc embryonic shield germinal disc germinal disk FMA:293863 NCIT:C34112 UMLS:C1283997 bilaminary embryonic disc bilaminary germ disc uberon bilaminar disk UBERON:0000091 bilaminar disc http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png Wikipedia A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. MP:0003886 embryonic disc MP:0003886 embryonic shield MP:0003886 germinal disc MP:0003886 germinal disk MP:0003886 UMLS:C1283997 ncithesaurus:Bilaminar_Embryonic_Disc bilaminary germ disc ISBN:9780878932504 bilaminar disk stage succeeding embryo, including mature structure In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 OGES:000024 WBls:0000022 WBls:0000093 WBls:0000103 postembryonic stage post-hatching stage uberon postembryonic UBERON:0000092 post-embryonic stage https://github.com/obophenotype/uberon/issues/344 stage succeeding embryo, including mature structure Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] cjm 2009-07-30T05:19:13Z membrane FMA:7145 membrane of organ uberon UBERON:0000094 membrane organ FMA-def Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] FMA:7145 portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia] A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. ZFA treats this as a subtype of NC. cjm 2009-07-30T07:57:38Z TAO:0002173 XAO:0004190 ZFA:0001648 uberon cardiac neural crest complex complexus cristae neuralis cardiacus UBERON:0000095 cardiac neural crest Wikipedia portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia] A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. ZFA treats this as a subtype of NC. ZFA cardiac neural crest complex complexus cristae neuralis cardiacus The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. FMA:73750 lung vascular network pulmonary vasculature vascular network of lung vasculature of lung uberon UBERON:0000102 lung vasculature The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. GOC:GO lung vascular network OBOL:automatic pulmonary vasculature FMA:73750 vascular network of lung OBOL:automatic vasculature of lung OBOL:automatic An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. FBdv:00000000 HsapDv:0000001 MmusDv:0000001 OGES:000011 ncithesaurus:Life entire life cycle entire lifespan life lifespan uberon UBERON:0000104 life cycle https://github.com/obophenotype/uberon/issues/532 An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. A spatiotemporal region encompassing some part of the life cycle of an organism. this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here the WBls class 'all stages' belongs here as it is the superclass of other WBls stages we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage developmental stage stage uberon UBERON:0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 NCIT:C12601 PdumDv:0000100 VHOG:0000745 XAO:1000001 ZFS:0000001 1-cell stage fertilized egg stage one cell stage uberon fertilized egg stage one-cell stage zygote zygotum UBERON:0000106 zygote stage A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] 2012-09-17 VHOG:0000745 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 fertilized egg stage BTO:0000854 one-cell stage VHOG:0000745 zygote VHOG:0000745 zygotum The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. BILS:0000107 BilaDO:0000006 EFO:0001290 FBdv:00000054 MESH:A16.254.270 MmusDv:0000004 OGES:000015 OGES:000020 PdumDv:0000200 XAO:1000004 ZFS:0000046 uberon UBERON:0000107 cleavage stage The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. GO:0040016 An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. consider adding a preceding stage 'morula stage' as part of cleavage BILS:0000108 BilaDO:0000007 EFO:0001282 HsapDv:0000006 MmusDv:0000007 OGES:000003 OGES:000016 OGES:000021 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg WBls:0000005 XAO:1000003 ZFS:0000045 uberon UBERON:0000108 blastula stage http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. BILS:0000109 BilaDO:0000008 EFO:0001296 FBdv:00005317 HsapDv:0000010 MmusDv:0000013 OGES:000004 OGES:000019 WBls:0000010 XAO:1000005 ZFS:0000047 uberon blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage UBERON:0000109 gastrula stage BILS A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. GO:0007369 blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. BILS:0000110 BilaDO:0000009 HsapDv:0000012 MmusDv:0000017 XAO:1000006 uberon UBERON:0000110 neurula stage https://github.com/obophenotype/uberon/issues/343 Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GO:0001841 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. BILS:0000111 BilaDO:0000010 HsapDv:0000015 MmusDv:0000018 OGES:000005 OGES:000032 uberon segmentation stage UBERON:0000111 organogenesis stage https://github.com/obophenotype/uberon/issues/533 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. The stage of being a sexually immature adult animal[XAO:1000010]. In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother) BILS:0000112 BTO:0002168 EFO:0001300 EV:0300051 MmusDv:0000043 OGES:000009 XAO:1000010 XtroDO:0000083 ZFS:0000051 immature stage juvenile stage uberon subadult stage UBERON:0000112 sexually immature stage https://github.com/obophenotype/uberon/issues/427 The stage of being a sexually immature adult animal[XAO:1000010]. XAO:1000010 immature stage VHOG:FB juvenile stage XAO:1000010 subadult stage The stage of being a sexually mature adult animal. adult stage BILS:0000113 EV:0300064 EV:0300070 MIAA:0000403 MmusDv:0000110 OGES:000026 OGES:000027 XAO:1000093 ZFS:0000044 uberon UBERON:0000113 post-juvenile adult stage https://github.com/obophenotype/uberon/issues/345 https://github.com/obophenotype/uberon/issues/499 The stage of being a sexually mature adult animal. the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces EMAPA:35521 FMA:27533 MA:0001782 connective tissue of lung pulmonary interstitium uberon lung interstitial tissue lung interstitium pulmonary connective tissue pulmonary interstitial tissue UBERON:0000114 lung connective tissue the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin ISBN:0-683-40008-8 MGI:anna MP:0002276 connective tissue of lung OBOL:automatic pulmonary interstitium FMA:27533 lung interstitial tissue MA:0001782 pulmonary connective tissue EMAPA:35521 The epithelial layer of the lung. A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469] BTO:0001653 EMAPA:32860 MA:0001783 epithelial tissue of lung epithelium of lung lung epithelial tissue uberon pulmonary epithelium UBERON:0000115 lung epithelium The epithelial layer of the lung. MP:0006382 epithelial tissue of lung OBOL:automatic epithelium of lung OBOL:automatic lung epithelial tissue OBOL:automatic pulmonary epithelium BTO:0001653 A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) EMAPA:37946 FMA:12224 segment of tracheobronchial tree respiratory conducting tube segment of tracheobronchial tree tracheobronchial tree segment uberon airway UBERON:0000117 respiratory tube A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. GO:0030323 in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) GO EMAPA:37946 MA:th segment of tracheobronchial tree FMA:12224 respiratory conducting tube MP:0004391 segment of tracheobronchial tree FMA:12224 tracheobronchial tree segment FMA:12224 Structure derived from foregut that becomes a lung[GO]. clarify successors - include bronchi? BTO:0001643 EHDAA2:0004089 NCIT:C34260 NCIT:C34282 UMLS:C1514420 UMLS:C1514897 uberon gemma pulmonalis gemma respiratoria lung bud primary lung bud respiratory diverticulum UBERON:0000118 lung bud http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png GO:0060441 EHDAA2 Structure derived from foregut that becomes a lung[GO]. GO:0060431 UMLS:C1514420 ncithesaurus:Primary_Bronchial_Bud UMLS:C1514897 ncithesaurus:Respiratory_Diverticulum gemma pulmonalis gemma respiratoria lung bud primary lung bud GO:0060572 respiratory diverticulum A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. UBERON:0005163 CARO:0001001 FBbt:00005099 NLX:147821 funiculus nerve fiber bundle neural fiber bundle uberon UBERON:0000122 neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBC:DOS FBbt:00005099 nerve fiber bundle FBbt:00005099 A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO) Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. nucleus AEO:0000136 FMA:83686 NCIT:C13197 NLX:28443 nervous system nucleus neuraxis nucleus neuronal nucleus nucleus of CNS uberon nucleus of neuraxis UBERON:0000125 neural nucleus A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO) NLX:28443 Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. GO_REF:0000021 neuraxis nucleus FMA:83686 neuronal nucleus AEO:0000136 nucleus of CNS NLX:28443 Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves EMAPA:37066 FMA:54501 NLX:28532 cranial neural nucleus nucleus of cranial nerve uberon nucleus nervi cranialis UBERON:0000126 cranial nerve nucleus http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves NLX:28532 EMAPA:37066 MA:th cranial neural nucleus FMA:54501 nucleus nervi cranialis the group of motor neurons residing in the pons that innervate the muscles of facial expression FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus. BAMS:7 BAMS:7N BAMS:VII BM:Pons-VII DHBA:12420 EHDAA2:0004638 EMAPA:35338 EV:0100267 FMA:54572 MA:0001014 NCIT:C12898 UMLS:C0228740 VHOG:0001412 facial VII nucleus facial nerve nucleus nucleus of facial nerve uberon facial VII motor nucleus UBERON:0000127 facial nucleus definitional the group of motor neurons residing in the pons that innervate the muscles of facial expression ISBN:0838580343 MP:0000909 FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus. FMA UMLS:C0228740 ncithesaurus:Facial_Nerve_Nucleus facial VII nucleus MA:0001014 nucleus of facial nerve FMA:54572 facial VII motor nucleus MA:0001014 uberon UBERON:0000153 anterior region of body lexical uberon UBERON:0000154 posterior region of body lexical A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. membrane FMA:30322 FMA:82500 MESH:D008566 NCIT:C12749 membranous organ component uberon UBERON:0000158 membranous layer A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. ncithesaurus:Membrane membranous organ component FMA:82500 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. requires alignment with EHDAA2 and complete developmental relationships BTO:0001978 CALOHA:TS-2160 EMAPA:18256 FMA:15703 MA:0000330 NCIT:C12375 UMLS:C0227411 galen:AnalCanal anal canal anal canal viewed anatomically anatomical anal canal uberon anal pad anus canalis analis cloaca cloacal chamber mesenteron pars analis recti UBERON:0000159 anal canal https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png Wikipathways:WP2062 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. UMLS:C0227411 ncithesaurus:Anal_Canal canalis analis canalis analis BTO:0001978 pars analis recti BTO:0001978 Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. This class is probably too inclusive intestine http://langual.org Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] intestinal In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EV:0100071 FMA:7199 GAID:295 MA:0000328 MA:0001524 MESH:A03.492.411 MIAA:0000043 NCIT:C12736 TAO:0001338 UMLS:C0021853 VHOG:0000056 WBbt:0005772 XAO:0000129 ZFA:0001338 galen:Intestine http://www.langual.org/langual_thesaurus.asp?termid=C0212 bowel uberon intestinal tract UBERON:0000160 intestine cjm Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. GOC:GO Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] 2012-06-20 AAO:0000246 AAO AAO:EJS The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000056 VHOG UMLS:C0021853 ncithesaurus:Intestine Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. in FMA, this is an anatomical conduit *space*, rather than anatomical conduit anatomical ostium ostium FMA:3724 anatomical orifice hilum uberon UBERON:0000161 orifice Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. FMA:3724 in FMA, this is an anatomical conduit *space*, rather than anatomical conduit FMA anatomical ostium FMA:3724 anatomical orifice FMA:3724 Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] cloacal Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs hindgut endoderm and proctodeal ectoderm. AAO:0000095 GAID:1206 MESH:D002988 NCIT:C34127 UMLS:C0008987 VHOG:0001186 XAO:0000244 ZFA:0005781 uberon cloacal chamber vent UBERON:0000162 cloaca ZFA AAO Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures ISBN:0073040584 most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults. A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] 2012-09-17 VHOG:0001186 VHOG Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] 2012-06-20 AAO:0000095 AAO AAO:BJB A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001186 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572 hindgut endoderm and proctodeal ectoderm. WP UMLS:C0008987 ncithesaurus:Cloaca cloacal chamber AAO:0000095 vent XAO:0000244 endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. EHDAA2:0000256 EHDAA:4895 EMAPA:27573 uberon cloaca UBERON:0000163 embryonic cloaca EHDAA2 EHDAA2 endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. MP:0010115 cloaca the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal urogenital sinus EHDAA2:0004060 EHDAA:5029 EHDAA:5919 EMAPA:17379 NCIT:C34322 UMLS:C0231057 VHOG:0000414 UGS fetal UGS sinus urogenitalis uberon UBERON:0000164 primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png MP-def the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females ISBN:0-683-40008-8 MP:0010116 The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] 2012-09-17 VHOG:0000414 VHOG In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] 2012-09-17 VHOG:0000414 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300 the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal MP urogenital sinus MP:0010116 UMLS:C0231057 ncithesaurus:Urogenital_Sinus UGS MP:0010116 fetal UGS sinus urogenitalis mouth The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] oral some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 CALOHA:TS-1315 EFO:0000825 EHDAA2:0001326 EHDAA:542 EMAPA:16262 FBbt:00003126 FMA:49184 GAID:75 MA:0000341 MA:0002474 MAT:0000038 MESH:D009055 MIAA:0000038 OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 VHOG:0000280 VHOG:0000812 XAO:0003029 ZFA:0000547 ZFA:0000590 galen:Mouth regio oralis adult mouth uberon cavital oralis cavitas oris cavum oris mouth cavity oral region oral vestibule rima oris stoma stomatodaeum trophic apparatus vestibule of mouth vestibulum oris UBERON:0000165 mouth https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts exceptions in some taxa The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] 2012-06-20 AAO:0010355 AAO AAO:BJB Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] 2012-09-17 VHOG:0000812 VHOG DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips FMA regio oralis BTO:0004698 regio oralis FMA:49184 FMA:TA cavital oralis cavitas oris BTO:0001090 cavum oris BTO:0001090 mouth cavity BTO:0001090 oral region EHDAA2:0001326 oral vestibule BTO:0001090 rima oris BTO:0001090 stomatodaeum VHOG:0000812 trophic apparatus vestibule of mouth BTO:0001090 vestibulum oris BTO:0001090 The orifice that connects the mouth to the exterior of the body. (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] FMA:59806 oral fissure oral orifice uberon mouth oral part of face UBERON:0000166 oral opening FMA The orifice that connects the mouth to the exterior of the body. (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] 2012-09-17 VHOG:0000280 VHOG DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007) oral fissure FMA:59806 oral orifice FMA:59806 mouth Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present) Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] AAO:0000053 AAO:0000960 BSA:0000107 CALOHA:TS-1315 EFO:0001975 EHDAA2:0001324 EHDAA:6970 EMAPA:17411 EMAPA:18399 EV:0100057 FMA:20292 HAO:0000669 NCIT:C12421 TAO:0001027 TGMA:0000102 UMLS:C0226896 VHOG:0000188 WBbt:0005255 XAO:0000126 ZFA:0001027 buccal cavity cavity of mouth uberon bucca UBERON:0000167 oral cavity Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present) ISBN:0073040584 Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000960 AAO AAO:EJS The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] 2012-09-17 VHOG:0000188 VHOG Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] 2012-09-17 VHOG:0000188 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32 UMLS:C0226896 ncithesaurus:Oral_Cavity buccal cavity FMA:20292 ISBN:0073040584 A section dividing a colon along a proximal-distal axis. FMA:222905 uberon segment of colon UBERON:0000168 proximal-distal subdivision of colon 4 cjm A section dividing a colon along a proximal-distal axis. segment of colon FMA:222905 1 1 1 1 The pair of anatomical structures comprised of a left lung and right lung. FMA:68877 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA lungs lungs pair pulmones set of lungs uberon UBERON:0000170 pair of lungs FMA-abduced The pair of anatomical structures comprised of a left lung and right lung. pulmones FMA:68877 FMA:TA Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. EMAPA:17607 SPD:0000428 TGMA:0001247 apparatus respiratorius organ breathing organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ uberon gas exchange organ UBERON:0000171 respiration organ Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. GO:0007585 apparatus respiratorius organ OBOL:automatic organ of apparatus respiratorius OBOL:automatic organ of respiratory system OBOL:automatic respiratory system organ OBOL:automatic A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity UBERON:0000324 UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 galen:Excretion excreted substance portion of excreted substance waste substance uberon excretion UBERON:0000174 excreta A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity GO:0007588 portion of excreted substance FMA:9674 waste substance AEO:0000184 excretion BTO:0000491 blood A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA TAO:0000007 UMLS:C0005767 VHOG:0000224 XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood uberon whole blood UBERON:0000178 blood Bgee:AN A fluid that is composed of blood plasma and erythrocytes. FMA:9670 A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000007 TAO ZFIN:curator Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] 2012-06-20 AAO:0000046 AAO AAO:LAP relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000046 AAO Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] 2012-09-17 VHOG:0000224 VHOG DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) UMLS:C0005767 ncithesaurus:Blood whole blood BTO:0000089 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. cjm 2009-04-08T04:38:19Z CARO:0000081 uberon blood or blood analog circulating fluid UBERON:0000179 haemolymphatic fluid Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. Dorsal part (roof region) of the telencephalon[GO]. In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume. In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus cjm 2009-04-18T12:03:09Z UBERON:0007333 BTO:0003399 DMBA:15903 EFO:0003534 TAO:0000505 TAO:0007007 ZFA:0000505 area dorsalis telencephali dorsal part of telencephalon dorsal telencephalic area dorsal telencephalon uberon UBERON:0000203 pallium https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/87 Dorsal part (roof region) of the telencephalon[GO]. GO:0021543 ISBN:0471888893 In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume. NCBITaxon:8782 In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus WP area dorsalis telencephali ZFA:0000505 dorsal part of telencephalon ISBN:0471888893 dorsal telencephalic area ZFA:0000505 dorsal telencephalon ZFA:0000505 Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ. Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496]. Portion of connective tissue that connects bone or cartilage.[TAO] Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG] this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament CALOHA:TS-2145 EFO:0001966 EMAPA:35493 FMA:21496 FMA:30319 MA:0000113 MESH:D008022 NCIT:C13046 OpenCyc:Mx4rvVjqpZwpEbGdrcN5Y29ycA TAO:0001682 UMLS:C0023685 VHOG:0001272 XAO:0004031 ZFA:0001675 galen:Ligament ligament organ uberon UBERON:0000211 ligament Knee:diagram.svg Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ. GO_REF:0000034 VSAO:0000073 Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496]. FMA:21496 Portion of connective tissue that connects bone or cartilage.[TAO] 2012-08-14 TAO:0001682 TAO TAO:wd Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG] 2012-09-17 VHOG:0001272 VHOG PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996) UMLS:C0023685 ncithesaurus:Ligament ligament organ FMA:21496 A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath TODO - add layer relations. 'tendon sheath' GAT in FMA. BTO:0000051 FMA:45087 FMA:76715 NCIT:C96299 UMLS:C0224856 synovial tendon sheath uberon vagina tendinis UBERON:0000304 tendon sheath A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath UMLS:C0224856 ncithesaurus:Tendon_Sheath synovial tendon sheath FMA:45087 vagina tendinis Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 MESH:A16.254.270.274 OGEM:000006 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg blastula embryo uberon blastosphere UBERON:0000307 blastula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. blastula embryo BILA:0000059 blastosphere The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity. defined generically to encompass both vertebrates and invertebrates the BTO class refers to earthworms. BTO:0000139 EMAPA:32761 FMA:10427 galen:BodyWall wall fo trunk trunk wall wall of trunk uberon UBERON:0000309 body wall The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity. MP:0003385 the BTO class refers to earthworms. BTO wall fo trunk FMA:10427 trunk wall FMA:10427 wall of trunk FMA:10427 breast The upper ventral region of the torso of an organism. The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. BTO:0000149 CALOHA:TS-2083 EV:0100124 FMA:9601 GAID:33 MESH:D001940 NCIT:C12971 OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA UMLS:C0006141 galen:Breast mammary part of chest mammary region uberon mamma UBERON:0000310 breast http://upload.wikimedia.org/wikipedia/commons/6/6e/Closeup_of_female_breast.jpg The upper ventral region of the torso of an organism. The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. WP,unvetted UMLS:C0006141 ncithesaurus:Breast mammary part of chest FMA:9601 mammary region FMA:9601 mamma A mucosa that is part of a cecum [Automatically generated definition]. BTO:0000213 FMA:14998 caecum mucosa caecum mucosa of organ caecum mucous membrane caecum organ mucosa cecal mucosa cecum mucosa of organ cecum mucous membrane cecum organ mucosa intestinum crassum caecum mucosa intestinum crassum caecum mucosa of organ intestinum crassum caecum mucous membrane intestinum crassum caecum organ mucosa mucosa of caecum mucosa of cecum mucosa of intestinum crassum caecum mucosa of organ of caecum mucosa of organ of cecum mucosa of organ of intestinum crassum caecum mucous membrane of caecum mucous membrane of cecum mucous membrane of intestinum crassum caecum organ mucosa of caecum organ mucosa of cecum organ mucosa of intestinum crassum caecum uberon UBERON:0000314 cecum mucosa A mucosa that is part of a cecum [Automatically generated definition]. OBOL:automatic caecum mucosa OBOL:automatic caecum mucosa of organ OBOL:automatic caecum mucous membrane OBOL:automatic caecum organ mucosa OBOL:automatic cecal mucosa FMA:14998 cecum mucosa of organ OBOL:automatic cecum mucous membrane OBOL:automatic cecum organ mucosa OBOL:automatic intestinum crassum caecum mucosa OBOL:automatic intestinum crassum caecum mucosa of organ OBOL:automatic intestinum crassum caecum mucous membrane OBOL:automatic intestinum crassum caecum organ mucosa OBOL:automatic mucosa of caecum OBOL:automatic mucosa of cecum OBOL:automatic mucosa of intestinum crassum caecum OBOL:automatic mucosa of organ of caecum OBOL:automatic mucosa of organ of cecum OBOL:automatic mucosa of organ of intestinum crassum caecum OBOL:automatic mucous membrane of caecum OBOL:automatic mucous membrane of cecum OBOL:automatic mucous membrane of intestinum crassum caecum OBOL:automatic organ mucosa of caecum OBOL:automatic organ mucosa of cecum OBOL:automatic organ mucosa of intestinum crassum caecum OBOL:automatic The space between the arachnoid and pia mater. BTO:0000230 EMAPA:32666 FMA:83716 GAID:689 MESH:D013346 uberon cavitas subarachnoidea cavum subarachnoideale spatium leptomeningeum spatium subarachnoideum subarachnoid cavity UBERON:0000315 subarachnoid space http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray769-en.svg http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray769.png ISBN:0471888893 The space between the arachnoid and pia mater. GOC:add cavitas subarachnoidea BTO:0000230 cavum subarachnoideale spatium leptomeningeum BTO:0000230 spatium subarachnoideum spatium subarachnoideum BTO:0000230 subarachnoid cavity BTO:0000230 A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. BTO:0000242 FMA:83689 MESH:D002582 cervix mucus uberon UBERON:0000316 cervical mucus A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. BTO:0000242 cervix mucus OBOL:automatic Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. UBERON:0003347 UBERON:0004981 BTO:0000271 CALOHA:TS-0164 EFO:0003038 EMAPA:27375 FMA:14984 FMA:85388 MA:0003194 colon mucosa colon mucous membrane colonic mucosa colonic mucous membrane large bowel mucosa mucosa of colon mucosa of large bowel uberon UBERON:0000317 colonic mucosa Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. colon mucosa FMA:14984 colon mucous membrane OBOL:automatic colonic mucous membrane FMA:14984 large bowel mucosa OBOL:automatic mucosa of colon FMA:14984 mucosa of large bowel OBOL:automatic A mucosa that is part of a duodenum [Automatically generated definition]. UBERON:0003348 BTO:0000367 CALOHA:TS-0213 EMAPA:27235 FMA:14942 MA:0003207 doudenal mucosa duodenal mucous membrane mucosa of duodenum mucous membrane of duodenum uberon duodenum mucosa UBERON:0000320 duodenal mucosa A mucosa that is part of a duodenum [Automatically generated definition]. OBOL:automatic doudenal mucosa FMA:14942 duodenal mucous membrane FMA:14942 mucosa of duodenum OBOL:automatic mucous membrane of duodenum OBOL:automatic duodenum mucosa BTO:0000367 An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus. Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919]. BTO:0000449 CALOHA:TS-0360 EFO:0001323 FBbt:00005333 FMA:63919 GAID:552 MESH:D005333 NCIT:C13235 OpenCyc:Mx4rvZfC2ZwpEbGdrcN5Y29ycA UMLS:C0015965 fetus uberon embryo late growth stage embryo late stage UBERON:0000323 late embryo An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. BGEE:ANiknejad Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919]. FMA:63919 UMLS:C0015965 ncithesaurus:Fetus fetus BTO:0000449 embryo late growth stage BTO:0000449 embryo late stage BTO:0000449 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. BTO:0000503 EMAPA:27181 FMA:14919 uberon UBERON:0000325 gastric gland cjm ISBN:0073040584 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. MGI:anna Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach. BTO:0000504 CALOHA:TS-2235 FMA:62973 GAID:1166 MESH:D010189 uberon pancreatic fluid pancreatic secretion succus pancreaticus UBERON:0000326 pancreatic juice Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach. GO:0030157 succus pancreaticus BTO:0000504 The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). We model the digestive tract as consisting of two parts: the wall and the lumen. BTO:0000547 FMA:45653 digestive tract wall wall of digestive tract wall of gut uberon wall of alimentary tract UBERON:0000328 gut wall The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). wall of gut FMA:45653 A mucosa that is part of a ileum [Automatically generated definition]. BTO:0000619 CALOHA:TS-0470 EMAPA:35424 FMA:14956 MA:0003216 ileal mucous membrane ileum mucosa ileum mucosa of organ ileum mucous membrane ileum organ mucosa mucosa of ileum mucosa of organ of ileum mucous membrane of ileum organ mucosa of ileum uberon UBERON:0000331 ileal mucosa A mucosa that is part of a ileum [Automatically generated definition]. OBOL:automatic ileal mucous membrane FMA:14956 ileum mucosa FMA:14956 ileum mucosa OBOL:automatic ileum mucosa of organ OBOL:automatic ileum mucous membrane OBOL:automatic ileum organ mucosa OBOL:automatic mucosa of ileum OBOL:automatic mucosa of organ of ileum OBOL:automatic mucous membrane of ileum OBOL:automatic organ mucosa of ileum OBOL:automatic bone marrow in which the fat cells predominate in the meshes of the reticular network. BTO:0000635 FMA:74596 medulla ossium flava yellow marrow uberon fat marrow UBERON:0000332 yellow bone marrow bone marrow in which the fat cells predominate in the meshes of the reticular network. medulla ossium flava BTO:0000635 yellow marrow BTO:0000635 fat marrow BTO:0000635 A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. Note that some sources treat 'intestinal gland' as synonymous with crypts BTO:0000640 FMA:15052 bowel mucosa gland bowel mucosa of organ gland bowel mucous membrane gland bowel organ mucosa gland gland of bowel mucosa gland of bowel mucosa of organ gland of bowel mucous membrane gland of bowel organ mucosa gland of intestinal mucosa gland of intestine mucosa gland of intestine mucosa of organ gland of intestine mucous membrane gland of intestine organ mucosa gland of mucosa of bowel gland of mucosa of intestine gland of mucosa of organ of bowel gland of mucosa of organ of intestine gland of mucous membrane of bowel gland of mucous membrane of intestine gland of organ mucosa of bowel gland of organ mucosa of intestine glandula intestinalis intestinal mucosa gland intestine mucosa gland intestine mucosa of organ gland intestine mucous membrane gland intestine organ mucosa gland mucosa of bowel gland mucosa of intestine gland mucosa of organ of bowel gland mucosa of organ of intestine gland mucous membrane of bowel gland mucous membrane of intestine gland organ mucosa of bowel gland organ mucosa of intestine gland uberon glandulae intestinales UBERON:0000333 intestinal gland A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. bowel mucosa gland OBOL:automatic bowel mucosa of organ gland OBOL:automatic bowel mucous membrane gland OBOL:automatic bowel organ mucosa gland OBOL:automatic gland of bowel mucosa OBOL:automatic gland of bowel mucosa of organ OBOL:automatic gland of bowel mucous membrane OBOL:automatic gland of bowel organ mucosa OBOL:automatic gland of intestinal mucosa OBOL:automatic gland of intestine mucosa OBOL:automatic gland of intestine mucosa of organ OBOL:automatic gland of intestine mucous membrane OBOL:automatic gland of intestine organ mucosa OBOL:automatic gland of mucosa of bowel OBOL:automatic gland of mucosa of intestine OBOL:automatic gland of mucosa of organ of bowel OBOL:automatic gland of mucosa of organ of intestine OBOL:automatic gland of mucous membrane of bowel OBOL:automatic gland of mucous membrane of intestine OBOL:automatic gland of organ mucosa of bowel OBOL:automatic gland of organ mucosa of intestine OBOL:automatic glandula intestinalis FMA:15052 intestinal mucosa gland OBOL:automatic intestine mucosa gland OBOL:automatic intestine mucosa of organ gland OBOL:automatic intestine mucous membrane gland OBOL:automatic intestine organ mucosa gland OBOL:automatic mucosa of bowel gland OBOL:automatic mucosa of intestine gland OBOL:automatic mucosa of organ of bowel gland OBOL:automatic mucosa of organ of intestine gland OBOL:automatic mucous membrane of bowel gland OBOL:automatic mucous membrane of intestine gland OBOL:automatic organ mucosa of bowel gland OBOL:automatic organ mucosa of intestine gland OBOL:automatic throat In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. gular The hyoid bone and the clavicle are the only bones located in the throat of mammals. BTO:0000828 EMAPA:37973 FMA:228738 NCIT:C54272 OpenCyc:Mx4rwQtO_JwpEbGdrcN5Y29ycA UMLS:C0230069 uberon gula UBERON:0000341 throat Throat:Diagram.png In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. EMAPA:37973 MA:th UMLS:C0230069 ncithesaurus:Throat gula A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] mucosal FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately AEO:0000199 BTO:0000886 CALOHA:TS-2031 EHDAA2_RETIRED:0003234 EV:0100382 FMA:85355 FMA:85358 GAID:297 MESH:D009092 NCIT:C13166 OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA UMLS:C0026724 galen:Mucosa mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa uberon region of mucosa tunica mucosa UBERON:0000344 mucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately FMA UMLS:C0026724 ncithesaurus:Mucosa mucosa of organ FMA:85355 mucosa of organ part FMA:85358 mucosal region FMA:85358 mucous membrane FMA:85355 organ mucosa FMA:85355 region of mucosa FMA:85358 tunica mucosa tunica mucosa BTO:0000886 The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead. Sensory medial ramus of the trigeminal nerve.[AAO] The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG] AAO:0010648 BTO:0000926 EHDAA2:0002088 EHDAA:3744 EMAPA:17800 FMA:52621 GAID:837 MA:0001104 MESH:D009882 NCIT:C33215 OpenCyc:Mx4rwEs_K5wpEbGdrcN5Y29ycA UMLS:C0029082 VHOG:0001349 cranial nerve V, branch V1 first branch of fifth cranial nerve first division of fifth cranial nerve first division of trigeminal nerve nervus ophthalmicus (V1) nervus ophthalmicus (Va) nervus ophthalmicus [v1] nervus ophthalmicus [va] ophthalmic division [V1] ophthalmic division [Va] ophthalmic division of fifth cranial nerve ophthalmic division of trigeminal nerve (V1) ophthalmic division of trigeminal nerve (Va) ophthalmic nerve [V1] ophthalmic nerve [Va] opthalmic nerve ramus opthalmicus profundus (ramus V1) rostral branch of trigeminal nerve trigeminal V nerve ophthalmic division uberon ciliary nerve ethmoidal nerve ophthalmic division profundal nerve profundus profundus nerve trigeminal nerve ophthalmic division UBERON:0000348 Terminology notes. This nerve is known by a ridiculous number of names[http://palaeos.com/vertebrates/glossary/glossaryPo.html] ophthalmic nerve may be a distinct nerve in teleosts multiple The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead. MP:0009798 Sensory medial ramus of the trigeminal nerve.[AAO] 2012-06-20 AAO:0010648 AAO AAO:EJS The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG] 2012-09-17 VHOG:0001349 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.177 UMLS:C0029082 ncithesaurus:Ophthalmic_Nerve cranial nerve V, branch V1 first branch of fifth cranial nerve first division of fifth cranial nerve FMA:52621 first division of trigeminal nerve FMA:52621 nervus ophthalmicus (V1) FMA:52621 nervus ophthalmicus (Va) FMA:52621 nervus ophthalmicus [v1] FMA:52621 FMA:TA nervus ophthalmicus [va] FMA:52621 FMA:TA ophthalmic division [V1] FMA:52621 ophthalmic division [Va] FMA:52621 ophthalmic division of fifth cranial nerve FMA:52621 ophthalmic division of trigeminal nerve (V1) FMA:52621 ophthalmic division of trigeminal nerve (Va) FMA:52621 ophthalmic nerve [V1] FMA:52621 ophthalmic nerve [Va] FMA:52621 opthalmic nerve ramus opthalmicus profundus (ramus V1) AAO:0010648 rostral branch of trigeminal nerve trigeminal V nerve ophthalmic division MA:0001104 ciliary nerve ethmoidal nerve ophthalmic division ophthalmic division BTO:0000926 profundal nerve profundus profundus nerve trigeminal nerve ophthalmic division EMAPA:17800 A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity. BTO:0000928 CALOHA:TS-1307 FMA:242000 GAID:615 MESH:A08.186.211.577 NCIT:C94541 OpenCyc:Mx4rwAeba5wpEbGdrcN5Y29ycA UMLS:C0023715 uberon visceral brain UBERON:0000349 includes the hippocampus, amygdala, anterior thalamic nuclei, and limbic cortex, which support a variety of functions including emotion, behavior, long term memory, and olfaction [Wikipedia] limbic system Brain:limbicsystem.jpg A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]. BIRNLEX:Limbic_system UMLS:C0023715 ncithesaurus:Limbic_System visceral brain ISBN:0123813611 functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. parenchymal Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated EHDAA:3015 EHDAA:3905 EHDAA:3999 EHDAA:4005 EHDAA:6899 EHDAA:6903 EHDAA:6994 EHDAA:8086 EHDAA:9182 EHDAA:9190 EHDAA:9196 EHDAA:9202 FMA:45732 NCIT:C74601 UMLS:C0933845 uberon UBERON:0000353 parenchyma functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin WP the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated FMA UMLS:C0933845 ncithesaurus:Parenchyma A mucosa that is part of a pharynx [Automatically generated definition]. UBERON:0003344 BTO:0001047 EMAPA:26957 FMA:55031 MA:0003143 mucosa of organ of pharynx mucosa of pharynx mucous membrane of pharynx organ mucosa of pharynx pharynx mucosa pharynx mucosa of organ pharynx mucous membrane pharynx organ mucosa tunica mucosa pharyngea tunica mucosa pharyngis uberon mucous membrane of the pharynx UBERON:0000355 pharyngeal mucosa A mucosa that is part of a pharynx [Automatically generated definition]. OBOL:automatic mucosa of organ of pharynx OBOL:automatic mucosa of pharynx OBOL:automatic mucous membrane of pharynx FMA:55031 mucous membrane of pharynx OBOL:automatic organ mucosa of pharynx OBOL:automatic pharynx mucosa OBOL:automatic pharynx mucosa of organ OBOL:automatic pharynx mucous membrane OBOL:automatic pharynx organ mucosa OBOL:automatic tunica mucosa pharyngea FMA:55031 FMA:TA mucous membrane of the pharynx BTO:0001047 The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]. Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm) BTO:0001099 CALOHA:TS-0076 EFO:0000295 EMAPA:36035 EV:0100394 FMA:83041 GAID:1153 MESH:A16.254.085 NCIT:C13739 UMLS:C1281743 uberon blastocystis blastula UBERON:0000358 blastocyst Blastocyst:English.svg The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]. GO:0001824 UMLS:C1281743 ncithesaurus:Blastocyst blastocystis blastula FMA:83041 the inner portion of the kidney consisting of the renal pyramids The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water BTO:0001167 CALOHA:TS-1157 EMAPA:19279 GAID:425 MA:0000373 MESH:D007679 NCIT:C12740 UMLS:C0022664 galen:MedullaOfKidney kidney medulla medulla of kidney medulla renalis pyramides renales renal medullae renal medullae set renal pyramids renal pyramids set uberon medullary pyramids renal marrow UBERON:0000362 renal medulla Illu:kidney.jpg the inner portion of the kidney consisting of the renal pyramids ISBN:0-683-40008-8 MGI:smb MP:0003014 UMLS:C0022664 ncithesaurus:Renal_Medulla kidney medulla OBOL:automatic medulla of kidney OBOL:automatic medulla renalis FMA:74268 FMA:TA pyramides renales FMA:74268 FMA:TA renal medullae FMA:86327 renal medullae set FMA:86327 renal pyramids FMA:74268 renal pyramids set FMA:74268 medullary pyramids FMA:74268 renal marrow BTO:0001167 The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini. AAO:0010688 AAO:0010703 BTO:0001375 EHDAA2:0002086 EMAPA:17798 FMA:52996 GAID:834 MA:0001101 MESH:D008340 NCIT:C32779 OpenCyc:Mx4rvcQKSpwpEbGdrcN5Y29ycA UMLS:C0024695 VHOG:0001345 inferior maxillary nerve mandibular division [V3] mandibular division [Vc] mandibular division of fifth cranial nerve mandibular division of trigeminal nerve [Vc; V3] mandibular nerve [V3] mandibular nerve [Vc] nervus mandibularis [Vc; V3] nervus mandibularis [v3] nervus mandibularis [vc] ramus mandibularis (ramus V3) third division of fifth cranial nerve third division of trigeminal nerve trigeminal V nerve mandibular division uberon n. mandibularis nervus mandibularis trigeminal nerve mandibular division UBERON:0000375 mandibular nerve http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini. MP:0009800 UMLS:C0024695 ncithesaurus:Inferior_Maxillary_Nerve inferior maxillary nerve FMA:52996 mandibular division [V3] FMA:52996 mandibular division [Vc] FMA:52996 mandibular division of fifth cranial nerve FMA:52996 mandibular division of trigeminal nerve [Vc; V3] FMA:52996 mandibular nerve [V3] FMA:52996 mandibular nerve [Vc] FMA:52996 nervus mandibularis [Vc; V3] FMA:52996 nervus mandibularis [v3] FMA:52996 FMA:TA nervus mandibularis [vc] FMA:52996 FMA:TA ramus mandibularis (ramus V3) AAO:0010688 third division of fifth cranial nerve FMA:52996 third division of trigeminal nerve FMA:52996 trigeminal V nerve mandibular division MA:0001101 n. mandibularis nervus mandibularis BTO:0001375 trigeminal nerve mandibular division EMAPA:17798 The part of the hindlimb between pelvis and the knee, corresponding to the femur. Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] Naming conventions for pod terms under discussion within phenoscape group. BTO:0001376 CALOHA:TS-2039 EFO:0001943 EHDAA2:0002130 EHDAA:5171 EHDAA:6200 EMAPA:17499 FMA:24967 GAID:50 MA:0000052 MESH:D013848 NCIT:C33763 OpenCyc:Mx4rvVjN7JwpEbGdrcN5Y29ycA UMLS:C0039866 VHOG:0000349 galen:Thigh hind limb stylopod hind limb stylopodium hind propodium hindlimb propodium hindlimb stylopod hindlimb stylopodium proximal segment of free lower limb stylopod of hind limb stylopod of hindlimb stylopod of lower limb thigh upper leg uberon femur UBERON:0000376 hindlimb stylopod http://upload.wikimedia.org/wikipedia/commons/4/4b/Gray1238.png MA The part of the hindlimb between pelvis and the knee, corresponding to the femur. Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000349 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 Naming conventions for pod terms under discussion within phenoscape group. https://github.com/obophenotype/uberon/issues/61 UMLS:C0039866 ncithesaurus:Thigh hind limb stylopod OBOL:automatic hind limb stylopodium VHOG:0000349 hind propodium AAO:0000887 hindlimb propodium AAO:0000887 hindlimb stylopod OBOL:automatic hindlimb stylopodium OBOL:automatic proximal segment of free lower limb FMA:24967 stylopod of hind limb OBOL:automatic stylopod of hindlimb OBOL:automatic upper leg MA:0000052 femur The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. Medial ramus (sensory) of the trigeminal nerve.[AAO] relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] AAO:0010670 BTO:0001378 EHDAA2:0002087 EMAPA:17799 FMA:52724 GAID:836 MA:0001103 MESH:D008442 OpenCyc:Mx4rvWNU9JwpEbGdrcN5Y29ycA VHOG:0001346 maxillary division [V2] maxillary division [Vb] maxillary division of fifth cranial nerve maxillary division of trigeminal nerve (Vb; V2) maxillary nerve [V2] maxillary nerve [Vb] nervus maxillaris (Vb; V2) nervus maxillaris [v2] nervus maxillaris [vb] ramus maxillaris (ramus V2) second division of fifth cranial nerve second division of trigeminal nerve trigeminal V nerve maxillary division uberon n. maxillaris nervus maxillaris trigeminal nerve maxillary division UBERON:0000377 maxillary nerve http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. MP:0009799 Medial ramus (sensory) of the trigeminal nerve.[AAO] 2012-06-20 AAO:0010670 AAO AAO:EJS relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] 2012-06-20 AAO:0010670 AAO maxillary division [V2] FMA:52724 maxillary division [Vb] FMA:52724 maxillary division of fifth cranial nerve FMA:52724 maxillary division of trigeminal nerve (Vb; V2) FMA:52724 maxillary nerve [V2] FMA:52724 maxillary nerve [Vb] FMA:52724 nervus maxillaris (Vb; V2) FMA:52724 nervus maxillaris [v2] FMA:52724 FMA:TA nervus maxillaris [vb] FMA:52724 FMA:TA ramus maxillaris (ramus V2) AAO:0010670 second division of fifth cranial nerve FMA:52724 second division of trigeminal nerve FMA:52724 trigeminal V nerve maxillary division MA:0001103 n. maxillaris nervus maxillaris BTO:0001378 trigeminal nerve maxillary division EMAPA:17799 The muscular portion of the tongue. The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] BTO:0001386 EHDAA2:0002065 EHDAA:9146 EMAPA:17883 FMA:46689 MA:0001596 NCIT:C49301 NCIT:C52707 UMLS:C0448325 UMLS:C1710437 VHOG:0001390 muscle of tongue muscle organ of tongue skeletal muscle tissue of tongue tongue skeletal muscle tongue skeletal muscle tissue uberon musculi linguae UBERON:0000378 tongue muscle http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png FEED:rd ISBN:1607950324 The muscular portion of the tongue. MP:0004136 The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0001390 VHOG DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005) UMLS:C0448325 ncithesaurus:Tongue_Muscle UMLS:C1710437 ncithesaurus:Tongue_Skeletal_Muscle_Tissue muscle of tongue FMA:46689 muscle organ of tongue OBOL:accepted skeletal muscle tissue of tongue OBOL:automatic tongue skeletal muscle OBOL:automatic tongue skeletal muscle tissue OBOL:automatic musculi linguae A mucosa that is part of a respiratory airway. BTO:0001390 FMA:7471 mucosa of organ of trachea mucosa of organ of windpipe mucosa of trachea mucosa of windpipe mucous membrane of trachea mucous membrane of windpipe organ mucosa of trachea organ mucosa of windpipe trachea mucosa trachea mucosa of organ trachea mucous membrane trachea organ mucosa tracheal mucous membrane tunica mucosa (tracheae) tunica mucosa tracheae windpipe mucosa windpipe mucosa of organ windpipe mucous membrane windpipe organ mucosa uberon UBERON:0000379 tracheal mucosa A mucosa that is part of a respiratory airway. OBOL:automatic mucosa of organ of trachea OBOL:automatic mucosa of organ of windpipe OBOL:automatic mucosa of trachea OBOL:automatic mucosa of windpipe OBOL:automatic mucous membrane of trachea FMA:7471 mucous membrane of trachea OBOL:automatic mucous membrane of windpipe OBOL:automatic organ mucosa of trachea OBOL:automatic organ mucosa of windpipe OBOL:automatic trachea mucosa OBOL:automatic trachea mucosa of organ OBOL:automatic trachea mucous membrane OBOL:automatic trachea organ mucosa OBOL:automatic tracheal mucous membrane FMA:7471 tunica mucosa (tracheae) FMA:7471 tunica mucosa tracheae FMA:7471 FMA:TA windpipe mucosa OBOL:automatic windpipe mucosa of organ OBOL:automatic windpipe mucous membrane OBOL:automatic windpipe organ mucosa OBOL:automatic The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 Anatomical system that consists of the muscles of the body.[VSAO] we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 EMAPA:35578 FBbt:00005069 FMA:72954 MA:0002888 MAT:0000025 MIAA:0000025 VSAO:0000033 XAO:0004042 muscle system muscle system of body muscular system musculature system set of all muscles set of muscles of body vertebrate muscular system uberon muskelsystem UBERON:0000383 musculature of body The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 Anatomical system that consists of the muscles of the body.[VSAO] 2012-08-14 VSAO:0000033 VSAO VSAO:curator we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA MA muscular system FMA:72954 musculature system BILA:0000088 set of all muscles FMA:72954 set of muscles of body FMA:72954 vertebrate muscular system BTO:0001369 muskelsystem BTO:0001485 Tissue that surrounds the lens nucleus BTO:0001632 CALOHA:TS-0542 FMA:58970 MESH:A09.371.509.225 cortex of lens uberon UBERON:0000389 lens cortex Tissue that surrounds the lens nucleus cortex of lens FMA:58970 The core of the crystalline lens, surrounded by the cortex. BTO:0001633 FMA:58971 MESH:A09.371.509.670 nucleus of lens uberon UBERON:0000390 lens nucleus The core of the crystalline lens, surrounded by the cortex. BTO:0001633 nucleus of lens FMA:58971 pia mater or arachnoid mater. check relationship to secondary meninx in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular BTO:0001634 CALOHA:TS-0546 FMA:231515 NCIT:C32979 NLXANAT:090207 UMLS:C0228126 leptomeninges uberon arachnoid mater and pia mater arachnoidea mater et pia mater pia-arachnoid pia-arachnoid of neuraxis UBERON:0000391 leptomeninx pia mater or arachnoid mater. in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular FMA UMLS:C0228126 ncithesaurus:Leptomeninges leptomeninges NLXANAT:090207 arachnoid mater and pia mater FMA:231515 arachnoidea mater et pia mater BTO:0001634 pia-arachnoid BTO:0001634 pia-arachnoid of neuraxis FMA:231515 An epithelium that is part of a colon [Automatically generated definition]. Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] BTO:0001709 CALOHA:TS-0163 EMAPA:18941 FMA:17302 MA:0003195 TAO:0005128 ZFA:0005128 colon epithelial tissue colon epithelium epithelial tissue of colon epithelial tissue of large bowel epithelium of colon epithelium of large bowel large bowel epithelial tissue large bowel epithelium posterior intestine epithelium uberon UBERON:0000397 colonic epithelium An epithelium that is part of a colon [Automatically generated definition]. OBOL:automatic Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] 2012-08-14 TAO:0005128 TAO ZFIN:curator colon epithelial tissue OBOL:automatic colon epithelium FMA:17302 colon epithelium OBOL:automatic epithelial tissue of colon OBOL:automatic epithelial tissue of large bowel OBOL:automatic epithelium of colon OBOL:automatic epithelium of large bowel OBOL:automatic large bowel epithelial tissue OBOL:automatic large bowel epithelium OBOL:automatic posterior intestine epithelium ZFA:0005128 The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted]. BTO:0001761 CALOHA:TS-0660 FMA:59644 vestibular part of nasal cavity uberon vestibulum nasale vestibulum nasi UBERON:0000402 nasal vestibule http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray994.png The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted]. vestibular part of nasal cavity FMA:59644 vestibulum nasale BTO:0001761 vestibulum nasi vestibulum nasi BTO:0001761 A gland in which the principal secretory cells are serous secreting cells. glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. BTO:0001837 EMAPA:37950 FMA:62889 uberon UBERON:0000409 serous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png A gland in which the principal secretory cells are serous secreting cells. glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. MP:0008052 EMAPA:37950 MA:th A mucosa that is part of a bronchus [Automatically generated definition]. BTO:0001846 FMA:62652 bronchi mucosa bronchi mucosa of organ bronchi mucous membrane bronchi organ mucosa bronchial trunk mucosa bronchial trunk mucosa of organ bronchial trunk mucous membrane bronchial trunk organ mucosa bronchus mucosa bronchus mucosa of organ bronchus mucous membrane bronchus organ mucosa mucosa of bronchi mucosa of bronchial trunk mucosa of bronchus mucosa of organ of bronchi mucosa of organ of bronchial trunk mucosa of organ of bronchus mucous membrane of bronchi mucous membrane of bronchial trunk mucous membrane of bronchus organ mucosa of bronchi organ mucosa of bronchial trunk organ mucosa of bronchus tunica mucosa bronchi uberon UBERON:0000410 bronchial mucosa A mucosa that is part of a bronchus [Automatically generated definition]. OBOL:automatic bronchi mucosa OBOL:automatic bronchi mucosa of organ OBOL:automatic bronchi mucous membrane OBOL:automatic bronchi organ mucosa OBOL:automatic bronchial trunk mucosa OBOL:automatic bronchial trunk mucosa of organ OBOL:automatic bronchial trunk mucous membrane OBOL:automatic bronchial trunk organ mucosa OBOL:automatic bronchus mucosa OBOL:automatic bronchus mucosa of organ OBOL:automatic bronchus mucous membrane OBOL:automatic bronchus organ mucosa OBOL:automatic mucosa of bronchi OBOL:automatic mucosa of bronchial trunk OBOL:automatic mucosa of bronchus OBOL:automatic mucosa of organ of bronchi OBOL:automatic mucosa of organ of bronchial trunk OBOL:automatic mucosa of organ of bronchus OBOL:automatic mucous membrane of bronchi OBOL:automatic mucous membrane of bronchial trunk OBOL:automatic mucous membrane of bronchus FMA:62652 mucous membrane of bronchus OBOL:automatic organ mucosa of bronchi OBOL:automatic organ mucosa of bronchial trunk OBOL:automatic organ mucosa of bronchus OBOL:automatic tunica mucosa bronchi FMA:62652 FMA:TA A gland in which the principal secretory cells are mucus secreting cells. In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] AAO:0010601 BTO:0001979 EMAPA:37913 FMA:62888 glandula mucosa uberon muciparous gland mucous secreting gland mucus gland mucus-secreting gland UBERON:0000414 mucous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png A gland in which the principal secretory cells are mucus secreting cells. In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] NCBITaxon:8292 ISBN:0073040584 EMAPA:37913 MA:th glandula mucosa muciparous gland BTO:0001979 An anatomical wall that is part of an artery [Automatically generated definition]. BTO:0002009 FMA:14155 galen:ArterialWall arterial wall wall of artery uberon UBERON:0000415 artery wall An anatomical wall that is part of an artery [Automatically generated definition]. OBOL:automatic arterial wall FMA:14155 wall of artery FMA:14155 The prostate epithelium. TODO - check 2 FMA IDs UBERON:0002452 BTO:0002397 CALOHA:TS-2065 EMAPA:35711 FMA:66812 FMA:79643 MA:0001737 NCIT:C13103 UMLS:C1179826 epithelial tissue of prostate epithelial tissue of prostate gland epithelium of prostate epithelium of prostate gland epithelium of prostatic gland prostate epithelial tissue prostate gland epithelial tissue prostate gland epithelium prostatic epithelium prostatic gland epithelium uberon UBERON:0000428 prostate epithelium The prostate epithelium. MP:0001168 UMLS:C1179826 ncithesaurus:Prostatic_Epithelium epithelial tissue of prostate OBOL:automatic epithelial tissue of prostate gland OBOL:automatic epithelium of prostate OBOL:automatic epithelium of prostate gland OBOL:automatic epithelium of prostatic gland FMA:79643 prostate epithelial tissue OBOL:automatic prostate gland epithelial tissue OBOL:automatic prostatic epithelium FMA:66812 The arachnoid trabeculae are delicate strands of connective tissue that loosely connect the two innermost layers of the meninges -- the arachnoid mater and the pia mater. They are found within the subarachnoid space where cerebrospinal fluid is also found. Embryologically, the trabeculae are the remnants of the common precursor that forms both the arachnoid and pial layers of the meninges. BTO:0002500 FMA:83979 uberon arachnoid trabeculae trabecula arachnoideum UBERON:0000439 arachnoid trabecula The arachnoid trabeculae are delicate strands of connective tissue that loosely connect the two innermost layers of the meninges -- the arachnoid mater and the pia mater. They are found within the subarachnoid space where cerebrospinal fluid is also found. Embryologically, the trabeculae are the remnants of the common precursor that forms both the arachnoid and pial layers of the meninges. arachnoid trabeculae trabecula arachnoideum A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]. trabecular BTO:0002501 FMA:85273 uberon UBERON:0000440 trabecula A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]. GO:0060343 A vein that drains the left pampiniform plexus and empties into the left renal vein. BTO:0002679 EMAPA:37383 FMA:14341 MA:0002220 NCIT:C52697 right spermatic vein vena testicularis (adrenalis) dextra uberon vena testicularis dextra vena testicularis sinistra UBERON:0000442 right testicular vein A vein that drains the left pampiniform plexus and empties into the left renal vein. Dorlands_Medical_Dictionary:MerckSource EMAPA:37383 MA:th right spermatic vein MA:0002220 vena testicularis (adrenalis) dextra FMA:14341 vena testicularis dextra BTO:0002679 vena testicularis sinistra BTO:0002680 A vein that drains the right pampiniform plexus and empties into the inferior vena cava. BTO:0002680 EMAPA:37167 FMA:14345 MA:0002219 NCIT:C52696 left spermatic vein uberon vena testicularis dextra vena testicularis sinistra UBERON:0000443 left testicular vein A vein that drains the right pampiniform plexus and empties into the inferior vena cava. Dorlands_Medical_Dictionary:MerckSource EMAPA:37167 MA:th left spermatic vein MA:0002219 vena testicularis dextra BTO:0002679 vena testicularis sinistra BTO:0002680 A portion of organism substance that is produced by exocrine glands. BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions UBERON:0006540 secretion AEO:0001005 BTO:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 NCIT:C34062 UMLS:C1516992 galen:Secretion bodily secretion exocrine gland fluid/secretion secreted substance uberon exocrine gland fluid exocrine gland fluid or secretion exocrine gland secretion external secretion UBERON:0000456 secretion of exocrine gland A portion of organism substance that is produced by exocrine glands. BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions BTO secretion FMA:9675 UMLS:C1516992 ncithesaurus:Exocrine_Gland_Fluid_or_Secretion bodily secretion MESH:D012634 exocrine gland fluid/secretion MA:0002504 external secretion BTO:0002977 Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses. BTO:0002996 FMA:70527 cavernous branch of cavernous part of internal carotid artery ramus sinus cavernosi (pars cavernosa) (arteria carotis interna) uberon UBERON:0000457 cavernous artery Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses. BTO:0002996 cavernous branch of cavernous part of internal carotid artery FMA:70527 ramus sinus cavernosi (pars cavernosa) (arteria carotis interna) FMA:70527 FMA:TA The region of the opening of the uterine cervix into the uterine cavity. BTO:0003002 FMA:86485 NCIT:C12309 UMLS:C0227837 uberon UBERON:0000458 endocervix The region of the opening of the uterine cervix into the uterine cavity. BTO:0003002 UMLS:C0227837 ncithesaurus:Endocervix An anatomical wall that is part of a uterus [Automatically generated definition]. BTO:0003083 FMA:17560 anatomical wall of uterus uterus anatomical wall uterus wall wall of uterus uberon UBERON:0000459 uterine wall An anatomical wall that is part of a uterus [Automatically generated definition]. OBOL:automatic anatomical wall of uterus OBOL:automatic uterus anatomical wall OBOL:automatic uterus wall OBOL:automatic wall of uterus OBOL:automatic organism substance Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. Damion Dooley AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 NCIT:C13236 SPD:0000008 TAO:0001487 TGMA:0001824 VHOG:0001726 XAO:0004001 ZFA:0001487 galen:BodySubstance body fluid or substance body substance organism substance portion of body substance portion of organism substance uberon UBERON:0000463 organism substance organism substance this relationship may be too strong and may be weakened in future Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. body fluid or substance MA:0002450 body substance FMA:9669 organism substance CARO:0000004 portion of body substance FMA:9669 portion of organism substance ZFA:0001487 Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. lumen space AAO:0010110 AEO:0000005 BILA:0000005 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 TAO:0001668 TGMA:0001825 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 lumen space uberon anatomical spaces UBERON:0000464 anatomical space Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. UMLS:C0524461 ncithesaurus:Lumen_Space anatomical spaces ZFA:0001643 material anatomical entity Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Anatomical entity that has mass. Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 VHOG:0001727 immaterial physical anatomical entity uberon UBERON:0000466 immaterial anatomical entity Anatomical entity that has no mass. immaterial physical anatomical entity FMA:67112 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. system AAO:0000007 AEO:0000011 BILA:0000011 BIRNLEX:14 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 NCIT:C12919 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system uberon anatomical systems UBERON:0000467 anatomical system Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. CARO:0000011 system GO:0048731 UMLS:C0460002 ncithesaurus:Organ_System body system BIRNLEX:14 connected anatomical system CARO:0000011 anatomical systems ZFA:0001439 Anatomical structure that is an individual member of a species and consists of more than one cell. TODO - split body and mc organism? body continues after death stage organismal organism AAO:0010026 AEO:0000191 BILA:0000012 BIRNLEX:18 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism animal uberon Koerper body whole body whole organism UBERON:0000468 multicellular organism Anatomical structure that is an individual member of a species and consists of more than one cell. CARO:0000012 organism FBbt:00000001 VHOG:0000671 WBbt:0007833 multi-cellular organism CARO:0000012 animal BTO:0000042 Koerper BTO:0001489 body AEO:0000103 BIRNLEX:18 FMA:256135 NCIT:C13041 whole body BTO:0001489 whole organism FBbt:00000001 Multi-tissue structure that is part of a compound organ. this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010017 AEO:0000019 BILA:0000019 CARO:0000019 EHDAA2:0003019 HAO:0000019 TAO:0001489 TGMA:0001835 XAO:0003039 ZFA:0001489 uberon compound organ components UBERON:0000471 compound organ component Multi-tissue structure that is part of a compound organ. CARO:0000019 compound organ components ZFA:0001489 testis A gonad of a male animal. A gonad produces and releases sperm. Male reproductive organ.[TAO] (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] testicular The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally UBERON:0002117 AAO:0000606 BILA:0000124 BSA:0000085 BTO:0001363 CALOHA:TS-1030 EFO:0000984 EHDAA2:0002007 EHDAA:8146 EMAPA:17972 EV:0100102 FBbt:00004928 FMA:7210 GAID:396 HAO:0001007 MA:0000411 MAT:0000132 MESH:D013737 MIAA:0000132 NCIT:C12412 OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA TAO:0000598 UMLS:C0039597 VHOG:0000252 WBbt:0006794 XAO:0000157 ZFA:0000598 galen:Testis gonad of male genitalia gonad of male reproductive system male gonad testicle uberon orchis testes testiculus UBERON:0000473 testis http://upload.wikimedia.org/wikipedia/commons/c/c3/Gray1144.png A gonad of a male animal. A gonad produces and releases sperm. Male reproductive organ.[TAO] 2012-08-14 TAO:0000598 TAO ZFIN:curator (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] 2012-09-17 VHOG:0000252 VHOG DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally ISBN:0123971756 NCBITaxon:40674 UMLS:C0039597 ncithesaurus:Testis gonad of male genitalia OBOL:automatic gonad of male reproductive system OBOL:automatic male gonad OBOL:automatic testicle FMA:7210 orchis BTO:0001363 testes testiculus BTO:0001363 The organs and associated structures associated with bearing offspring in a female animal. By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] BTO:0000083 CALOHA:TS-1303 EFO:0000969 EHDAA2:0000506 EHDAA:8116 EMAPA:17959 EV:0100110 FBbt:00004864 FMA:45663 GAID:364 HAO:0000324 MA:0000381 MESH:D005836 MIAA:0000028 NCIT:C12402 OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA TGMA:0000635 UMLS:C0700038 VHOG:0000726 WBbt:0006748 WikipediaCategory:Female_reproductive_system XAO:0000156 female organism genitalia female organism reproductive system genitalia of female organism reproductive system of female organism uberon female genital system female genital tract female genitalia female genitals female reproductive tract gynaecological tissue systema genitale femininum UBERON:0000474 female reproductive system http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg The organs and associated structures associated with bearing offspring in a female animal. MP:0001119 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000726 VHOG ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43 UMLS:C0700038 ncithesaurus:Female_Reproductive_System female organism genitalia OBOL:automatic female organism reproductive system OBOL:automatic genitalia of female organism OBOL:automatic reproductive system of female organism OBOL:automatic female genitals XAO:0000156 female reproductive tract MA:0000381 gynaecological tissue BTO:0000083 systema genitale femininum BTO:0000083 Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency AAO:0010053 AEO:0000032 BILA:0000032 BIRNLEX:7 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 NCIT:C32221 OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA TAO:0001308 TGMA:0001840 UMLS:C0229962 VHOG:0001758 XAO:0003013 ZFA:0001308 galen:BodyPart anatomic region uberon body part body region cardinal body part UBERON:0000475 organism subdivision CARO Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. CARO:0000032 CARO:DOS UMLS:C0229962 ncithesaurus:Body_Part anatomic region MA:0002433 body region FMA:7153 cardinal body part FMA:7153 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 uberon acellular anatomical structures UBERON:0000476 acellular anatomical structure CARO Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. acellular anatomical structures ZFA:0000382 anatomical cluster Anatomical group that has its parts adjacent to one another. Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3] AAO:0010009 AEO:0000041 BILA:0000041 CARO:0000041 EHDAA2:0003041 FBbt:00007277 FMA:49443 HAO:0000041 TADS:0000605 TAO:0001478 TGMA:0001842 VHOG:0001737 XAO:0003160 ZFA:0001478 uberon UBERON:0000477 anatomical cluster Anatomical group that has its parts adjacent to one another. A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. AAO:0010020 AEO:0000042 BILA:0000042 CALOHA:TS-2119 CARO:0000042 EHDAA2:0003042 EHDAA:46 FBbt:00005835 FMA:85537 HAO:0000042 NCIT:C34055 TAO:0000020 TGMA:0001843 UMLS:C1282438 VHOG:0000292 XAO:0004005 ZFA:0000020 extra-embryonic structure uberon extraembryonic structures extraembryonic tissue UBERON:0000478 see also conceptus extraembryonic component in EHDAA2. extraembryonic structure A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. CARO:DOS UMLS:C1282438 ncithesaurus:Extraembryonic_Structure extraembryonic structures ZFA:0000020 tissue Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. changed label and definition to reflect CARO2 AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 BIRNLEX:19 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 tissue CARO Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 UMLS:C0040300 ncithesaurus:Tissue portion of tissue CARO:0000043 simple tissue AEO:0000043 multi-tissue structure Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. AAO:0010048 AEO:0000055 BILA:0000055 CARO:0000055 EHDAA2:0003055 FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 VHOG:0001762 XAO:0003037 ZFA:0001488 uberon multi-tissue structures UBERON:0000481 multi-tissue structure CARO Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. CARO:0000055 multi-tissue structures ZFA:0001488 Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] epithelial AAO:0000144 AAO:0010055 AEO:0000066 BILA:0000066 BTO:0000416 CALOHA:TS-0288 CARO:0000066 EHDAA2:0003066 EMAPA:32738 FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 MA:0003060 MESH:D004848 NCIT:C12710 TAO:0001486 UMLS:C0014609 VHOG:0000387 XAO:0003045 ZFA:0001486 epithelial tissue portion of epithelium uberon UBERON:0000483 epithelium Tkanka:nablonkowa.png Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] 2012-09-17 VHOG:0000387 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 UMLS:C0014609 ncithesaurus:Epithelium portion of epithelium FMA:9639 Unilaminar epithelium that consists of a single layer of cuboidal cells. needs to be synchronized with CL - there is no distinct cuboidal cell in CL AAO:0010064 AEO:0000067 BILA:0000067 CARO:0000067 EHDAA2:0003067 FMA:45566 HAO:0000067 NCIT:C33553 TAO:0001497 UMLS:C0836134 XAO:0004009 ZFA:0001497 epithelium simplex cuboideum uberon simple cuboidal epithelia UBERON:0000484 simple cuboidal epithelium http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png Unilaminar epithelium that consists of a single layer of cuboidal cells. UMLS:C0836134 ncithesaurus:Simple_Cuboidal_Epithelium simple cuboidal epithelia ZFA:0001497 Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] columnar epithelium columnar epithlium AAO:0010063 AEO:0000068 BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 FBbt:00007027 FMA:45567 HAO:0000068 NCIT:C33552 TAO:0001496 UMLS:C0836135 XAO:0004008 ZFA:0001496 epithelium simplex columnare simple columnar epithelium uberon simple columnar epithelia UBERON:0000485 simple columnar epithelium http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] FMA:FMA columnar epithelium EHDAA2:0003068 columnar epithlium AEO:0000068 UMLS:C0836135 ncithesaurus:Simple_Columnar_Epithelium simple columnar epithelia ZFA:0001496 Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] Epithelium that consists of more than one layer of epithelial cells.[CARO] AAO:0010059 AEO:0000069 BILA:0000069 BTO:0002074 CARO:0000069 EHDAA2:0003069 FMA:45562 HAO:0000069 NCIT:C33622 TAO:0001494 UMLS:C0682575 XAO:0004006 ZFA:0001494 stratified epithelium uberon laminated epithelium UBERON:0000486 multilaminar epithelium Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] FMA:FMA Epithelium that consists of more than one layer of epithelial cells.[CARO] 2012-06-20 CARO:0000069 CARO FMA:45562 UMLS:C0682575 ncithesaurus:Stratified_Epithelium laminated epithelium BTO:0002074 Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 BTO:0002073 CARO:0000070 EHDAA2:0003070 FMA:45565 HAO:0000070 NCIT:C13178 TAO:0001498 UMLS:C0836133 XAO:0004010 ZFA:0001498 epithelium simplex squamosum uberon simple squamous epithelia UBERON:0000487 simple squamous epithelium Illu:epithelium.jpg Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] FMA:45565 Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] 2012-06-20 CARO:0000070 CARO FMA:45565 UMLS:C0836133 ncithesaurus:Simple_Squamous_Epithelium simple squamous epithelia ZFA:0001498 Epithelium that consists of epithelial cells not arranged in one ore more layers. AAO:0010057 AEO:0000071 BILA:0000071 CARO:0000071 EHDAA2:0003071 FMA:61741 HAO:0000071 TAO:0001493 XAO:0004004 ZFA:0001493 heterogenous epithelium uberon atypical epithelia UBERON:0000488 atypical epithelium Epithelium that consists of epithelial cells not arranged in one ore more layers. atypical epithelia ZFA:0001493 Compound organ that contains one or more macroscopic anatomical spaces. this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 CARO:0000072 EHDAA2:0003072 FMA:55671 HAO:0000072 TAO:0001490 TGMA:0001857 VHOG:0001730 XAO:0003165 ZFA:0001490 cavitated organ uberon cavitated compound organs UBERON:0000489 cavitated compound organ Compound organ that contains one or more macroscopic anatomical spaces. cavitated organ FMA:55671 cavitated compound organs ZFA:0001490 Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 BTO:0002073 CARO:0000073 EHDAA2:0003073 FMA:45561 HAO:0000073 NCIT:C33554 TAO:0001495 UMLS:C0682574 XAO:0004007 ZFA:0001495 simple epithelium uberon unilaminar epithelia UBERON:0000490 unilaminar epithelium Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] FMA:45561 Epithelium that consists of a single layer of epithelial cells.[CARO] 2012-06-20 CARO:0000073 CARO FMA:45561 UMLS:C0682574 ncithesaurus:Simple_Epithelium simple epithelium FMA:45561 unilaminar epithelia ZFA:0001495 Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. mucoid mucous CALOHA:TS-2144 ENVO:02000040 FMA:66938 GAID:1164 MESH:D009093 NCIT:C13259 OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA UMLS:C0026727 galen:Mucus uberon UBERON:0000912 mucus Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. UMLS:C0026727 ncithesaurus:Mucus Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. ENVO:02000042 FMA:9673 NCIT:C120839 intercellular fluid tissue fluid uberon UBERON:0000913 interstitial fluid Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. intercellular fluid ENVO:02000042 tissue fluid ENVO:02000042 Subdivision of trunk that lies between the head and the abdomen. note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest EMAPA:35862 FMA:259209 MA:0000022 thorax uberon anterior subdivision of trunk upper body upper trunk UBERON:0000915 thoracic segment of trunk FMA Subdivision of trunk that lies between the head and the abdomen. thorax MA:0000022 upper trunk FMA:259209 The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class abdominal celiac BTO:0000020 CALOHA:TS-0001 EFO:0000968 EMAPA:35102 EV:0100011 FMA:9577 GAID:16 MA:0000029 MAT:0000298 MESH:A01.047 MIAA:0000298 OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA galen:Abdomen abdominopelvic region abdominopelvis uberon adult abdomen belly celiac region UBERON:0000916 abdomen MA The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. abdominopelvic region FMA:9577 abdominopelvis FMA:9577 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryonic Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA UMLS:C0013935 VHOG:0001766 XAO:0000113 ZFA:0000103 embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo https://github.com/obophenotype/uberon/issues/503 Wrinkledfrog:embryos.jpg Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. BTO:0000379 FB:FBrf0039741 FB:FBrf0041814 GO:0009790 Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo ZFA UMLS:C0013935 ncithesaurus:Embryo embryonic organism BILA:0000056 developing organism BILA:0000056 A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 FBbt:00000110 FMA:69069 GAID:1303 MESH:A16.254.425 NCIT:C12950 NCIT:C54105 TAO:0001122 UMLS:C0920502 UMLS:C1708239 VHOG:0001223 XAO:0003011 ZFA:0001122 germinal layer primary germ layer uberon embryonic germ layer embryonic germ layers UBERON:0000923 Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] germ layer A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0001223 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 embryonic tissue FMA:69069 UMLS:C0920502 ncithesaurus:Embryonic_Tissue UMLS:C1708239 ncithesaurus:Germinal_Layer germinal layer ncithesaurus:Germinal_Layer primary germ layer GO:0001704 ZFA:0001122 Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] ectodermal AAO:0000137 BILA:0000036 BTO:0000315 CALOHA:TS-0216 EFO:0000414 EHDAA2:0000428 EMAPA:16069 EV:0100003 FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 MAT:0000173 MESH:A16.254.425.273 MIAA:0000173 NCIT:C12703 TAO:0000016 UMLS:C0013574 VHOG:0000153 XAO:0000001 ZFA:0000016 embryonic ectoderm uberon UBERON:0000924 ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png Bgee:AN Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] 2012-06-20 AAO:0000137 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000153 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 UMLS:C0013574 ncithesaurus:Ectoderm embryonic ectoderm VHOG:0000153 Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal AAO:0000139 BILA:0000038 BTO:0000800 CALOHA:TS-0273 EFO:0002545 EHDAA2:0000436 EMAPA:16062 EV:0100005 FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 MESH:A16.254.425.407 MIAA:0000175 NCIT:C12706 TAO:0000017 UMLS:C0014144 VHOG:0000154 XAO:0000090 ZFA:0000017 uberon entoderm UBERON:0000925 endoderm http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png Bgee:AN Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000154 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 UMLS:C0014144 ncithesaurus:Endoderm entoderm The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] mesodermal sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 CALOHA:TS-0623 EFO:0001981 EHDAA2:0001128 EHDAA:124 EHDAA:160 EHDAA:183 EMAPA:16083 EV:0100006 FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 MESH:A16.254.425.660 MIAA:0000174 NCIT:C12750 TAO:0000041 UMLS:C0025485 VHOG:0000152 XAO:0000050 ZFA:0000041 uberon embryonic mesoderm entire mesoderm mesodermal mantle UBERON:0000926 mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png sometimes not considered primary Bgee:AN The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] 2012-06-20 AAO:0000304 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000152 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UMLS:C0025485 ncithesaurus:Mesoderm embryonic mesoderm VHOG:0000152 entire mesoderm Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx stomodeal This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 TGMA:0000135 UMLS:C1514977 XAO:0000269 ZFA:0001290 mouth primordium primitive oral cavity stomatodeum stomodaeum uberon mouth pit oral ectoderm oral pit UBERON:0000930 stomodeum http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] 2012-08-14 TAO:0001290 TAO ZFIN:curator the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx MP:0012522 NCBITaxon:40674 stomodeal-hypophyseal primordium XAO:0000269 UMLS:C1514977 ncithesaurus:Stomodeum mouth primordium XAO:0000269 primitive oral cavity stomatodeum mouth pit EMAPA:16263 oral ectoderm ZFA:0001290 ZFIN:ZDB-PUB-100726-23 oral pit EMAPA:16263 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] proctodeal AAO:0011087 EHDAA2:0000121 EMAPA:25038 FBbt:00000123 NCIT:C34278 TAO:0000066 UMLS:C0231054 VHOG:0000139 XAO:0001019 ZFA:0000066 embryonic proctodaeum proctodaeum amnioproctodeal invagination uberon anal pit anus porus UBERON:0000931 proctodeum https://github.com/obophenotype/uberon/issues/685 EHDAA2 EHDAA2 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. ZFA:0000066 An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] 2012-08-14 TAO:0000066 TAO ZFIN:curator Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] 2012-06-20 AAO:0011087 AAO ZFA:0000066 UMLS:C0231054 ncithesaurus:Proctodeum amnioproctodeal invagination FBbt:00000123 anal pit VHOG:0000139 anus porus XAO:0001019 stomach An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. stomach http://langual.org Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa AAO:0000579 ANISEED:1235297 BTO:0001307 CALOHA:TS-0980 EFO:0000837 EHDAA2:0001915 EHDAA:2993 EMAPA:17021 EV:0100070 FMA:7148 GAID:293 MA:0000353 MAT:0000051 MESH:A03.492.766 MIAA:0000051 NCIT:C12391 OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA TAO:0002121 UMLS:C0038351 VHOG:0000408 XAO:0000128 galen:Stomach http://www.langual.org/langual_thesaurus.asp?termid=C0211 stomach chamber uberon anterior intestine gaster mesenteron ventriculus maw (mammal) UBERON:0000945 stomach Stomach:diagram.svg cjm cjm An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. ISBN:0073040584 Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] 2012-06-20 AAO:0000579 AAO AAO:EJS It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] 2012-09-17 VHOG:0000408 VHOG DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000) We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa WP:Stomach#In_other_animals UMLS:C0038351 ncithesaurus:Stomach gaster BTO:0001307 ventriculus aorta The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] aortic All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches AAO:0010213 BTO:0000135 CALOHA:TS-0046 EFO:0000265 EMAPA:18601 EV:0100027 FMA:3734 GAID:469 MA:0000062 MAT:0000035 MESH:D001011 MIAA:0000035 NCIT:C12669 OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA UMLS:C0003483 VHOG:0001523 XAO:0003010 galen:Aorta trunk of aortic tree trunk of systemic arterial tree dorsal aorta uberon arteria maxima UBERON:0000947 aorta Aorta:scheme.jpg MA EHDAA2 The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation ISBN:0-683-40008-8 MESH:A07.231.114.056 MP:0000272 This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. WP The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] 2012-06-20 AAO:0010213 AAO AAO:BJB When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0001523 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0003483 ncithesaurus:Aorta dorsal aorta ZFA:0000014 arteria maxima heart A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. heart (animal) http://langual.org Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] cardiac AAO:0010210 BILA:0000020 BTO:0000562 CALOHA:TS-0445 EFO:0000815 EHDAA2:0000738 EHDAA:420 EMAPA:16105 EV:0100018 FMA:7088 GAID:174 MA:0000072 MAT:0000036 MESH:D006321 MIAA:0000036 NCIT:C12727 OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA TAO:0000114 UMLS:C0018787 VHOG:0000276 XAO:0000064 ZFA:0000114 galen:Heart http://www.langual.org/langual_thesaurus.asp?termid=C0201 chambered heart vertebrate heart branchial heart uberon Herz@de cardium UBERON:0000948 Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart MA A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] 2012-08-14 TAO:0000114 TAO ZFIN:curator Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] 2012-06-20 AAO:0010210 AAO AAO:BJB relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0010210 AAO As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] 2012-09-17 VHOG:0000276 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 UMLS:C0018787 ncithesaurus:Heart chambered heart branchial heart Herz@de BTO:0000562 cardium EMAPA:16105 Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] endocrine AAO:0010279 CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 FBbt:00005068 FMA:9668 GAID:439 MA:0000012 MESH:D004703 NCIT:C12705 TAO:0001158 UMLS:C0014136 VHOG:0000098 XAO:0000158 ZFA:0001158 endocrine glandular system endocrine system systema endocrinum uberon UBERON:0000949 endocrine system Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. NLM:endocrine+system Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] 2012-06-20 AAO:0010279 AAO AAO:BJB Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] 2012-09-17 VHOG:0000098 VHOG DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009) UMLS:C0014136 ncithesaurus:Endocrine_System endocrine glandular system EHDAA2:0002224 brain The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion brain http://langual.org Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br BAMS:Brain BILA:0000135 BIRNLEX:796 BTO:0000142 CALOHA:TS-0095 DHBA:10155 EFO:0000302 EHDAA2:0000183 EHDAA:2641 EHDAA:6485 EMAPA:16894 EV:0100164 FBbt:00005095 FMA:50801 GAID:571 HBA:4005 MA:0000168 MAT:0000098 MBA:8 MBA:997 MESH:D001921 MIAA:0000098 NCIT:C12439 OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA PBA:3999 TAO:0000008 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 XAO:0000010 ZFA:0000008 galen:Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 http://www.langual.org/langual_thesaurus.asp?termid=C0199 uberon encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain UBERON:0000955 brain GO FMA Bgee:AN The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] 2012-08-14 TAO:0000008 TAO ZFIN:curator Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] 2012-06-20 AAO:0010478 AAO AAO:BJB The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000157 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 UMLS:C0006104 BIRNLEX:796 UMLS:C0006104 ncithesaurus:Brain UMLS:C1269537 BIRNLEX:796 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 BIRNLEX:796 encephalon BTO:0000142 suprasegmental levels of nervous system NeuroNames:21 suprasegmental structures NeuroNames:21 the brain NeuroNames:21 cerebral cortex The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus). The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]. Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG] hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743] BAMS:C BAMS:CTX BAMS:Cerebral_cortex BAMS:Cx BIRNLEX:1494 BM:Tel-Cx BTO:0000233 CALOHA:TS-0091 DHBA:10159 EFO:0000328 EHDAA2:0000234 EHDAA:5464 EMAPA:17544 EV:0100166 FMA:61830 GAID:629 HBA:4008 MA:0000185 MAT:0000108 MBA:688 MESH:A08.186.211.730.885.213 MIAA:0000108 NCIT:C12443 PBA:128011354 UMLS:C0007776 VHOG:0000722 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=39 cortex of cerebral hemisphere uberon brain cortex cortex cerebralis cortex cerebri cortical plate (CTXpl) cortical plate (areas) pallium of the brain UBERON:0000956 cerebral cortex http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg FMA GO ISBN:0471888893 FMA MA The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. BIRNLEX:1494 The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]. Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG] 2012-09-17 VHOG:0000722 VHOG DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969) UMLS:C0007776 BIRNLEX:1494 UMLS:C0007776 ncithesaurus:Cortex http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=39 BIRNLEX:1494 cortex of cerebral hemisphere BTO:0000233 FMA:61830 brain cortex BTO:0000233 cortex cerebralis NeuroNames:39 cortex cerebri cortical plate (CTXpl) NeuroNames:39 cortical plate (areas) NeuroNames:39 pallium of the brain BTO:0000233 Middle part of an organ, surrounded by the cortex. this class is used in a very general sense medullary FMA:61108 galen:Medulla medulla uberon UBERON:0000958 medulla of organ Middle part of an organ, surrounded by the cortex. medulla FMA:61108 The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. BAMS:cern FMA:5859 NCIT:C32299 NLXANAT:20090207 UMLS:C0228815 cervical nerve cervical nerve tree cervical spinal nerve nervus cervicalis uberon UBERON:0000962 Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP] nerve of cervical vertebra http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. UMLS:C0228815 ncithesaurus:Cervical_Nerve cervical nerve FMA:5859 nervus cervicalis FMA:5859 FMA:TA the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure corneal Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water AAO:0010344 BTO:0000286 CALOHA:TS-0171 EFO:0000377 EHDAA2:0000316 EHDAA:10199 EMAPA:17161 EV:0100341 FMA:58238 GAID:892 MA:0000266 MESH:D003315 NCIT:C12342 OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA TAO:0000640 UMLS:C0010031 VHOG:0000164 XAO:0000180 ZFA:0000640 cornea of camera-type eye uberon corneas tunica cornea UBERON:0000964 cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg XAO MA MA FMA-isa definitional the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure ISBN:0-683-40008-8 MESH:A09.371.060.217 MP:0001312 UMLS:C0010031 ncithesaurus:Cornea cornea of camera-type eye GO:0061303 corneas ZFA:0000640 Transparent part of camera-type eye that helps to refract light to be focused on the retina. The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] This class excludes compound eye corneal lenses. AAO:0010348 BTO:0000723 CALOHA:TS-0545 EHDAA:9057 EMAPA:17838 EV:0100343 FMA:58241 MA:0000275 MAT:0000141 MESH:A09.371.509 MIAA:0000141 NCIT:C12743 OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000975 TAO:0000035 UMLS:C0023317 VHOG:0000169 XAO:0000008 ZFA:0000035 camera-type eye lens eye lens lens lens crystallina uberon crystalline lens lenses ocular lens UBERON:0000965 The lens is avascular and nourished by diffusion from the aqueous and vitreous lens of camera-type eye Transparent part of camera-type eye that helps to refract light to be focused on the retina. The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000169 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) UMLS:C0023317 ncithesaurus:Crystalline_Lens camera-type eye lens GO:0002088 eye lens lens lens crystallina crystalline lens BTO:0000723 lenses ZFA:0000035 ocular lens BTO:0000723 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] retinal AAO:0010352 BAMS:R BIRNLEX:1153 BTO:0001175 CALOHA:TS-0865 EFO:0000832 EHDAA2:0001627 EHDAA:4757 EMAPA:17168 EV:0100348 FMA:58301 GAID:755 MA:0000276 MAT:0000142 MBA:304325711 MESH:D012160 MIAA:0000142 NCIT:C12343 NIFSTD_RETIRED:birnlex_1156 OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA TAO:0000152 UMLS:C0035298 UMLS:C1278894 VHOG:0000229 XAO:0000009 ZFA:0000152 inner layer of eyeball retina of camera-type eye tunica interna of eyeball uberon Netzhaut retinas UBERON:0000966 Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png EHDAA2 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. ZFIN:curator The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000152 TAO ZFIN:curator The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000229 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) UMLS:C0035298 BIRNLEX:1153 UMLS:C0035298 ncithesaurus:Retina UMLS:C1278894 BIRNLEX:1153 retina of camera-type eye GO:0060041 Netzhaut BTO:0001175 retinas ZFA:0000152 eye An organ that detects light. eye This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) http://langual.org ocular optic Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 MIAA:0000140 OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA http://www.langual.org/langual_thesaurus.asp?termid=C0256 uberon light-detecting organ visual apparatus UBERON:0000970 eye An organ that detects light. visual apparatus EV:0100336 An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck. cervical AEO:0000108 BTO:0000420 CALOHA:TS-2045 EFO:0000967 EHDAA2:0003108 EMAPA:35587 FMA:7155 GAID:86 MA:0000024 MAT:0000297 MESH:D009333 MIAA:0000297 NCIT:C13063 OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA UMLS:C0027530 galen:Neck uberon collum neck (volume) UBERON:0000974 neck Female:neck.jpg An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. ISBN:9780674021839 UMLS:C0027530 ncithesaurus:Neck collum neck (volume) FMA:7155 Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah] Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] humeral AAO:0000679 CALOHA:TS-2202 EFO:0001398 EMAPA:19106 FMA:13303 GAID:183 MA:0001356 MESH:A02.835.232.087.412 NCIT:C12731 UMLS:C0020164 VHOG:0001158 XAO:0003210 galen:Humerus humeri humerus bone uberon mesomere 1 of pectoral appendage proximal metapterygial mesomere of pectoral appendage proximal metapterygial mesomere of pectoral fin UBERON:0000976 humerus http://upload.wikimedia.org/wikipedia/commons/6/67/Illu_upper_extremity.jpg definitional Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah] AAO:0000679 PHENOSCAPE:mah Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO] 2012-06-20 AAO:0000679 AAO AAO:LAP Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001158 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 UMLS:C0020164 ncithesaurus:Humerus humeri PHENOSCAPE:ad mesomere 1 of pectoral appendage ISBN:0226313409 proximal metapterygial mesomere of pectoral appendage ISBN:0226313409 proximal metapterygial mesomere of pectoral fin ISBN:0226313409 The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] pleural In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86 BTO:0001791 CALOHA:TS-2081 EFO:0001980 EMAPA:16775 EV:0100044 FMA:9583 GAID:360 MA:0000433 MESH:D010994 NCIT:C12469 OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA UMLS:C0032225 VHOG:0000394 wall of pleural sac uberon pleura pleural tissue UBERON:0000977 pleura http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). ISBN:0-683-40008-8 MP:0010820 UBERON:cjm BGEE:AN ISBN:978-0030223693 The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] 2012-09-17 VHOG:0000394 VHOG ISBN:0124020607 UMLS:C0032225 ncithesaurus:Pleural_Tissue pleural tissue BTO:0001791 NCIT:C12469 The portion of the hindlimb that contains both the stylopod and zeugopod. Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For BTO:0000721 CALOHA:TS-2206 EFO:0001411 EHDAA2:0000972 EHDAA:5151 EHDAA:6176 EHDAA:8289 EMAPA:17489 GAID:49 MA:0000047 MESH:D035002 OpenCyc:Mx4rvViYzZwpEbGdrcN5Y29ycA VHOG:0000345 tetrapod leg uberon lower extremity UBERON:0000978 we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot leg The portion of the hindlimb that contains both the stylopod and zeugopod. Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000345 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For 3 lower extremity MESH:A01.378.610 Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]. Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO] Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] femoral AAO:0000887 AAO:0000889 BTO:0001284 CALOHA:TS-0322 EFO:0001396 EMAPA:19143 FMA:9611 GAID:199 MA:0001359 MESH:A02.835.232.500.247 NCIT:C12717 OpenCyc:Mx4rvVjOJJwpEbGdrcN5Y29ycA UMLS:C0015811 VHOG:0001159 VSAO:0000186 XAO:0003214 galen:Femur thigh bone uberon femoral bone mesomere 1 of pevlic appendage os femorale os femoris os longissimum proximal metapterygial mesomere of pelvic appendage proximal metapterygial mesomere of pelvic fin UBERON:0000981 femur http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png MA definitional Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]. VSAO:0000186 Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO] 2012-08-14 VSAO:0000186 VSAO VSAO:NI Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO] 2012-06-20 AAO:0000889 AAO AAO:LAP Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001159 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 UMLS:C0015811 ncithesaurus:Femur femoral bone BTO:0001284 mesomere 1 of pevlic appendage ISBN:0226313409 os femorale BTO:0001284 os femoris BTO:0001284 os longissimum proximal metapterygial mesomere of pelvic appendage ISBN:0226313409 proximal metapterygial mesomere of pelvic fin ISBN:0226313409 Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 BTO:0001686 CALOHA:TS-2023 EFO:0000948 EMAPA:35456 FMA:7490 GAID:102 MA:0000319 MAT:0000188 MESH:D007596 MIAA:0000188 NCIT:C13044 OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0003182 TAO:0000367 UMLS:C0022417 VHOG:0001276 VSAO:0000101 XAO:0000171 ZFA:0001596 galen:Joint uberon articular joint joints UBERON:0000982 skeletal joint Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. GO_REF:0000034 VSAO:0000101 Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] 2012-08-14 VSAO:0000101 VSAO PSPUB:0000170 Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] 2012-08-14 TAO:0000367 TAO TAO:pem articulation VSAO:0000101 joint FMA:7490 VSAO:0000101 UMLS:C0022417 ncithesaurus:Joint articular joint BTO:0001686 joints ZFA:0001596 A metapodium region that is part of a pes. mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton CALOHA:TS-2221 FMA:24997 MA:0000049 hind metapodium metatarsal part of foot metatarsal region regio metatarsalis hindlimb cannon region hindlimb equine cannon region uberon metatarsus UBERON:0000983 metatarsus region PHENOSCAPE:ni A metapodium region that is part of a pes. OBOL:automatic hind metapodium AAO:0000221 MA:th metatarsal part of foot FMA:24997 metatarsal region FMA:24997 regio metatarsalis FMA:24997 FMA:TA hindlimb cannon region NCBITaxon:9788 hindlimb equine cannon region NCBITaxon:9788 metatarsus MA:0000049 The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] BAMS:PONS BAMS:Pons BIRNLEX:733 BM:Pons BTO:0001101 CALOHA:TS-0813 DHBA:10661 EFO:0001394 EHDAA2:0004394 EMAPA:17563 EV:0100253 FMA:67943 GAID:578 HBA:9131 MA:0000204 MAT:0000115 MBA:771 MESH:D011149 MIAA:0000115 NCIT:C12511 UMLS:C0032639 UMLS:C1280999 VHOG:0001176 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=547 pons Varolii pons of Varolius uberon pons cerebri UBERON:0000988 pons http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png neuronames The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. VHOG:0001176 The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] 2012-09-17 VHOG:0001176 VHOG During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] 2012-09-17 VHOG:0001176 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474 UMLS:C0032639 BIRNLEX:733 UMLS:C0032639 ncithesaurus:Pons_Varolii UMLS:C1280999 BIRNLEX:733 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=547 BIRNLEX:733 pons Varolii ncithesaurus:Pons_Varolii pons cerebri NeuroNames:547 A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination penile phallic Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca BTO:0000405 CALOHA:TS-0758 EFO:0000987 EHDAA2:0001433 EHDAA:9380 EMAPA:18682 EMAPA_RETIRED:18996 EV:0100107 FMA:9707 GAID:389 MA:0000408 MAT:0000186 MESH:D010413 MIAA:0000186 NCIT:C12409 OpenCyc:Mx4rvVjkCZwpEbGdrcN5Y29ycA UMLS:C0030851 VHOG:0000727 galen:Penis uberon penes phallus UBERON:0000989 penis http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg Wikipedia Wikipedia EHDAA2 A intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination ISBN:0-683-40008-8 MP:0005187 Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca WP UMLS:C0030851 ncithesaurus:Penis penes Anatomical system that has as its parts the organs concerned with reproduction. consider splitting genitalia from reproductive system Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] AAO:0010258 BILA:0000103 BTO:0000081 CALOHA:TS-1318 EFO:0000809 EHDAA2:0001603 EHDAA:5923 EMAPA:17381 EV:0100100 FBbt:00004857 FMA:7160 GAID:363 HAO:0000374 HAO:0000895 MA:0000326 MIAA:0000305 NCIT:C12841 OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA TAO:0000632 UMLS:C1261210 VHOG:0000182 WBbt:0005747 XAO:0000142 ZFA:0000632 uberon Geschlechtsorgan animal reproductive system genital system genital tract genitalia organa genitalia reproductive tissue reproductive tract systemata genitalia UBERON:0000990 reproductive system http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg Anatomical system that has as its parts the organs concerned with reproduction. Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] 2012-06-20 AAO:0010258 AAO AAO:BJB Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] 2012-09-17 VHOG:0000182 VHOG PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007) UMLS:C1261210 ncithesaurus:Reproductive_System Geschlechtsorgan BTO:0000081 animal reproductive system BTO:0000081 genitalia organa genitalia BTO:0000081 reproductive tissue BTO:0000081 systemata genitalia Reproductive organ that produces and releases eggs (ovary) or sperm (testis). Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] gonadal FMA xref is a 'general anatomical term' AAO:0000213 BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:17383 FBbt:00004858 FMA:18250 GAID:368 HAO:0000379 MA:0002420 MESH:D006066 NCIT:C12725 OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA TAO:0000413 UMLS:C0018067 VHOG:0000397 WBbt:0005175 XAO:0003146 ZFA:0000413 gonada uberon gonads UBERON:0000991 gonad Reproductive organ that produces and releases eggs (ovary) or sperm (testis). ISBN:0140512888 ZFA:0000413 ZFIN:curator Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] 2012-06-20 AAO:0000213 AAO AAO:BJB The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] 2012-08-14 TAO:0000413 TAO ZFIN:curator Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] 2012-09-17 VHOG:0000397 VHOG DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) FMA xref is a 'general anatomical term' FMA UMLS:C0018067 ncithesaurus:Gonad gonads ZFA:0000413 ovary the gonad of a female organism which contains germ cells Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] Female reproductive organ.[TAO] (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] ovarian Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo AAO:0000371 BILA:0000125 BSA:0000080 BTO:0000975 CALOHA:TS-0730 EFO:0000973 EHDAA2:0001360 EHDAA:8124 EMAPA:17962 EV:0100111 FBbt:00004865 FMA:7209 GAID:367 MA:0000384 MESH:D010053 MIAA:0000125 NCIT:C12404 OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA TAO:0000403 UMLS:C0029939 VHOG:0000251 XAO:0000258 ZFA:0000403 animal ovary female gonad female organism genitalia gonad female organism genitalia gonada female organism reproductive system gonad female organism reproductive system gonada female reproductive system gonad female reproductive system gonada genitalia of female organism gonad genitalia of female organism gonada gonad of female organism genitalia gonad of female organism reproductive system gonad of female reproductive system gonad of genitalia of female organism gonad of reproductive system of female organism gonada of female organism genitalia gonada of female organism reproductive system gonada of female reproductive system gonada of genitalia of female organism gonada of reproductive system of female organism ovum-producing ovary reproductive system of female organism gonad reproductive system of female organism gonada uberon ovaries ovarium UBERON:0000992 ovary Female:anatomy.png http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png the gonad of a female organism which contains germ cells ISBN:0-683-40008-8 MP:0001126 Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] 2012-06-20 AAO:0000371 AAO AAO:BJB Female reproductive organ.[TAO] 2012-08-14 TAO:0000403 TAO ZFIN:curator (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] 2012-09-17 VHOG:0000251 VHOG DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo WP UMLS:C0029939 ncithesaurus:Ovary animal ovary EFO:0000973 female organism genitalia gonad OBOL:automatic female organism genitalia gonada OBOL:automatic female organism reproductive system gonad OBOL:automatic female organism reproductive system gonada OBOL:automatic female reproductive system gonad OBOL:automatic female reproductive system gonada OBOL:automatic genitalia of female organism gonad OBOL:automatic genitalia of female organism gonada OBOL:automatic gonad of female organism genitalia OBOL:automatic gonad of female organism reproductive system OBOL:automatic gonad of female reproductive system OBOL:automatic gonad of genitalia of female organism OBOL:automatic gonad of reproductive system of female organism OBOL:automatic gonada of female organism genitalia OBOL:automatic gonada of female organism reproductive system OBOL:automatic gonada of female reproductive system OBOL:automatic gonada of genitalia of female organism OBOL:automatic gonada of reproductive system of female organism OBOL:automatic ovum-producing ovary GO:0061039 reproductive system of female organism gonad OBOL:automatic reproductive system of female organism gonada OBOL:automatic ovaries ovarium A tube or collection of tubes in an animal from the ovaries to the outside of the body. sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP] in birds divided into infundibulum, magnum, isthmus, uterus, and vagina AAO:0010533 BSA:0000083 BTO:0000980 EFO:0000974 EMAPA:18984 GAID:366 MAT:0000126 MESH:D010057 MIAA:0000126 NCIT:C77957 TAO:0000560 UMLS:C0029954 VHOG:0001136 XAO:0003052 ZFA:0000560 ovarian duct ovarian tube uterine tube uberon female reproductive tracts oviducts tuba uterina tuba uterinae tubular parts of female reproductive system UBERON:0000993 oviduct A tube or collection of tubes in an animal from the ovaries to the outside of the body. A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] 2012-09-17 VHOG:0001136 VHOG In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] 2012-09-17 VHOG:0001136 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688 UMLS:C0029954 ncithesaurus:Oviduct ovarian duct ovarian tube female reproductive tracts oviducts ZFA:0000560 tuba uterina BTO:0000980 tuba uterinae BTO:0000980 tubular parts of female reproductive system uterus the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] uterine Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus] BTO:0001424 CALOHA:TS-1102 EFO:0000975 EMAPA:29915 EV:0100113 FMA:17558 GAID:172 MA:0000389 MAT:0000127 MESH:D014599 MIAA:0000127 NCIT:C12405 OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA UMLS:C0042149 VHOG:0001137 galen:Uterus uberon UBERON:0000995 uterus Female:anatomy.png http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png cjm the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth MGI:csmith MP:0001120 The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] 2012-09-17 VHOG:0001137 VHOG An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] 2012-09-17 VHOG:0001137 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678 UMLS:C0042149 ncithesaurus:Uterus vagina A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] vaginal 'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688 BTO:0000243 CALOHA:TS-1103 EFO:0000976 EMAPA:18986 EV:0100117 FMA:19949 GAID:381 MA:0000394 MAT:0000128 MESH:D014621 MIAA:0000128 NCIT:C12407 OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA UMLS:C0042232 VHOG:0001138 galen:Vagina uberon distal oviductal region distal portion of oviduct vaginae UBERON:0000996 vagina http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg http://upload.wikimedia.org/wikipedia/commons/a/a4/Vaginal_opening_-_english_description.jpg cjm FMA Wikipedia A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] 2012-11-29 FMA:19949 FMA The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] 2012-09-17 VHOG:0001138 VHOG The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] 2012-09-17 VHOG:0001138 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 UMLS:C0042232 ncithesaurus:Vagina vaginae external genital organs of the female mammal[WP]. The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG] vulval BTO:0003101 CALOHA:TS-1168 EFO:0000978 EMAPA:36631 EV:0100118 FMA:20462 GAID:383 MA:0000395 MAT:0000169 MESH:D014844 MIAA:0000169 NCIT:C12408 OpenCyc:Mx4rvgAWeJwpEbGdrcN5Y29ycA UMLS:C0042993 VHOG:0001458 galen:Vulva female pudendum mammalian vulva puboperineal region pudendum femininum skin of female pudendum skin of vulva vulva uberon pudendum pudendum femininum pudendum muliebre UBERON:0000997 mammalian vulva http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg external genital organs of the female mammal[WP]. The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG] 2012-09-17 VHOG:0001458 VHOG UMLS:C0042993 ncithesaurus:Vulva female pudendum BTO:0003101 female pudendum FMA:20462 puboperineal region FMA:20462 pudendum femininum FMA:20462 FMA:TA vulva MA:0000395 pudendum BTO:0003101 pudendum femininum pudendum muliebre BTO:0003101 Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct. Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG] (In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG] The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70% of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid. seminal gland AAO:0010788 BTO:0001234 CALOHA:TS-0919 EFO:0000986 EMAPA:19180 EV:0100106 FMA:19386 GAID:394 MA:0000410 MAT:0000171 MESH:D012669 MIAA:0000171 NCIT:C12787 OpenCyc:Mx4rwTtRpJwpEbGdrcN5Y29ycA UMLS:C0036628 VHOG:0001379 uberon glandula seminalis glandula vesiculosa gonecyst vas efferens vesicula seminalis vesiculae seminales vesicular gland vesicular glands vesicular seminalis vesiculæ seminales UBERON:0000998 seminal vesicle http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct. BTO:0001234 Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG] 2012-09-17 VHOG:0001379 VHOG (In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG] 2012-09-17 VHOG:0001379 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556 UMLS:C0036628 ncithesaurus:Seminal_Vesicle glandula seminalis BTO:0001234 glandula vesiculosa BTO:0001234 vesicula seminalis vesicula seminalis BTO:0001234 vesiculae seminales vesiculae seminales vesicular gland vesicular glands vesicular seminalis vesiculæ seminales The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted]. BTO:0001580 CALOHA:TS-0211 EFO:0000985 EMAPA:19088 FMA:19325 GAID:388 MA:0003247 MAT:0000170 MESH:D004543 MIAA:0000170 NCIT:C32493 OpenCyc:Mx4rwOt7MJwpEbGdrcN5Y29ycA UMLS:C0013747 ductus ejaculatorii ductus ejaculatorius uberon ductus ejaculatorii UBERON:0000999 ejaculatory duct Male:anatomy.png The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted]. UMLS:C0013747 ncithesaurus:Ejaculatory_Duct ductus ejaculatorii BTO:0001580 ductus ejaculatorius BTO:0001580 ductus ejaculatorii A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG] Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall. BTO:0001427 CALOHA:TS-1105 EFO:0000981 EMAPA:18681 EV:0100105 FMA:19234 GAID:404 MA:0000413 MESH:D014649 MIAA:0000129 NCIT:C12813 OpenCyc:Mx4rvjv7bpwpEbGdrcN5Y29ycA UMLS:C0042360 VHOG:0001135 galen:VasDeferens deferent duct ductus deferens vas deferen uberon sperm duct vasa deferentia UBERON:0001000 vas deferens http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg FMA A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct ISBN:0-683-40008-8 MGI:pvb MP:0002769 The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG] 2012-09-17 VHOG:0001135 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.670 Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall. WP UMLS:C0042360 ncithesaurus:Vas_Deferens ductus deferens The outer epithelial layer of the skin that is superficial to the dermis. A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] relationship loss: subclass external integument structures (AAO:0000961)[AAO] (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] epidermal Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes). epidermis skin AAO:0000143 BTO:0000404 CALOHA:TS-0283 EFO:0000954 EMAPA:17528 EV:0100153 FMA:70596 GAID:932 MA:0000153 MAT:0000154 MESH:D004817 MIAA:0000154 NCIT:C12708 TAO:0000105 UMLS:C0014520 VHOG:0000077 XAO:0000028 ZFA:0000105 vertebrate epidermis uberon UBERON:0001003 skin epidermis The outer epithelial layer of the skin that is superficial to the dermis. ISBN:0073040584 A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000105 TAO ZFIN:curator The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] 2012-06-20 AAO:0000143 AAO AAO:BJB relationship loss: subclass external integument structures (AAO:0000961)[AAO] 2012-06-20 AAO:0000143 AAO (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] 2012-09-17 VHOG:0000077 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72 UMLS:C0014520 ncithesaurus:Epidermis Functional system which consists of structures involved in respiration. The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] AAO:0000541 BTO:0000203 CALOHA:TS-1319 EFO:0000804 EHDAA2:0001604 EHDAA:2203 EMAPA:16727 EV:0100036 FMA:7158 GAID:78 MA:0000327 MAT:0000030 MESH:D012137 MIAA:0000030 NCIT:C12779 OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA TAO:0000272 UMLS:C0035237 VHOG:0000202 XAO:0000117 ZFA:0000272 apparatus respiratorius respiratory system uberon Atmungssystem apparatus respiratorius systema respiratorium UBERON:0001004 respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg Functional system which consists of structures involved in respiration. The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] 2012-06-20 AAO:0000541 AAO AAO:BJB There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] 2012-09-17 VHOG:0000202 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23 UMLS:C0035237 ncithesaurus:Respiratory_System Atmungssystem BTO:0000203 apparatus respiratorius BTO:0000203 systema respiratorium An airway through which respiratory air passes in organisms. This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends airway airways FMA:265130 uberon UBERON:0001005 respiratory airway An airway through which respiratory air passes in organisms. airway airways Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] digestive many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 EV:0100056 FBbt:00005055 FMA:7152 GAID:278 MA:0002431 MAT:0000018 MESH:D004064 MIAA:0000018 TADS:0000170 TAO:0000339 WBbt:0005748 XAO:0000125 ZFA:0000339 galen:DigestiveSystem ncithesaurus:Digestive_System uberon alimentary system alimentary tract gastrointestinal system gut UBERON:0001007 digestive system Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. FB:gg NLM:alimentary+system An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] 2012-06-20 AAO:0000129 AAO AAO:BJB many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class MA The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans AAO:0010257 BILA:0000015 BTO:0001244 BTO:0003092 CALOHA:TS-1323 EFO:0000803 EHDAA2:0001601 EHDAA:5901 EMAPA:17366 EV:0100095 FBbt:00005056 FMA:7159 GAID:391 MA:0000325 MAT:0000027 MESH:D014551 MIAA:0000027 NCIT:C12413 TADS:0000162 TAO:0000163 UMLS:C1508753 VHOG:0000723 WBbt:0005736 XAO:0000143 ZFA:0000163 galen:UrinaryTract excretory system renal system systema urinaria systema urinarium urinary system urinary tract uberon renal or urinary system renal/urinary system UBERON:0001008 renal system The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. GO:0072001 An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] 2012-06-20 AAO:0010257 AAO AAO:BJB Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] 2012-09-17 VHOG:0000723 VHOG ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406 In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels GO This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans UMLS:C1508753 ncithesaurus:Urinary_System renal system GO:0001977 systema urinaria FMA:7159 systema urinarium BTO:0003092 renal or urinary system EHDAA:5901 organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. the cardiovascular system and the lymphatic system are parts of the circulatory system Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 FBbt:00005057 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA VHOG:0001248 uberon systema cardiovasculare UBERON:0001009 circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. WBbt coelomocyte currently classified as circulating cell Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] 2012-06-20 AAO:0000959 AAO AAO:BJB We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] 2012-09-17 VHOG:0001248 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 systema cardiovasculare adipose tissue Portion of connective tissue composed of adipocytes enmeshed in areolar tissue Connective tissue in which fat is stored.[TAO] Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] adipose In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen. in FMA this is dense irregular connective tissue AAO:0000001 AEO:000020 BTO:0001487 CALOHA:TS-0013 EFO:0000790 EHDAA2:0003120 EMAPA:35112 EV:0100381 FMA:20110 GAID:920 MA:0000009 MAT:0000015 MESH:D000273 MIAA:0000015 NCIT:C12472 OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA TAO:0002134 UMLS:C0001527 VHOG:0001284 XAO:0003049 ZFA:0005345 galen:FattyTissue fat fat tissue fatty tissue uberon adipose bodyfat fatty depot UBERON:0001013 adipose tissue FMA Portion of connective tissue composed of adipocytes enmeshed in areolar tissue MESH:A10.165.114 MGI:cwg MP:0000003 Connective tissue in which fat is stored.[TAO] 2012-08-14 TAO:0002134 TAO ZFIN:curator Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] 2012-06-20 AAO:0000001 AAO AAO:LAP relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] 2012-06-20 AAO:0000001 AAO Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] 2012-09-17 VHOG:0001284 VHOG DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007) in FMA this is dense irregular connective tissue FMA UMLS:C0001527 ncithesaurus:Adipose_Tissue fat MA:0000009 adipose BTO:0001487 bodyfat BTO:0001487 A subdivision of the muscular system corresponding to a subdisivision of an organism. In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. AAO:0011066 BTO:0000887 EFO:0001949 EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 NCIT:C13056 OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA TAO:0000548 UMLS:C0026845 VSAO:0005038 WBbt:0005737 ZFA:0000548 muscle group muscles set musculature musculi set of muscles set of skeletal muscles uberon muscle system muscles musculature system UBERON:0001015 musculature http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png A subdivision of the muscular system corresponding to a subdisivision of an organism. In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. FMA UMLS:C0026845 ncithesaurus:Muscle musculi FMA:32558 FMA:TA set of muscles FMA:32558 set of skeletal muscles MA:0000165 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] nervous neural AAO:0000324 BILA:0000079 BIRNLEX:844 BTO:0001484 CALOHA:TS-1313 EFO:0000802 EHDAA2:0001246 EHDAA:826 EMAPA:16469 EV:0100162 FBbt:00005093 FMA:7157 GAID:466 MA:0000016 MAT:0000026 MESH:D009420 MIAA:0000026 NCIT:C12755 OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA TAO:0000396 UMLS:C0027763 VHOG:0000402 WBbt:0005735 XAO:0000177 ZFA:0000396 neurological system nerve net uberon systema nervosum UBERON:0001016 nervous system http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png Bgee:AN The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. BIRNLEX:844 ISBN:0-14-051288-8 ISBN:3110148986 NLM:nervous+system WB:rynl ZFIN:curator A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000396 TAO ZFIN:curator Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] 2012-06-20 AAO:0000324 AAO AAO:BJB Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] 2012-09-17 VHOG:0000402 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 UMLS:C0027763 ncithesaurus:Nervous_System neurological system GO:0050877 nerve net systema nervosum The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] The brain and spinal cord. Kimmel et al, 1995.[TAO] The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 BIRNLEX:1099 BTO:0000227 CALOHA:TS-0150 EFO:0000908 EHDAA2:0000225 EHDAA:828 EMAPA:16470 EMAPA:16754 EV:0100163 FBbt:00005094 FMA:55675 GAID:570 MA:0000167 MAT:0000457 MESH:D002490 NCIT:C12438 OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA TAO:0000012 UMLS:C0927232 VHOG:0000293 XAO:0000215 ZFA:0000012 CNS systema nervosum centrale cerebrospinal axis uberon neuraxis UBERON:0001017 central nervous system FBbt cjm Bgee:AN The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. GO:0021551 Part of the nervous system which includes the brain and spinal cord.[AAO] 2012-06-20 AAO:0000090 AAO AAO:BJB The brain and spinal cord. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000012 TAO ZFIN:curator The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). BIRNLEX:1099 (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] 2012-09-17 VHOG:0000293 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) UMLS:C0927232 BIRNLEX:1099 UMLS:C0927232 ncithesaurus:Central_Nervous_System CNS systema nervosum centrale FMA:55675 FMA:TA cerebrospinal axis FMA:55675 neuraxis FMA:55675 An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. A portion of tissue which is a fasiculated group of axons.[TAO] nervous AAO:0011070 AEO:0000137 BAMS:n BIRNLEX:1615 BSA:0000098 BTO:0000925 BTO:0001027 CALOHA:TS-0772 EHDAA2:0003137 EHDAA:2851 EHDAA:3776 EHDAA:4657 EMAPA:32808 EMAPA:32815 EV:0100371 FBbt:00005105 FMA:65132 FMA:65239 GAID:747 GAID:758 MA:0000217 MA:0000228 MESH:D010525 NCIT:C12466 NCIT:C12768 NLX:147826 OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA TAO:0007009 UMLS:C0027740 UMLS:C0031119 VHOG:0000901 XAO:0000204 XAO:0003047 ZFA:0007009 galen:Nerve nerves peripheral nerve uberon neural subtree UBERON:0001021 nerve FBbt An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. FBbt:00005105 A portion of tissue which is a fasiculated group of axons.[TAO] 2012-08-14 TAO:0007009 TAO ZFIN:curator UMLS:C0027740 ncithesaurus:Nerve UMLS:C0031119 ncithesaurus:Peripheral_Nerve nerves TAO:0007009 peripheral nerve neural subtree FMA:65132 A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. AEO:0000201 EHDAA2:0003200 FBbt:00005136 FMA:5868 OpenCyc:Mx4rv0GdXpwpEbGdrcN5Y29ycA nervus sensorius uberon afferent nerve UBERON:0001027 sensory nerve A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. UBERON:cjm nervus sensorius Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 MIAA:0000031 NLXANAT:090816 TAO:0000282 VHOG:0001674 XAO:0003194 ZFA:0000282 organa sensuum sense organ subsystem sense organs sense organs set sensory subsystem sensory systems uberon organa sensuum sensory organ system set of sense organs UBERON:0001032 sensory system http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] 2012-09-17 VHOG:0001674 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) organa sensuum FMA:75259 FMA:TA sense organs FMA:75259 sense organs set FMA:75259 sensory systems TAO:0000282 organa sensuum set of sense organs FMA:75259 The sensory system for the sense of taste. The sensory system for the sense of taste[NLXANAT:090803]. The sensory system used for the sense of taste.[AAO] gustatory in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes AAO:0010577 BILA:0000143 EFO:0000830 FMA:7194 MA:0002446 MAT:0000275 MIAA:0000275 NLXANAT:090803 TAO:0001101 XAO:0003197 ZFA:0001101 gustatory organ system taste system uberon UBERON:0001033 gustatory system The sensory system for the sense of taste. NLXANAT:090803 The sensory system for the sense of taste[NLXANAT:090803]. NLXANAT:090803 The sensory system used for the sense of taste.[AAO] 2012-06-20 AAO:0010577 AAO AAO:EJS in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes ZFA A filament, mostly protein, that grows from follicles found in the dermis[WP]. TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales) this class defines an individual hair BTO:0001501 CALOHA:TS-0430 EFO:0000958 EMAPA:18769 EV:0100157 FMA:53667 GAID:71 MA:0000155 MAT:0000160 MESH:D006197 MIAA:0000160 NCIT:C32705 OpenCyc:Mx4rvVjOX5wpEbGdrcN5Y29ycA-Mp88EdaAAACgycbRww UMLS:C0018494 VHOG:0001191 hair uberon coat hair coat/ hair fur microchaeta quill setulae vibrissa whisker UBERON:0001037 strand of hair http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png FMA FMA FMA A filament, mostly protein, that grows from follicles found in the dermis[WP]. UMLS:C0018494 ncithesaurus:Hair quill vibrissa whisker A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. consider splitting class One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG] the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)] BTO:0001471 CALOHA:TS-1130 EFO:0003078 EHDAA2:0002212 EHDAA:164 EMAPA:16085 FMA:87180 GAID:1301 MESH:A16.254.403.981 NCIT:C14128 UMLS:C0043425 VHOG:0000830 uberon saccus vitellinus vesicula umbilicalis UBERON:0001040 yolk sac http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png https://github.com/obophenotype/uberon/issues/635 EHDAA2 ISBN:0073040584 ISBN:0073040584 A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]. One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG] 2012-09-17 VHOG:0000830 VHOG the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells MP:0001718 Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] 2012-09-17 VHOG:0000830 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 UMLS:C0043425 ncithesaurus:Yolk_Sac saccus vitellinus vesicula umbilicalis Anterior subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] AAO:0011042 BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 FBbt:00005379 FMA:45616 MA:0001526 NCIT:C34180 TGMA:0001014 UMLS:C0231051 VHOG:0000285 XAO:0000232 uberon praeenteron proenteron UBERON:0001041 foregut http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png Anterior subdivision of a digestive tract. The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. MP:0000474 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000285 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0231051 ncithesaurus:Foregut praeenteron proenteron A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme pharynx AAO:0000967 BTO:0001049 CALOHA:TS-0785 EFO:0000836 EHDAA2:0001458 EHDAA:2947 EMAPA:16706 EV:0100065 FMA:46688 GAID:155 MA:0000432 MESH:A03.867 NCIT:C12425 OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA TAO:0000056 UMLS:C0031354 VHOG:0000462 XAO:0003227 ZFA:0000056 galen:Pharynx uberon UBERON:0001042 Consider generalizing to deuterostome pharynx chordate pharynx EHDAA2 A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. MESH:A03.867 Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000967 AAO AAO:EJS Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000056 TAO ZFIN:curator Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000462 VHOG relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] 2012-09-17 VHOG:0000462 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503 MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme MA pharynx FMA:46688 UMLS:C0031354 ncithesaurus:Pharynx Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] esophageal esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) AAO:0000145 ANISEED:1235301 BTO:0000959 CALOHA:TS-0700 EFO:0000835 EHDAA2:0001285 EHDAA:2937 EMAPA:16833 EV:0100069 FMA:7131 GAID:291 MA:0000352 MAT:0000048 MESH:A03.365 MIAA:0000048 NCIT:C12389 OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA TAO:0000204 UMLS:C0014876 VHOG:0000450 XAO:0000127 ZFA:0000204 galen:Esophagus gullet oesophagus uberon UBERON:0001043 esophagus http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] 2012-06-20 AAO:0000145 AAO AAO:EJS The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] 2012-09-17 VHOG:0000450 VHOG DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996) esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) MA UMLS:C0014876 ncithesaurus:Esophagus saliva-secreting exocrine glands of the oral cavity[GO] currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals. A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG] The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands BTO:0001203 CALOHA:TS-0892 EFO:0000859 EHDAA2:0001775 EHDAA:7987 EMAPA:17751 EV:0100059 FBbt:00005382 FMA:9597 GAID:937 MA:0000346 MAT:0000079 MESH:D012469 MIAA:0000079 NCIT:C12426 OpenCyc:Mx4rvVjl5ZwpEbGdrcN5Y29ycA UMLS:C0036098 VHOG:0000376 galen:SalivaryGland salivary gland uberon glandulae salivariae UBERON:0001044 saliva-secreting gland http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg saliva-secreting exocrine glands of the oral cavity[GO] GO:0007431 currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals. 3 A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000376 VHOG In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG] 2012-09-17 VHOG:0000376 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211 UMLS:C0036098 ncithesaurus:Salivary_Gland salivary gland MA:0000346 glandulae salivariae Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon in FMA this represents an embryonic region. BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 FBbt:00005383 FMA:45617 MA:0001564 NCIT:C34210 TGMA:0001036 UMLS:C0231052 VHOG:0000290 XAO:0000103 uberon mesenteron UBERON:0001045 midgut http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. GO:0007494 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000290 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon WP in FMA this represents an embryonic region. FMA UMLS:C0231052 ncithesaurus:Midgut mesenteron The caudalmost subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class the caudal portion of the primitive digestive tube of the embryo The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] in FMA this class has no children. In MA it has a single child hindgut epithelium AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 FBbt:00005384 FMA:45618 MA:0001527 NCIT:C34188 TGMA:0001020 UMLS:C0231053 VHOG:0000459 XAO:0000104 uberon metenteron UBERON:0001046 hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png Wikipedia The caudalmost subdivision of a digestive tract. the caudal portion of the primitive digestive tube of the embryo MP:0008786 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000459 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 in FMA this class has no children. In MA it has a single child hindgut epithelium FMA UMLS:C0231053 ncithesaurus:Hindgut metenteron Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. AEO:0000171 BTO:0001886 EFO:0001652 EHDAA2:0003171 FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 UMLS:C0678727 XAO:0003043 uberon bud future organ placode primordia rudiment UBERON:0001048 primordium EHDAA2 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. BTO:0001886 FB:DJS FB:FBrf0089570 UMLS:C0678727 ncithesaurus:Primordium placode FBbt:00005495 primordia XAO:0003043 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 DHBA:10154 EHDAA2:0001254 EHDAA:2869 EHDAA:908 EMAPA:16164 EMAPA:16757 FMA:293882 MAT:0000069 MIAA:0000069 NCIT:C34226 TAO:0001135 UMLS:C0231024 VHOG:0000307 XAO:0003204 ZFA:0001135 uberon neural primordium presumptive central nervous system tubus neuralis UBERON:0001049 neural tube http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] 2012-06-20 AAO:0010617 AAO AAO:JOR The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000307 VHOG (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000307 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium GO:0021915 UMLS:C0231024 ncithesaurus:Neural_Tube tubus neuralis Bottom part of the pharynx that connects to the esophagus. The inferior portion of the pharynx, between the epiglottis and the larynx. [TFD][VHOG] hypopharyngeal BTO:0001740 CALOHA:TS-2020 EFO:0001388 EHDAA2:0004574 EV:0100068 FMA:54880 GAID:338 MA:0001796 MESH:A03.867.490 NCIT:C12246 OpenCyc:Mx4rvq5O0JwpEbGdrcN5Y29ycA UMLS:C0020629 VHOG:0000445 laryngeal pharynx laryngopharynx uberon pars laryngea pharyngis UBERON:0001051 hypopharynx Illu:pharynx.jpg Bottom part of the pharynx that connects to the esophagus. The inferior portion of the pharynx, between the epiglottis and the larynx. [TFD][VHOG] 2012-09-17 VHOG:0000445 VHOG UMLS:C0020629 ncithesaurus:Hypopharynx laryngeal pharynx FMA:54877 laryngopharynx FMA:54877 pars laryngea pharyngis pars laryngea pharyngis BTO:0001740 rectum the terminal portion of the intestinal tube, terminating with the anus The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] rectal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html AAO:0010401 BTO:0001158 CALOHA:TS-1180 EFO:0000848 EHDAA2:0001592 EHDAA:5836 EMAPA:17896 EV:0100081 FMA:14544 GAID:311 MA:0000336 MAT:0000050 MESH:A03.492.411.495.767 MIAA:0000050 NCIT:C12390 OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA UMLS:C0034896 VHOG:0001751 XAO:0000238 galen:Rectum terminal portion of intestine uberon intestinum rectum rectal sac terminal portion of large intestine UBERON:0001052 rectum http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif 4 cjm MA EHDAA2 ISBN:0073040584 the terminal portion of the intestinal tube, terminating with the anus ISBN:0-683-40008-8 MP:0000492 The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0001751 VHOG UMLS:C0034896 ncithesaurus:Rectum intestinum rectum BTO:0001158 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. FMA:62955 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct. UBERON:0005627 pancreatic duct BTO:0002362 EHDAA2:0001396 EHDAA:6905 EMAPA:17510 FMA:16003 GAID:337 MA:0000126 MESH:D010183 NCIT:C12272 RETIRED_EHDAA2:0002177 UMLS:C0030288 VHOG:0000256 chief pancreatic duct duct of Wirsung main pancreatic duct uberon canal of Wirsung ductus pancreatis ventralis hepaticopancreatic duct UBERON:0001064 ventral pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png FMA EHDAA2 A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] 2012-09-17 VHOG:0000256 VHOG DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005) Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct. WP pancreatic duct MESH:A03.734.667 UMLS:C0030288 ncithesaurus:Pancreatic_Duct chief pancreatic duct FMA:16003 duct of Wirsung main pancreatic duct MA:0000126 canal of Wirsung BTO:0002362 hepaticopancreatic duct BTO:0002362 A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core. strictly speaking the term intervertebral disk [applies to intervertebral cartilage] BTO:0003625 EFO:0001370 EMAPA:32739 FMA:10446 GAID:105 MA:0000110 MESH:A02.165.410 NCIT:C49571 OpenCyc:Mx4rv11AcpwpEbGdrcN5Y29ycA UMLS:C0021815 discus intervertebralis intervertebral disc spinal disc uberon intervertebral fibrocartilage spinal disk UBERON:0001066 whose gel-like core is nucleus puloposus, by this definition only in mammals intervertebral disk http://upload.wikimedia.org/wikipedia/commons/9/92/Gray301.png A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core. ISBN:0073040584 UMLS:C0021815 ncithesaurus:Intervertebral_Disc discus intervertebralis FMA:10446 FMA:TA spinal disc intervertebral fibrocartilage BTO:0003625 spinal disk BTO:0003625 A zone of skin that is part of a back [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region EMAPA:36392 FMA:10462 FMA:22985 MA:0000498 back skin back zone of skin skin, dorsal region zone of skin of back uberon UBERON:0001068 skin of back MA MA A zone of skin that is part of a back [Automatically generated definition]. OBOL:automatic back zone of skin OBOL:automatic skin, dorsal region zone of skin of back OBOL:automatic A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP] not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO AAO:0010218 AAO:0010416 BTO:0004696 EFO:0001953 EHDAA2:0000461 EMAPA:18611 FMA:10635 GAID:480 MA:0001929 MESH:D002342 NCIT:C32551 OpenCyc:Mx4rwVJkPZwpEbGdrcN5Y29ycA UMLS:C0007275 VHOG:0000265 XAO:0000345 external carotid uberon arteria carotis externa UBERON:0001070 external carotid artery https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif MA FMA EHDAA2 FMA A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP] MGI:anna UMLS:C0007275 ncithesaurus:External_Carotid_Artery external carotid AAO:0010218 arteria carotis externa It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. EMAPA:37117 FMA:10665 MA:0002052 NCIT:C53005 UMLS:C0226271 superficial branch of transverse cervical artery uberon UBERON:0001071 The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] superficial cervical artery It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. EMAPA:37117 MA:th UMLS:C0226271 ncithesaurus:Superficial_Cervical_Artery superficial branch of transverse cervical artery A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] AAO:0011083 BTO:0002682 EHDAA2:0000611 EMAPA:18416 FMA:10951 GAID:548 MA:0000480 MESH:D014682 NCIT:C12815 UMLS:C0042458 VHOG:0001194 XAO:0000388 galen:InferiorVenaCava inferior caval vein inferior vena cava posterior vena cava uberon caudal vena cava postcava vena cava inferior UBERON:0001072 posterior vena cava http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png lexical A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. FMA:10951 Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] 2012-09-17 VHOG:0001194 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 UMLS:C0042458 ncithesaurus:Inferior_Vena_Cava inferior caval vein inferior vena cava posterior vena cava caudal vena cava VHOG:0001194 vena cava inferior vena cava inferior BTO:0002682 A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice EMAPA:37601 FMA:11338 MA:0000332 ileocaecal junction uberon UBERON:0001073 ileocecal junction A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice EMAPA:37601 MA:th A potential space between the visceral and parietal layers of the pericardium. Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal) BSA:0000091 EHDAA2:0001434 EMAPA:16131 EMAPA:16132 FMA:11350 MA:0000053 NCIT:C38662 TAO:0002220 UMLS:C0225972 VHOG:0000556 ZFA:0001655 galen:PericardialSpace cavity of pericardial sac pericardial space uberon cavitas pericardiaca UBERON:0001074 pericardial cavity MA FMA Wikipedia A potential space between the visceral and parietal layers of the pericardium. Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO] 2012-08-14 TAO:0002220 TAO ZFIN:curator In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000556 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal) ZFA UMLS:C0225972 ncithesaurus:Pericardial_Cavity pericardial space cavitas pericardiaca Ossified form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]. Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO] Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO] The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra]. The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO] VSAO definition states it surrounds notochord but not applicable to post-natal. AAO:0000697 EMAPA:36588 FMA:11945 MA:0001457 NCIT:C12852 OpenCyc:Mx4rvXU4VpwpEbGdrcN5Y29ycA TAO:0000126 UMLS:C0223084 ZFA:0000126 body of vertebra corpus vertebra corpus vertebrae (vertebrale) vertebral body arcocentrum autocentrum holocentrum uberon centra corpus vertebrae vertebral centra vertebral centrum UBERON:0001075 bony vertebral centrum http://upload.wikimedia.org/wikipedia/commons/6/63/Corpusvertebrae.png Ossified form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]. VSAO:0000183 VSAO:curator Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO] 2012-08-14 TAO:0000126 TAO ZFIN:curator Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO] 2012-06-20 AAO:0000697 AAO AAO:Duellman_and_Trueb_2008 The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra]. The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO] 2012-09-06 VSAO:0000183 VSAO Curator VSAO definition states it surrounds notochord but not applicable to post-natal. VSAO UMLS:C0223084 ncithesaurus:Vertebral_Body body of vertebra FMA:11945 corpus vertebra corpus vertebrae (vertebrale) FMA:11945 vertebral body FMA:11945 arcocentrum autocentrum ZFA:0000126 holocentrum centra PHENOSCAPE:ad corpus vertebrae vertebral centra PHENOSCAPE:ad vertebral centrum MA:0001457 The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted]. Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae. AAO:0000698 FMA:11949 MA:0001456 XAO:0003102 processus transversus processus transversus vertebrae transverse process vertebra transverse process uberon diapophyses diapophysis UBERON:0001077 transverse process of vertebra http://upload.wikimedia.org/wikipedia/commons/a/a1/Processustransversusvertebrae.PNG The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted]. Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae. AAO:0000698 Endocardium that is part of the cardiac ventricle. EMAPA:32747 FMA:12148 MA:0000079 TAO:0002247 VHOG:0000607 ZFA:0001615 cardiac ventricle endocardium endocardium of cardiac ventricle endocardium of heart ventricle endocardium of lower chamber of heart endocardium of ventricle of heart heart ventricle endocardium lower chamber of heart endocardium ventricle endocardium ventricle of heart endocardium ventricular endocardium uberon ventricle endocardial tissue UBERON:0001081 endocardium of ventricle Endocardium that is part of the cardiac ventricle. ZFIN:curator cardiac ventricle endocardium OBOL:automatic endocardium of cardiac ventricle OBOL:automatic endocardium of heart ventricle OBOL:automatic endocardium of lower chamber of heart OBOL:automatic endocardium of ventricle of heart OBOL:automatic heart ventricle endocardium OBOL:automatic lower chamber of heart endocardium OBOL:automatic ventricle of heart endocardium OBOL:automatic ventricle endocardial tissue VHOG:0000607 An epicardial layer that lines a cardiac ventricle The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO] FMA:12150 TAO:0005058 ZFA:0005058 cardiac ventricle epicardium ventricular epicardium uberon UBERON:0001082 epicardium of ventricle An epicardial layer that lines a cardiac ventricle The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO] 2012-08-14 TAO:0005058 TAO ZFIN:curator cardiac ventricle epicardium OBOL:automatic Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] EFO:0003088 EMAPA:32748 FMA:12151 MA:0000082 TAO:0005061 VHOG:0000604 ZFA:0005061 ventricle myocardium ventricular myocardium uberon ventricle cardiac muscle UBERON:0001083 myocardium of ventricle Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. ZFIN:curator Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] 2012-08-14 TAO:0005061 TAO ZFIN:curator As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] 2012-09-17 VHOG:0000604 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 ventricle cardiac muscle VHOG:0000604 A zone of skin that is part of a head [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region FMA:12166 FMA:24756 MA:0000582 NCIT:C52757 UMLS:C0205029 adult head zone of skin head skin head zone of skin zone of skin of adult head zone of skin of head uberon UBERON:0001084 skin of head A zone of skin that is part of a head [Automatically generated definition]. OBOL:automatic UMLS:C0205029 ncithesaurus:Head_Skin adult head zone of skin OBOL:automatic head zone of skin OBOL:automatic zone of skin of adult head OBOL:automatic zone of skin of head OBOL:automatic A zone of skin that is part of a trunk [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region EMAPA:37278 FMA:12167 FMA:23093 MA:0000517 NCIT:C12295 UMLS:C0205031 torso zone of skin trunk skin trunk zone of skin zone of skin of torso zone of skin of trunk uberon UBERON:0001085 skin of trunk A zone of skin that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37278 MA:th UMLS:C0205031 ncithesaurus:Skin_of_the_Trunk torso zone of skin OBOL:automatic trunk zone of skin OBOL:automatic zone of skin of torso OBOL:automatic zone of skin of trunk OBOL:automatic Transudate contained in the pleural cavity. BTO:0003080 FMA:12273 MA:0002532 MAT:0000500 ncithesaurus:Pleural_Fluid uberon UBERON:0001087 pleural fluid Transudate contained in the pleural cavity. FMA:12273 Excretion that is the output of a kidney kidney excreta from some taxa (e.g. in aves) may not be liquid BTO:0001419 CALOHA:TS-1092 EFO:0001939 EMAPA:36554 ENVO:00002047 FMA:12274 GAID:1189 MA:0002545 MAT:0000058 MESH:D014556 MIAA:0000058 NCIT:C13283 OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA UMLS:C0042036 galen:Urine uberon UBERON:0001088 urine Excretion that is the output of a kidney UMLS:C0042036 ncithesaurus:Urine Secretion produced by a sweat gland. BTO:0001254 ENVO:02000025 FMA:12275 GAID:1172 MA:0002539 MESH:D013542 NCIT:C13280 OpenCyc:Mx4rvVjJtZwpEbGdrcN5Y29ycA UMLS:C0038984 uberon skin exudate UBERON:0001089 sweat Secretion produced by a sweat gland. FMA:12275 UMLS:C0038984 ncithesaurus:Sweat skin exudate BTO:0001254 Joint fluid is a transudate of plasma that is actively secreted by synovial cells. Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] It provides nutrients and lubrication for articular cartilage The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 NCIT:C33718 TAO:0005154 UMLS:C0039097 ZFA:0005154 galen:SynovialFluid joint fluid uberon UBERON:0001090 synovial fluid FMA Joint fluid is a transudate of plasma that is actively secreted by synovial cells. Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] 2012-08-14 TAO:0005154 TAO ZFIN:curator UMLS:C0039097 ncithesaurus:Synovial_Fluid joint fluid Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food. we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeeous tooth. Note that sea cucumbers develop calcareous tooth-like structures The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG] dental absent in living platypus, present in toothed Miocene platypus Obduron dicksoni AEO:0000220 BTO:0000397 CALOHA:TS-1055 EFO:0000839 EHDAA2:0004605 EMAPA:32906 EV:0100063 FMA:12516 GAID:1260 MA:0000348 MAT:0000041 MESH:A14.254.860 MIAA:0000041 NCIT:C12506 OpenCyc:Mx4rvVjUEZwpEbGdrcN5Y29ycA TAO:0001625 UMLS:C0040426 VHOG:0001733 XAO:0000431 ZFA:0000694 dental element dentine containing tooth tooth vertebrate tooth uberon UBERON:0001091 calcareous tooth http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg XAO-modified ZFA-modified cjm Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food. The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG] 2012-09-17 VHOG:0001733 VHOG PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009) absent in living platypus, present in toothed Miocene platypus Obduron dicksoni UMLS:C0040426 ncithesaurus:Tooth dental element Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] we deliberately merge the MA classes as we believe them equivalent UBERON:0006070 caudal vertebra EMAPA:18374 FMA:12527 MA:0000310 MA:0001420 NCIT:C32334 OpenCyc:Mx4rv9IEzZwpEbGdrcN5Y29ycA TAO:0000326 UMLS:C0223616 XAO:0003079 ZFA:0000326 galen:CoccygealVertebra caudal vertebrae caudal vertebral bone caudal vertebral bone element coccygeal segment coccygeal vertebra fused tail vertebra uberon coccygea tail vertebra UBERON:0001095 Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae caudal vertebra Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] 2012-08-14 TAO:0000326 TAO ZFIN:curator we deliberately merge the MA classes as we believe them equivalent MA caudal vertebra FMA:12527 UMLS:C0223616 ncithesaurus:Coccygeal_Vertebra caudal vertebrae coccygeal vertebra FMA:12527 fused tail vertebra coccygea MA:0001420 tail vertebra MA:0000310 An anatomical wall that is part of a esophagus [Automatically generated definition]. EMAPA:35326 FMA:12611 MA:0002691 anatomical wall of esophagus anatomical wall of gullet anatomical wall of oesophagus esophageal wall esophagus anatomical wall esophagus wall gullet anatomical wall gullet wall oesophagus anatomical wall oesophagus wall wall of gullet wall of oesophagus uberon UBERON:0001096 wall of esophagus An anatomical wall that is part of a esophagus [Automatically generated definition]. OBOL:automatic anatomical wall of esophagus OBOL:automatic anatomical wall of gullet OBOL:automatic anatomical wall of oesophagus OBOL:automatic esophagus anatomical wall OBOL:automatic gullet anatomical wall OBOL:automatic gullet wall OBOL:automatic oesophagus anatomical wall OBOL:automatic oesophagus wall OBOL:automatic wall of gullet OBOL:automatic wall of oesophagus OBOL:automatic A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] phrenic The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3] The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution) barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus breathing control originate from the cervical somites, likely C3-C5[PMID:23586979] BTO:0000341 CALOHA:TS-0198 EFO:0000937 EHDAA2:0003495 EMAPA:17701 EV:0100376 FMA:13295 GAID:158 MA:0001904 MAT:0000502 MESH:D003964 NCIT:C12702 OpenCyc:Mx4rvVivz5wpEbGdrcN5Y29ycA UMLS:C0011980 VHOG:0000713 diaphragm muscle diaphragm of thorax thoracic diaphragm uberon midriff phren UBERON:0001103 diaphragm definitional A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control MP:0002279 The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. GO:0060539 The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] 2012-09-17 VHOG:0000713 VHOG ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278 UMLS:C0011980 ncithesaurus:Diaphragm diaphragm muscle BTO:0000341 midriff BTO:0000341 phren BTO:0000341 Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe. some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts EMAPA:18306 FMA:13361 MA:0000360 NCIT:C49579 UMLS:C0447541 hepatic lobe liver lobe lobus hepatis uberon UBERON:0001113 lobe of liver FMA Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe. UMLS:C0447541 ncithesaurus:Liver_Lobe The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted]. Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO] EHDAA2:0001008 EHDAA:4001 EMAPA:18311 FMA:13362 MA:0000363 NCIT:C33481 TAO:0005173 UMLS:C0227481 VHOG:0001424 ZFA:0005173 liver right lobe lobus hepaticus dexter right liver lobe uberon 2nd lobe gall bladder lobe lobus hepatis dexter right hepatic lobe second lobe UBERON:0001114 right lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted]. Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO] 2012-08-14 TAO:0005173 TAO ZFIN:curator UMLS:C0227481 ncithesaurus:Right_Lobe_of_the_Liver lobus hepaticus dexter right liver lobe ZFA:0005173 2nd lobe TAO:0005173 gall bladder lobe ZFA:0005173 lobus hepatis dexter right hepatic lobe EMAPA:18311 second lobe TAO:0005173 The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]. Portion of the liver which develops on the fish's left side.[TAO] EHDAA2:0001000 EHDAA:3995 EMAPA:18307 FMA:13363 MA:0000361 NCIT:C32965 TAO:0005172 UMLS:C0227486 VHOG:0001423 ZFA:0005172 left liver lobe liver left lobe lobus hepaticus sinister uberon left hepatic lobe lobus hepatis sinister UBERON:0001115 left lobe of liver http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]. Portion of the liver which develops on the fish's left side.[TAO] 2012-08-14 TAO:0005172 TAO ZFIN:curator UMLS:C0227486 ncithesaurus:Left_Lobe_of_the_Liver lobus hepaticus sinister left hepatic lobe EMAPA:18307 lobus hepatis sinister A lobe of tissue that is part of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] EHDAA2:0002032 EMAPA:18196 FMA:13367 MA:0000131 NCIT:C33784 UMLS:C0447647 VHOG:0000732 lobus (glandula thyroidea) lobus glandulae thyroideae thyroid gland lobe thyroid lobe uberon lobuli glandulae thyroideae UBERON:0001118 The lobes of the thyroid gland are conical in shape, the apex of each being directed upward and lateralward as far as the junction of the middle with the lower third of the thyroid cartilage; the base looks downward, and is on a level with the fifth or sixth tracheal ring. Each lobe is about 5 cm. long; its greatest width is about 3 cm. , and its thickness about 2 cm. The lateral or superficial surface is convex, and covered by the skin, the superficial and deep fasciæ, the Sternocleidomastoideus, the superior belly of the Omohyoideus, the Sternohyoideus and Sternothyreoideus, and beneath the last muscle by the pretracheal layer of the deep fascia, which forms a capsule for the gland. The deep or medial surface is moulded over the underlying structures, viz. , the thyroid and cricoid cartilages, the trachea, the Constrictor pharyngis inferior and posterior part of the Cricothyreoideus, the esophagus (particularly on the left side of the neck), the superior and inferior thyroid arteries, and the recurrent nerves. The anterior border is thin, and inclines obliquely from above downward toward the middle line of the neck, while the posterior border is thick and overlaps the common carotid artery, and, as a rule, the parathyroids lobe of thyroid gland http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png FMA-abduced-lr A lobe of tissue that is part of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] 2012-09-17 VHOG:0000732 VHOG UMLS:C0447647 ncithesaurus:Thyroid_Gland_Lobe lobus glandulae thyroideae FMA:13367 FMA:TA lobuli glandulae thyroideae A lobe of thyroid gland that is in the right side of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001759 EMAPA:18198 FMA:13368 MA:0000729 NCIT:C33491 UMLS:C0229581 VHOG:0000733 lobus dexter (glandula thyroidea) right thyroid lobe thyroid gland right lobe uberon UBERON:0001119 right lobe of thyroid gland A lobe of thyroid gland that is in the right side of a thyroid gland. OBOL:automatic Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] 2012-09-17 VHOG:0000733 VHOG UMLS:C0229581 ncithesaurus:Right_Thyroid_Gland_Lobe A lobe of thyroid gland that is in the left side of a thyroid gland. Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000965 EMAPA:18197 FMA:13369 MA:0000728 NCIT:C32973 UMLS:C0229582 VHOG:0000734 left thyroid lobe lobus sinister (glandula thyroidea) thyroid gland left lobe uberon UBERON:0001120 left lobe of thyroid gland A lobe of thyroid gland that is in the left side of a thyroid gland. OBOL:automatic Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG] 2012-09-17 VHOG:0000734 VHOG UMLS:C0229582 ncithesaurus:Left_Thyroid_Gland_Lobe Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton Anatomical cluster that consists of all the vertebra in the body.[VSAO] The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG] Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG] spine AAO:0000699 AAO:0000734 BTO:0000818 EFO:0001369 EHDA:10119 EMAPA:35919 FMA:13478 GAID:106 MA:0002416 MESH:D013131 NCIT:C12998 NCIT:C33588 NIF_Subcellular:sao1145756102 OpenCyc:Mx4rv2j-CpwpEbGdrcN5Y29ycA OpenCyc:Mx4rv6GF55wpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkFEpwpEbGdrcN5Y29ycA TAO:0001559 UMLS:C0037949 UMLS:C1519455 VHOG:0001142 VSAO:0000185 XAO:0003074 ZFA:0001559 galen:SpinalColumn backbone vertebral column skeleton uberon columna vertebralis dorsal spine spinal column vertebral region UBERON:0001130 vertebral column cjm Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. VSAO:0000185 Anatomical cluster that consists of all the vertebra in the body.[VSAO] 2012-08-14 VSAO:0000185 VSAO VSAO:curator The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0001142 VHOG Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG] 2012-09-17 VHOG:0001142 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53 spine FMA:13478 UMLS:C0037949 ncithesaurus:Vertebral_Column UMLS:C1519455 ncithesaurus:Spinal_Cord_Column backbone FMA:13478 vertebral column skeleton AAO:0000699 columna vertebralis BTO:0000818 dorsal spine BTO:0000818 spinal column MESH:A02.835.232.834 A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch. Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO] AAO:0000729 EMAPA:37803 FMA:13479 MA:0001454 OpenCyc:Mx4rv_EvQZwpEbGdrcN5Y29ycA vertebra neural canal uberon foramen vertebrale UBERON:0001131 vertebral foramen http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch. Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO] 2012-06-20 AAO:0000729 AAO AAO:LAP EMAPA:37803 MA:th foramen vertebrale The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism. Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG] Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO] The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG] Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP] In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity. AAO:0010545 BTO:0000997 CALOHA:TS-0745 EFO:0000862 EMAPA:32812 EV:0100134 FMA:13890 GAID:452 MA:0000128 MAT:0000082 MESH:D010280 MIAA:0000082 NCIT:C12765 UMLS:C0030518 VHOG:0001188 XAO:0000167 parathyroid uberon epithelial body parathyroid secreting cell UBERON:0001132 parathyroid gland The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism. ISBN:0-683-40008-8 MP:0000678 Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG] 2012-09-17 VHOG:0001188 VHOG Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO] 2012-06-20 AAO:0010545 AAO AAO:BJB The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG] 2012-09-17 VHOG:0001188 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity. UMLS:C0030518 ncithesaurus:Parathyroid_Gland epithelial body XAO:0000167 Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit UBERON:0007096 AAO:0010245 AEO:0000142 BILA:0000134 BTO:0000199 CALOHA:TS-0440 EHDAA2:0003142 EMAPA:32688 FMA:14068 TAO:0005280 ZFA:0005280 galen:CardiacMuscle galen:CardiacMuscleTissue ncithesaurus:Heart_Muscle cardiac muscle cardiac muscle muscle tissue cardiac muscle textus muscularis heart muscle muscle tissue heart muscle textus muscularis heart myocardium muscle tissue heart myocardium textus muscularis muscle of heart muscle tissue muscle of heart textus muscularis muscle tissue of cardiac muscle muscle tissue of heart muscle muscle tissue of heart myocardium muscle tissue of muscle of heart muscle tissue of myocardium myocardium muscle tissue myocardium textus muscularis textus muscularis of cardiac muscle textus muscularis of heart muscle textus muscularis of heart myocardium textus muscularis of muscle of heart textus muscularis of myocardium uberon cardiac musculature UBERON:0001133 cardiac muscle tissue ZFA Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. ZFA:0005280 cardiac muscle muscle tissue OBOL:automatic cardiac muscle textus muscularis OBOL:automatic heart muscle muscle tissue OBOL:automatic heart muscle textus muscularis OBOL:automatic heart myocardium muscle tissue OBOL:automatic heart myocardium textus muscularis OBOL:automatic muscle of heart muscle tissue OBOL:automatic muscle of heart textus muscularis OBOL:automatic muscle tissue of cardiac muscle OBOL:automatic muscle tissue of heart muscle OBOL:automatic muscle tissue of heart myocardium OBOL:automatic muscle tissue of muscle of heart OBOL:automatic muscle tissue of myocardium OBOL:automatic myocardium muscle tissue OBOL:automatic myocardium textus muscularis OBOL:automatic textus muscularis of cardiac muscle OBOL:automatic textus muscularis of heart muscle OBOL:automatic textus muscularis of heart myocardium OBOL:automatic textus muscularis of muscle of heart OBOL:automatic textus muscularis of myocardium OBOL:automatic cardiac musculature BILA:0000134 Muscle tissue that consists primarily of skeletal muscle fibers. TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] skeletal muscle EMAPA:32716 FMA:14069 MA:0002439 NCIT:C13050 UMLS:C0242692 uberon skeletal muscle system somatic muscle UBERON:0001134 skeletal muscle tissue Skeletal:muscle.jpg Muscle tissue that consists primarily of skeletal muscle fibers. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] 2012-08-14 TAO:0005277 TAO ZFIN:curator Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] FMA:14069 FMA This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] 2012-09-17 VHOG:0000319 VHOG PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999) UMLS:C0242692 ncithesaurus:Skeletal_Muscle_Tissue skeletal muscle system BTO:0001103 somatic muscle BTO:0001103 Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. AAO:0010244 AEO:0000141 BTO:0001260 CALOHA:TS-0943 EFO:0000889 EHDAA2:0003141 EMAPA:32717 EV:0100378 FBbt:00003525 FMA:14070 GAID:167 MA:0000166 MAT:0000303 MESH:D009130 MIAA:0000303 NCIT:C12437 OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA TAO:0005274 UMLS:C1267092 VHOG:0001246 WBbt:0005781 XAO:0000175 ZFA:0005274 galen:SmoothMuscle galen:SmoothMuscleTissue involuntary muscle non-striated muscle smooth muscle textus muscularis nonstriatus visceral muscle visceral muscle tissue uberon textus muscularis levis; textus muscularis nonstriatus UBERON:0001135 smooth muscle tissue Glatte:Muskelzellen.jpg Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. GO:0006939 A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] 2012-08-14 TAO:0005274 TAO ZFIN:curator Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] 2012-06-20 AAO:0010244 AAO AAO:CAM (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] 2012-09-17 VHOG:0001246 VHOG DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) UMLS:C1267092 ncithesaurus:Smooth_Muscle_Tissue textus muscularis nonstriatus FMA:14070 FMA:TA visceral muscle visceral muscle tissue textus muscularis levis; textus muscularis nonstriatus Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 CALOHA:TS-1183 EHDAA2_RETIRED:0003111 EHDAA:2331 EHDAA:2349 EHDAA:295 EHDAA:6073 EHDAA:640 EHDAA:646 EMAPA:32856 FMA:14074 MA:0000565 NCIT:C33105 UMLS:C0086610 uberon UBERON:0001136 mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). FMA:14074 UMLS:C0086610 ncithesaurus:Mesothelium A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. dorsal In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body BTO:0001713 CALOHA:TS-2223 EFO:0001405 FMA:14181 GAID:30 MESH:A01.176 NCIT:C13062 OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA UMLS:C0004600 galen:Back back back of body proper dorsal part of organism uberon UBERON:0001137 dorsum http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. BSPO:0000063 UBERONREF:0000006 UMLS:C0004600 ncithesaurus:Back back FMA:14181 back of body proper FMA:14181 In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002783 EHDAA2:0001951 EHDAA:5414 EMAPA:18643 FMA:14332 MA:0002179 NCIT:C33687 OpenCyc:Mx4rwFjmM5wpEbGdrcN5Y29ycA UMLS:C0226742 VHOG:0000552 uberon upper mesenteric vein vena mesenterica superior UBERON:0001138 superior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. UMLS:C0226742 ncithesaurus:Superior_Mesenteric_Vein upper mesenteric vein BTO:0002783 vena mesenterica superior Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. in EHDAA2, the renal vein is part of the kidney BTO:0002681 EHDAA2:0001602 EHDAA:8722 EMAPA:28376 FMA:14334 GAID:544 MA:0002210 MESH:D012082 NCIT:C33462 OpenCyc:Mx4rvdUXKJwpEbGdrcN5Y29ycA UMLS:C0035092 galen:RenalVein kidney vein renal venous tree vein of kidney uberon venae renales UBERON:0001140 renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. ISBN:0-683-40008-8 MGI:csmith MP:0011323 The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. in EHDAA2, the renal vein is part of the kidney EHDAA2 UMLS:C0035092 ncithesaurus:Renal_Vein kidney vein OBOL:automatic vein of kidney OBOL:automatic venae renales A renal vein that drains the right kidney A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]. EMAPA:37381 FMA:14335 MA:0002212 NCIT:C52695 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvdUXKJwpEbGdrcN5Y29ycA UMLS:C0508000 uberon UBERON:0001141 right renal vein A renal vein that drains the right kidney A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]. ncithesaurus:Right_Renal_Vein EMAPA:37381 MA:th UMLS:C0508000 ncithesaurus:Right_Renal_Vein A renal vein that drains the left kidney A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]. EMAPA:37166 FMA:14336 MA:0002211 NCIT:C52693 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvdUXKJwpEbGdrcN5Y29ycA UMLS:C0508001 uberon UBERON:0001142 left renal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png A renal vein that drains the left kidney A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]. ncithesaurus:Left_Renal_Vein EMAPA:37166 MA:th UMLS:C0508001 ncithesaurus:Left_Renal_Vein Vein that carries blood away from the liver[ZFA]. todo - add developmental relationships for other taxa AAO:0010216 EMAPA:19221 FMA:14337 GAID:534 MA:0003015 MESH:D006503 NCIT:C32736 OpenCyc:Mx4rv5GivJwpEbGdrcN5Y29ycA TAO:0000670 UMLS:C0019155 XAO:0000387 ZFA:0000670 galen:HepaticVein liver vein vein of liver vena hepatica uberon hepatic veins venae hepaticae UBERON:0001143 hepatic vein http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png FMA-abduced-lr Vein that carries blood away from the liver[ZFA]. ZFA:0000670 UMLS:C0019155 ncithesaurus:Hepatic_Vein liver vein OBOL:automatic vein of liver OBOL:automatic vena hepatica hepatic veins venae hepaticae A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis. TODO - check testicular vs spermatic vein (MA:0002218) In humans, the right testicular vein generally joins the inferior vena cava; the left testicular vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. The veins emerge from the back of the testis, and receive tributaries from the epididymis; they unite and form a convoluted plexus, called the pampiniform plexus, which constitutes the greater mass of the spermatic cord; the vessels composing this plexus are very numerous, and ascend along the cord, in front of the ductus deferens. Below the subcutaneous inguinal ring, they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins, which ascend on the Psoas major, behind the peritoneum, lying one on either side of the internal spermatic artery. These unite to form a single vein, which opens, on the right side, into the inferior vena cava (at an acute angle), on the left side into the left renal vein (at a right angle). The spermatic veins are provided with valves. The left spermatic vein passes behind the iliac colon and is thus exposed to pressure from the contents of that part of the bowel BTO:0002678 EMAPA:18647 FMA:14344 MA:0002218 MA:0002234 NCIT:C53050 OpenCyc:Mx4rv1WIHpwpEbGdrcN5Y29ycA UMLS:C0226718 male gonadal vein spermatic vein testicle vein testicular venous tree vein of testicle uberon vena tesicularis vena testicularis dextra vena testicularis sinistra venae spermaticae UBERON:0001144 testicular vein http://upload.wikimedia.org/wikipedia/commons/1/1b/Gray590.png A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis. UMLS:C0226718 ncithesaurus:Spermatic_Vein male gonadal vein spermatic vein testicle vein OBOL:automatic testicular venous tree vein of testicle OBOL:automatic vena tesicularis BTO:0002678 vena testicularis dextra vena testicularis sinistra venae spermaticae A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. EMAPA:18644 FMA:14346 MA:0002186 NCIT:C53058 OpenCyc:Mx4rvrST5ZwpEbGdrcN5Y29ycA UMLS:C0226720 female reproductive system gonad vein female reproductive system gonada vein gonad of female reproductive system vein gonada of female reproductive system vein ovary vein vein of female reproductive system gonad vein of female reproductive system gonada vein of gonad of female reproductive system vein of gonada of female reproductive system vein of ovary uberon vena ovarica dextra vena ovarica sinistra UBERON:0001145 ovarian vein http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. UMLS:C0226720 ncithesaurus:Ovarian_Vein female reproductive system gonad vein OBOL:automatic female reproductive system gonada vein OBOL:automatic gonad of female reproductive system vein OBOL:automatic gonada of female reproductive system vein OBOL:automatic ovary vein OBOL:automatic vein of female reproductive system gonad OBOL:automatic vein of female reproductive system gonada OBOL:automatic vein of gonad of female reproductive system OBOL:automatic vein of gonada of female reproductive system OBOL:automatic vein of ovary OBOL:automatic vena ovarica dextra vena ovarica sinistra A vein that drains the adrenal gland. EHDAA2:0001966 EHDAA:8731 FMA:14348 MA:0002081 MA:0002229 NCIT:C53129 UMLS:C0226717 uberon adrenal vein UBERON:0001146 suprarenal vein http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png A vein that drains the adrenal gland. UMLS:C0226717 ncithesaurus:Suprarenal_Vein adrenal vein MA:0002081 the tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct Duct that connects the gall bladder and the common bile duct.[TAO] The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] EHDAA2:0000333 EHDAA:3045 EMAPA:16841 FMA:14539 GAID:290 MA:0000355 MESH:A03.159.183.419 NCIT:C32421 OpenCyc:Mx4rveBeC5wpEbGdrcN5Y29ycA TAO:0005166 UMLS:C0010672 VHOG:0000213 ZFA:0005166 galen:CysticDuct uberon ductus cysticus UBERON:0001152 cystic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png FMA EHDAA2 the tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct ISBN:0-683-40008-8 MP:0009493 Duct that connects the gall bladder and the common bile duct.[TAO] 2012-08-14 TAO:0005166 TAO ZFIN:Curator The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000213 VHOG UMLS:C0010672 ncithesaurus:Cystic_Duct ductus cysticus A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. caecal A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. BTO:0000166 CALOHA:TS-0122 EFO:0000850 EHDAA2:0000206 EHDAA:3913 EMAPA:35197 EV:0100397 FMA:14541 GAID:307 MA:0000334 MESH:A03.492.411.495.209 MIAA:0000288 NCIT:C12381 OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA UMLS:C0007531 VHOG:0001559 galen:Cecum caecum cecum intestinum crassum caecum caeca ceca uberon blind intestine blindgut intestinum caecum intestinum crassum cecum UBERON:0001153 Taxon notes: in some herbivorous lizards, a cecum is present between small and large intestines[Kardong] caecum http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg EHDAA2 Wikipedia Wikipedia A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. WP UMLS:C0007531 ncithesaurus:Cecum caecum VHOG:0001559 cecum FMA:14541 caeca NCBITaxon:8782 ceca NCBITaxon:8782 blind intestine BTO:0000166 blindgut BTO:0000166 intestinum caecum BTO:0000166 intestinum crassum cecum BTO:0000166 A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]. A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG] appendiceal vermix BTO:0000084 CALOHA:TS-1267 EFO:0000849 EHDAA2:0000588 EMAPA:35140 EV:0100076 EV:0100080 FMA:14542 GAID:308 MA:0001540 MAT:0000287 MESH:A03.492.411.495.209.290 MIAA:0000287 NCIT:C12380 OpenCyc:Mx4rvVjGgJwpEbGdrcN5Y29ycA UMLS:C0003617 VHOG:0001306 galen:AppendixVermiformis appendix appendix vermiformis caecal appendix cecal appendix uberon apex of caecum apex of cecum appendix vermiformis UBERON:0001154 vermiform appendix http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png MA Wikipedia A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]. FMA:14542 A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG] 2012-09-17 VHOG:0001306 VHOG DOI:10.1111/j.1420-9101.2009.01809.x Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009) UMLS:C0003617 ncithesaurus:Vermiform_Appendix appendix vermiformis FMA:14542 FMA:TA apex of caecum EMAPA:35140 apex of cecum VHOG:0001306 appendix vermiformis colon Last portion of the large intestine before it becomes the rectum. TODO - abstract this such that it legitimately covers all vertebrates The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] colonic In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP] In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN] it extracts water and salt from solid wastes before they are eliminated from the body[WP] AAO:0010400 BTO:0000269 CALOHA:TS-0158 EFO:0000361 EMAPA:18939 EV:0100079 FMA:14543 GAID:309 MA:0000335 MAP:0000001 MAT:0000526 MESH:A03.492.411.495.356 NCIT:C12382 OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA TAO:0000706 UMLS:C0009368 VHOG:0000648 XAO:0000243 ZFA:0000706 galen:Colon large bowel posterior intestine uberon hindgut UBERON:0001155 colon 3 cjm FMA Last portion of the large intestine before it becomes the rectum. ZFIN:curator The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] 2012-06-20 AAO:0010400 AAO UBERON:0001155 The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0000706 TAO ZFIN:curator Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000648 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0009368 ncithesaurus:Colon Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified] in MA, this is a subclass of colon BTO:0000270 CALOHA:TS-0057 EFO:0000843 EMAPA:35151 FMA:14545 MA:0001541 MAT:0000311 MIAA:0000311 NCIT:C12265 OpenCyc:Mx4rv3H0FZwpEbGdrcN5Y29ycA UMLS:C0227375 galen:AscendingColon colon ascendens uberon spiral colon UBERON:0001156 ascending colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg FMA Wikipedia Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified] FMA:14545 in MA, this is a subclass of colon MA UMLS:C0227375 ncithesaurus:Ascending_Colon colon ascendens spiral colon The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]. BTO:0000272 CALOHA:TS-2052 EFO:0000844 EMAPA:35880 FMA:14546 MA:0001543 MAT:0000312 MIAA:0000312 NCIT:C12385 OpenCyc:Mx4rvg7qyJwpEbGdrcN5Y29ycA UMLS:C0227386 galen:TransverseColon colon transversum uberon UBERON:0001157 transverse colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg FMA Wikipedia The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]. BTO:0000272 UMLS:C0227386 ncithesaurus:Transverse_Colon colon transversum The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. BTO:0000641 CALOHA:TS-2010 EFO:0000845 EMAPA:35285 FMA:14547 MA:0001542 MAT:0000313 MIAA:0000313 NCIT:C12268 OpenCyc:Mx4rwHsNhpwpEbGdrcN5Y29ycA UMLS:C0227389 galen:DescendingColon colon descendens uberon UBERON:0001158 descending colon http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray1223.png FMA Wikipedia The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. BTO:0000641 UMLS:C0227389 ncithesaurus:Descending_Colon colon descendens The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. BTO:0000645 CALOHA:TS-2044 EFO:0000846 EMAPA:36391 FMA:14548 MAT:0000314 MESH:A03.492.411.495.356.668 MIAA:0000314 NCIT:C12384 NCIT:C33550 OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA UMLS:C0227391 UMLS:C0682612 galen:SigmoidColon uberon colon sigmoideum pelvic colon sigmoid colon sigmoid flexure UBERON:0001159 sigmoid colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg FMA Wikipedia The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. UMLS:C0227391 ncithesaurus:Sigmoid_Colon UMLS:C0682612 ncithesaurus:Sigmoid_Flexure colon sigmoideum The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]. we include this as zone of stomach even though it is not distinguished by gland type BTO:0000505 EMAPA:35810 FMA:14560 MA:0002559 NCIT:C12258 UMLS:C0227230 galen:GastricCorpus corpus gastricum (ventriculare) gastric body stomach body uberon corpus gastricum corpus ventriculare corpus ventriculi gastric corpus UBERON:0001161 body of stomach http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg FMA The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]. GO:0014845 UMLS:C0227230 ncithesaurus:Body_of_Stomach corpus gastricum corpus gastricum BTO:0000505 corpus ventriculare BTO:0000505 corpus ventriculi BTO:0000505 The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP] There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that 'The gastric cardia is now clearly considered to be part of the stomach'[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP] We follow Kardong in defining stomach regions by glands. UBERON:0004712 BTO:0000198 EMAPA:35811 FMA:14561 GAID:319 MA:0001609 MESH:A03.492.766.163 NCIT:C12256 UMLS:C0007144 cardial part of stomach gastric cardia pars cardiaca (gaster) pars cardiaca gastricae stomach cardiac region uberon antrum cardiacum cardiac antrum cardiac orifice cardiac region cardial orifice UBERON:0001162 cardia of stomach Illu:stomach.jpg The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP] BTO:0000198 UMLS:C0007144 ncithesaurus:Cardia pars cardiaca gastricae FMA:14561 FMA:TA stomach cardiac region MA:0001609 antrum cardiacum antrum cardiacum cardiac orifice cardiac region cardial orifice the area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells antrum BTO:0001732 EFO:0002555 EMAPA:17891 FMA:14579 GAID:332 MA:0001624 MESH:A03.492.766.716 NCIT:C12259 UMLS:C0034193 galen:PyloricAntrum antrum of stomach stomach pyloric antrum uberon antrum of Willis antrum pylori antrum pyloricum gastric antrum stomach antrum UBERON:0001165 pyloric antrum http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg FMA Wikipedia the area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells ISBN:0-683-40008-8 MP:0010790 UMLS:C0034193 ncithesaurus:Antrum_Pylori antrum of Willis BTO:0001732 antrum pylori BTO:0001732 antrum pyloricum antrum pyloricum BTO:0001732 gastric antrum BTO:0001732 the stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum We follow Kardong in defining stomach regions by glands The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] pyloric BTO:0001146 EHDAA2:0001580 EHDAA:4860 EMAPA:17631 FMA:14581 GAID:333 MA:0002560 MESH:A03.492.766.799 NCIT:C12260 UMLS:C0034196 VHOG:0000420 galen:Pylorus pars pylorica pars pylorica gastricae pyloric part of stomach pyloric region stomach pyloric region uberon valvula pylori UBERON:0001166 pylorus http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg the stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum MGI:csmith MP:0010785 The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000420 VHOG Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000420 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0034196 ncithesaurus:Pylorus pars pylorica pars pylorica gastricae FMA:14581 FMA:TA stomach pyloric region EHDAA2:0001580 valvula pylori the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between EMAPA:35826 FMA:14582 MA:0002692 galen:WallOfStomach anatomical wall of stomach anatomical wall of ventriculus gastric wall stomach anatomical wall stomach wall ventriculus anatomical wall ventriculus wall wall of ventriculus uberon UBERON:0001167 wall of stomach the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between MGI:csmith MP:0010783 anatomical wall of stomach OBOL:automatic anatomical wall of ventriculus OBOL:automatic stomach anatomical wall OBOL:automatic ventriculus anatomical wall OBOL:automatic ventriculus wall OBOL:automatic wall of ventriculus OBOL:automatic An anatomical wall that is part of a small intestine [Automatically generated definition]. EMAPA:35785 FMA:14615 MA:0002696 NCIT:C33573 UMLS:C1519375 anatomical wall of small bowel anatomical wall of small intestine small bowel anatomical wall small bowel wall small intestinal wall small intestine anatomical wall small intestine wall wall of small bowel uberon UBERON:0001168 wall of small intestine An anatomical wall that is part of a small intestine [Automatically generated definition]. OBOL:automatic UMLS:C1519375 ncithesaurus:Small_Intestinal_Wall_Tissue anatomical wall of small bowel OBOL:automatic anatomical wall of small intestine OBOL:automatic small bowel anatomical wall OBOL:automatic small bowel wall OBOL:automatic small intestine anatomical wall OBOL:automatic wall of small bowel OBOL:automatic An anatomical wall that is part of a large intestine [Automatically generated definition]. EMAPA:35470 FMA:14619 MA:0002695 anatomical wall of large intestine large intestinal wall large intestine anatomical wall large intestine wall uberon UBERON:0001169 wall of large intestine An anatomical wall that is part of a large intestine [Automatically generated definition]. OBOL:automatic anatomical wall of large intestine OBOL:automatic large intestine anatomical wall OBOL:automatic The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP]. EMAPA:37745 FMA:14643 MA:0001555 mesentery (proper) mesentery proper small intestinal mesentery small intestine mesentery uberon UBERON:0001170 mesentery of small intestine FMA The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP]. EMAPA:37745 MA:th mesentery (proper) mesentery proper FMA:14643 small intestinal mesentery FMA:14643 small intestine mesentery OBOL:automatic The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. FMA:14653 MA:0002498 NCIT:C33341 UMLS:C0682620 uberon UBERON:0001171 portal lobule FMA MA MP The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. MP:0008992 UMLS:C0682620 ncithesaurus:Portal_Lobule The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids. EMAPA:35497 FMA:14654 MA:0002496 NCIT:C32992 UMLS:C0227519 liver acinus portal acinus uberon UBERON:0001172 hepatic acinus cjm The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids. UMLS:C0227519 ncithesaurus:Liver_Acinus A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] AAO:0011020 EMAPA:35172 FMA:14665 UMLS:C0005423 XAO:0000455 uberon biliary tract UBERON:0001173 The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP] biliary tree A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] 2012-06-20 AAO:0011020 AAO UBERON:0001173 UMLS:C0005423 ncithesaurus:Biliary_Tract biliary tract MA:0001273 the part of the biliary tree formed by the union of the cystic duct and the common hepatic duct Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO] The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] EHDAA2:0000303 EHDAA:3981 EMAPA:17201 FMA:14667 GAID:282 MA:0001631 MESH:D003135 NCIT:C12698 TAO:0005165 UMLS:C0009437 VHOG:0000214 ZFA:0005165 galen:CommonBileDuct ductus choledochus (biliaris) uberon ductus choledochus UBERON:0001174 common bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png the part of the biliary tree formed by the union of the cystic duct and the common hepatic duct MGI:csmith MP:0009495 Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO] 2012-08-14 TAO:0005165 TAO ZFIN:Curator The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000214 VHOG UMLS:C0009437 ncithesaurus:Common_Bile_Duct ductus choledochus Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]. TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] EMAPA:19101 FMA:14668 GAID:286 MA:0002660 MESH:D006500 NCIT:C32356 UMLS:C0019149 VHOG:0000220 uberon ductus hepaticus communis hepatic duct UBERON:0001175 common hepatic duct http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg FMA MA Wikipedia Wikipedia definitional Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]. ZFIN:curator The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000220 VHOG UMLS:C0019149 ncithesaurus:Common_Hepatic_Duct ductus hepaticus communis The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct. The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] EHDAA2:0001727 EHDAA:3992 EMAPA:32797 FMA:14669 MA:0001639 NCIT:C33476 UMLS:C0227557 VHOG:0000217 uberon ductus hepaticus dexter UBERON:0001176 right hepatic duct The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct. The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] 2012-09-17 VHOG:0000217 VHOG UMLS:C0227557 ncithesaurus:Right_Hepatic_Duct ductus hepaticus dexter The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct. The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] EHDAA2:0000941 EHDAA:3990 EMAPA:32795 FMA:14670 MA:0001638 NCIT:C32960 UMLS:C0227560 VHOG:0000218 uberon ductus hepaticus sinister UBERON:0001177 left hepatic duct The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct. The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] 2012-09-17 VHOG:0000218 VHOG UMLS:C0227560 ncithesaurus:Left_Hepatic_Duct ductus hepaticus sinister The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. EMAPA:16592 FMA:14703 TAO:0005132 VHOG:0001528 ZFA:0005132 visceral serous membrane of peritoneum uberon UBERON:0001178 visceral peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. visceral serous membrane of peritoneum UBERON:cjm Anatomical cavity bounded by visceral and parietal peritoneum The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] BTO:0001782 EHDAA2:0001446 EMAPA:16138 FMA:14704 GAID:24 MA:0000054 MESH:A01.047.025.600.678 NCIT:C12769 UMLS:C1704247 VHOG:0000852 uberon cavitas peritonealis saccus serosus peritonei UBERON:0001179 peritoneal cavity Wikipedia Anatomical cavity bounded by visceral and parietal peritoneum The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG] 2012-09-17 VHOG:0000852 VHOG In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000852 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 UMLS:C1704247 ncithesaurus:Peritoneal_Cavity cavitas peritonealis cavitas peritonealis BTO:0001782 saccus serosus peritonei Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted]. IMA BTO:0002302 EHDAA2:0000817 EHDAA:4345 EMAPA:18618 FMA:14750 GAID:501 MA:0002004 MESH:D017537 NCIT:C32780 OpenCyc:Mx4rv-t-S5wpEbGdrcN5Y29ycA UMLS:C0162860 VHOG:0001116 galen:InferiorMesentericArtery inferior mesenteric arterial tree uberon arteria mesenterica inferior UBERON:0001183 inferior mesenteric artery http://upload.wikimedia.org/wikipedia/commons/e/e4/Gray538.png Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted]. IMA UMLS:C0162860 ncithesaurus:Inferior_Mesenteric_Artery arteria mesenterica inferior arteria mesenterica inferior BTO:0002302 One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates. renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability. Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO] The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia] AAO:0010223 BTO:0001165 EFO:0002552 EHDAA2:0004100 EHDAA:5321 EHDAA:8594 EMAPA:28373 FMA:14751 GAID:507 MA:0002035 MESH:D012077 NCIT:C12778 OpenCyc:Mx4rveOFHpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001600 TAO:0000420 UMLS:C0035065 ZFA:0000420 galen:RenalArtery renal arterial tree uberon arteria renalis renal arteries UBERON:0001184 renal artery http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates. ISBN:0073040584 Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO] 2012-06-20 AAO:0010223 AAO AAO:BJB The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia] Wikipedia UMLS:C0035065 ncithesaurus:Renal_Artery arteria renalis renal arteries Renal artery that supplies the right kidney EMAPA:37380 FMA:14752 MA:0002037 NCIT:C52740 OpenCyc:Mx4rtW8I0KgEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rveOFHpwpEbGdrcN5Y29ycA UMLS:C0226332 right renal arterial tree uberon UBERON:0001185 The right [renal artery] passes behind the inferior vena cava, the right renal vein, the head of the pancreas, and the descending part of the duodenum[WP] right renal artery http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png Renal artery that supplies the right kidney EMAPA:37380 MA:th UMLS:C0226332 ncithesaurus:Right_Renal_Artery Renal artery that supplies the left kidney EMAPA:37098 FMA:14753 MA:0002036 NCIT:C52741 OpenCyc:Mx4rtW8I0agEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rveOFHpwpEbGdrcN5Y29ycA UMLS:C0226333 left renal arterial tree uberon UBERON:0001186 The left [renal artery] is somewhat higher than the right; it lies behind the left renal vein, the body of the pancreas and the splenic vein, and is crossed by the inferior mesenteric vein[WP] left renal artery Renal artery that supplies the left kidney EMAPA:37098 MA:th UMLS:C0226333 ncithesaurus:Left_Renal_Artery One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad. EMAPA:18621 FMA:14758 MA:0002063 testicular arterial tree uberon arteria testicularis internal spermatic internal spermatic arteries internal spermatic artery internal spermatic vessels spermatic arteries spermatic artery spermatic vessels testicular arteries UBERON:0001187 testicular artery http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad. arteria testicularis internal spermatic internal spermatic arteries internal spermatic artery internal spermatic vessels spermatic arteries spermatic artery spermatic vessels testicular arteries A testicular artery that supplies a right testicle. EMAPA:37382 FMA:14759 MA:0002042 NCIT:C52738 UMLS:C0734076 right spermatic artery trunk of right testicular arterial tree uberon UBERON:0001188 right testicular artery A testicular artery that supplies a right testicle. OBOL:automatic EMAPA:37382 MA:th UMLS:C0734076 ncithesaurus:Right_Spermatic_Artery A testicular artery that supplies a left testicle. EMAPA:37099 FMA:14760 MA:0002041 NCIT:C52739 UMLS:C0734077 left spermatic artery trunk of left testicular arterial tree uberon UBERON:0001189 left testicular artery A testicular artery that supplies a left testicle. OBOL:automatic EMAPA:37099 MA:th UMLS:C0734077 ncithesaurus:Left_Spermatic_Artery An artery that supplies an ovary. In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. EMAPA:18620 FMA:14761 MA:0002012 NCIT:C33242 OpenCyc:Mx4rwOa9PZwpEbGdrcN5Y29ycA UMLS:C0226411 ovarian arterial tree uberon arteria ovarica UBERON:0001190 ovarian artery http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png An artery that supplies an ovary. OBOL:automatic In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. UMLS:C0226411 ncithesaurus:Ovarian_Artery arteria ovarica The common iliac arteries are two large arteries, about 4cm long in adults but more than a centimetre in diameter, that originate from the aortic bifurcation. The arteries run inferolaterally, along the medial border of the psoas muscles to the pelvic brim, where they bifurcate into the external iliac artery and internal iliac artery. The common iliac artery, and all of its branches, exist as paired structures (that is to say, there is one on the left side and one on the right). The distribution of the common iliac artery is basically the pelvis and lower limb on the corresponding side. Both common iliac arteries are accompanied along their course by common iliac veins. [WP,unvetted]. EHDAA2:0000311 EHDAA:2553 EMAPA:17310 FMA:14764 MA:0001972 NCIT:C32357 OpenCyc:Mx4rvkZ7ZpwpEbGdrcN5Y29ycA UMLS:C1261084 common iliac arterial tree uberon arteria iliaca communis UBERON:0001191 See notes for parent class common iliac artery http://upload.wikimedia.org/wikipedia/commons/6/6e/Iliac_artery_bifurcation_and_aorta.PNG MA The common iliac arteries are two large arteries, about 4cm long in adults but more than a centimetre in diameter, that originate from the aortic bifurcation. The arteries run inferolaterally, along the medial border of the psoas muscles to the pelvic brim, where they bifurcate into the external iliac artery and internal iliac artery. The common iliac artery, and all of its branches, exist as paired structures (that is to say, there is one on the left side and one on the right). The distribution of the common iliac artery is basically the pelvis and lower limb on the corresponding side. Both common iliac arteries are accompanied along their course by common iliac veins. [WP,unvetted]. UMLS:C1261084 ncithesaurus:Common_Iliac_Artery arteria iliaca communis An artery that supplies the liver. currently defined in a generic fashion. Artery that supplies blood to the liver.[TAO] BTO:0004307 EMAPA:17859 FMA:14769 GAID:496 MA:0001963 MESH:D006499 NCIT:C32729 OpenCyc:Mx4rvzKtFpwpEbGdrcN5Y29ycA TAO:0005161 UMLS:C0019145 ZFA:0005161 galen:HepaticArtery arteria hepatica propria uberon arteria hepatica UBERON:0001193 hepatic artery http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png An artery that supplies the liver. Artery that supplies blood to the liver.[TAO] 2012-08-14 TAO:0005161 TAO ZFIN:curator UMLS:C0019145 ncithesaurus:Hepatic_Artery arteria hepatica propria arteria hepatica BTO:0004307 An artery that supplies the spleen. EMAPA:19216 FMA:14773 GAID:510 MA:0001991 MA:0003177 MESH:D013157 NCIT:C33597 OpenCyc:Mx4rv0cb2ZwpEbGdrcN5Y29ycA UMLS:C0037996 galen:SplenicArtery arteria splenica lienal artery uberon arteria lienalis UBERON:0001194 splenic artery https://github.com/obophenotype/uberon/issues/268 http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png An artery that supplies the spleen. UMLS:C0037996 ncithesaurus:Splenic_Artery arteria splenica lienal artery MA:0001991 arteria lienalis The mucosal layer that lines the stomach. The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. BTO:0001308 CALOHA:TS-0404 EMAPA:35817 FMA:14907 GAID:321 MA:0002683 MESH:A03.492.766.440 NCIT:C32656 OpenCyc:Mx8NhB4rvcD6KJwpEbGdrcN5Y29ycB4rvmKNOpwpEbGdrcN5Y29ycB4rvVj5FpwpEbGdrcN5Y29ycB4rvVjlqpwpEbGdrcN5Y29ycA UMLS:C0017136 galen:GastricMucosa gastric mucosa gastric mucous membrane mucosa of organ of stomach mucosa of organ of ventriculus mucosa of ventriculus mucous membrane of stomach mucous membrane of ventriculus organ mucosa of stomach organ mucosa of ventriculus stomach mucosa stomach mucosa of organ stomach mucous membrane stomach organ mucosa tunica mucosa (gaster) tunica mucosa gastricae ventriculus mucosa ventriculus mucosa of organ ventriculus mucous membrane ventriculus organ mucosa uberon Magenschleimhaut tunica mucosa gastris UBERON:0001199 mucosa of stomach Wikipedia:File:Normal_gastric_mucosa_intermed_mag.jpg The mucosal layer that lines the stomach. The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. UMLS:C0017136 ncithesaurus:Gastric_Mucosa mucosa of organ of stomach OBOL:automatic mucosa of organ of ventriculus OBOL:automatic mucosa of ventriculus OBOL:automatic mucous membrane of ventriculus OBOL:automatic organ mucosa of stomach OBOL:automatic organ mucosa of ventriculus OBOL:automatic stomach mucosa of organ OBOL:automatic stomach mucous membrane OBOL:automatic stomach organ mucosa OBOL:automatic tunica mucosa gastricae FMA:14907 FMA:TA ventriculus mucosa OBOL:automatic ventriculus mucosa of organ OBOL:automatic ventriculus mucous membrane OBOL:automatic ventriculus organ mucosa OBOL:automatic Magenschleimhaut BTO:0001308 tunica mucosa gastris tunica mucosa gastris BTO:0001308 the fibrous connective tissue layer beneath the stomach mucosa BTO:0002110 EMAPA:35825 FMA:14908 MA:0002685 NCIT:C32663 UMLS:C0227211 gastric submucosa stomach submucosa submucosa of ventriculus tela submucosa (gaster) tela submucosa gastricae ventriculus submucosa uberon submucous layer of stomach tela submucosa ventriculi UBERON:0001200 submucosa of stomach the fibrous connective tissue layer beneath the stomach mucosa MGI:csmith MP:0010794 UMLS:C0227211 ncithesaurus:Gastric_Submucosa submucosa of ventriculus OBOL:automatic tela submucosa gastricae FMA:14908 FMA:TA ventriculus submucosa OBOL:automatic submucous layer of stomach BTO:0002110 tela submucosa ventriculi BTO:0002110 the outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum TODO - check serosa/peritoneum EMAPA:35822 FMA:14914 MA:0001626 NCIT:C32662 UMLS:C1517453 anatomical wall of stomach serosa anatomical wall of stomach serous membrane anatomical wall of ventriculus serosa anatomical wall of ventriculus serous membrane gastric wall serosa gastric wall serous membrane serosa of anatomical wall of stomach serosa of anatomical wall of ventriculus serosa of gastric wall serosa of stomach anatomical wall serosa of stomach wall serosa of ventriculus anatomical wall serosa of ventriculus wall serosa of wall of stomach serosa of wall of ventriculus serous coat of stomach serous membrane of anatomical wall of stomach serous membrane of anatomical wall of ventriculus serous membrane of gastric wall serous membrane of stomach anatomical wall serous membrane of stomach wall serous membrane of ventriculus anatomical wall serous membrane of ventriculus wall serous membrane of wall of stomach serous membrane of wall of ventriculus stomach anatomical wall serosa stomach anatomical wall serous membrane stomach serosa stomach wall serosa stomach wall serous membrane tunica serosa (gaster) tunica serosa gastricae ventriculus anatomical wall serosa ventriculus anatomical wall serous membrane ventriculus wall serosa ventriculus wall serous membrane visceral peritoneum of stomach wall of stomach serosa wall of stomach serous membrane wall of ventriculus serosa wall of ventriculus serous membrane uberon gastric serosa UBERON:0001201 serosa of stomach the outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum MGI:csmith MP:0010793 UMLS:C1517453 ncithesaurus:Gastric_Serosal_Surface anatomical wall of stomach serosa OBOL:automatic anatomical wall of stomach serous membrane OBOL:automatic anatomical wall of ventriculus serosa OBOL:automatic anatomical wall of ventriculus serous membrane OBOL:automatic gastric wall serosa OBOL:automatic gastric wall serous membrane OBOL:automatic serosa of anatomical wall of stomach OBOL:automatic serosa of anatomical wall of ventriculus OBOL:automatic serosa of gastric wall OBOL:automatic serosa of stomach anatomical wall OBOL:automatic serosa of stomach wall OBOL:automatic serosa of ventriculus anatomical wall OBOL:automatic serosa of ventriculus wall OBOL:automatic serosa of wall of stomach OBOL:automatic serosa of wall of ventriculus OBOL:automatic serous membrane of anatomical wall of stomach OBOL:automatic serous membrane of anatomical wall of ventriculus OBOL:automatic serous membrane of gastric wall OBOL:automatic serous membrane of stomach anatomical wall OBOL:automatic serous membrane of stomach wall OBOL:automatic serous membrane of ventriculus anatomical wall OBOL:automatic serous membrane of ventriculus wall OBOL:automatic serous membrane of wall of stomach OBOL:automatic serous membrane of wall of ventriculus OBOL:automatic stomach anatomical wall serosa OBOL:automatic stomach anatomical wall serous membrane OBOL:automatic stomach wall serosa OBOL:automatic stomach wall serous membrane OBOL:automatic tunica serosa gastricae FMA:14914 FMA:TA ventriculus anatomical wall serosa OBOL:automatic ventriculus anatomical wall serous membrane OBOL:automatic ventriculus wall serosa OBOL:automatic ventriculus wall serous membrane OBOL:automatic wall of stomach serosa OBOL:automatic wall of stomach serous membrane OBOL:automatic wall of ventriculus serosa OBOL:automatic wall of ventriculus serous membrane OBOL:automatic A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]. (...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG] AAO:0011093 EMAPA:19251 FMA:14916 MA:0002952 NCIT:C33433 OpenCyc:Mx4rvly2ZZwpEbGdrcN5Y29ycA UMLS:C0227238 VHOG:0001466 XAO:0000457 pyloric valve uberon UBERON:0001202 pyloric sphincter A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]. (...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG] 2012-09-17 VHOG:0001466 VHOG UMLS:C0227238 ncithesaurus:Pyloric_Sphincter pyloric valve A mucosa that is part of a small intestine [Automatically generated definition]. BTO:0001259 CALOHA:TS-0941 EMAPA:35780 FMA:14933 MA:0002686 NCIT:C33568 UMLS:C0227261 mucosa of organ of small bowel mucosa of organ of small intestine mucosa of small bowel mucous membrane of small bowel mucous membrane of small intestine organ mucosa of small bowel organ mucosa of small intestine small bowel mucosa small bowel mucosa of organ small bowel mucous membrane small bowel organ mucosa small intestinal mucosa small intestine mucosa small intestine mucosa of organ small intestine mucous membrane small intestine organ mucosa tunica mucosa (intestinum tenue) tunica mucosa intestini tenuis uberon UBERON:0001204 mucosa of small intestine A mucosa that is part of a small intestine [Automatically generated definition]. OBOL:automatic UMLS:C0227261 ncithesaurus:Small_Intestinal_Mucosa mucosa of organ of small bowel OBOL:automatic mucosa of organ of small intestine OBOL:automatic mucosa of small bowel OBOL:automatic mucous membrane of small bowel OBOL:automatic organ mucosa of small bowel OBOL:automatic organ mucosa of small intestine OBOL:automatic small bowel mucosa OBOL:automatic small bowel mucosa of organ OBOL:automatic small bowel mucous membrane OBOL:automatic small bowel organ mucosa OBOL:automatic small intestine mucosa of organ OBOL:automatic small intestine organ mucosa OBOL:automatic tunica mucosa intestini tenuis FMA:14933 FMA:TA submucosal tissue in the small intestines. BTO:0002112 EMAPA:37564 FMA:14934 MA:0001562 NCIT:C33572 UMLS:C0227268 small bowel submucosa small intestinal submucosa small intestine submucosa submucosa of small bowel tela submucosa (intestinum tenue) tela submucosa intestini tenuis uberon UBERON:0001205 submucosa of small intestine submucosal tissue in the small intestines. EMAPA:37564 MA:th UMLS:C0227268 ncithesaurus:Small_Intestinal_Submucosa small bowel submucosa OBOL:automatic submucosa of small bowel OBOL:automatic tela submucosa intestini tenuis BTO:0002112 A serous membrane that is part of a small intestine [Automatically generated definition]. duodenum, 1st part serosa, 2nd - 4th adventitia EMAPA:37561 FMA:14938 MA:0001558 serosa of small bowel serous coat of small intestine serous membrane of small bowel serous membrane of small intestine small bowel serosa small bowel serous membrane small intestinal serosa small intestine serosa small intestine serous membrane tunica serosa (intestinum tenue) tunica serosa intestini tenuis visceral peritoneum of small intestine uberon UBERON:0001206 serosa of small intestine A serous membrane that is part of a small intestine [Automatically generated definition]. OBOL:automatic EMAPA:37561 MA:th serosa of small bowel OBOL:automatic serous membrane of small bowel OBOL:automatic serous membrane of small intestine OBOL:automatic small bowel serosa OBOL:automatic small bowel serous membrane OBOL:automatic small intestine serous membrane OBOL:automatic tunica serosa intestini tenuis FMA:14938 FMA:TA A mucosa that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2106 EMAPA:35467 FMA:14969 MA:0002688 NCIT:C32926 UMLS:C0734203 large intestinal mucosa large intestine mucosa large intestine mucosa of organ large intestine mucous membrane large intestine organ mucosa mucosa of organ of large intestine mucous membrane of large intestine organ mucosa of large intestine tunica mucosa intestini crassi uberon UBERON:0001207 mucosa of large intestine A mucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic UMLS:C0734203 ncithesaurus:Large_Intestinal_Mucosa large intestine mucosa of organ OBOL:automatic large intestine mucous membrane OBOL:automatic large intestine organ mucosa OBOL:automatic mucosa of organ of large intestine OBOL:automatic organ mucosa of large intestine OBOL:automatic tunica mucosa intestini crassi FMA:14969 FMA:TA A submucosa that is part of a large intestine [Automatically generated definition]. BTO:0002111 EMAPA:37560 FMA:14970 MA:0002690 NCIT:C32930 UMLS:C0734204 large intestinal submucosa large intestine submucosa tela submucosa intestini crassi uberon submucous layer of large intestine UBERON:0001208 submucosa of large intestine A submucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37560 MA:th UMLS:C0734204 ncithesaurus:Large_Intestinal_Submucosa tela submucosa intestini crassi FMA:14970 FMA:TA submucous layer of large intestine BTO:0002111 A serous membrane that is part of a large intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37557 FMA:14975 MA:0001546 NCIT:C32929 UMLS:C1517727 large intestinal serosa large intestine serosa large intestine serous membrane serous coat of large intestine serous membrane of large intestine tunica serosa intestini crassi visceral peritoneum of large intestine uberon UBERON:0001209 serosa of large intestine A serous membrane that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37557 MA:th UMLS:C1517727 ncithesaurus:Large_Intestinal_Serosal_Surface large intestine serous membrane OBOL:automatic serous membrane of large intestine OBOL:automatic tunica serosa intestini crassi FMA:14975 FMA:TA A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. currently defined as equivalent to any submucosal gland in the duodenum. Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds BTO:0002376 EMAPA:36522 FMA:15060 GAID:314 MA:0001551 MESH:A03.492.411.620.270.322 NCIT:C13010 UMLS:C0006323 Brunner's gland gland of Brunner submucosal gland of duodenum uberon glandula duodenales glandula duodenales Brunneri UBERON:0001212 duodenal gland compound tubular FMA, modified A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds ISBN:9780521617147 UMLS:C0006323 ncithesaurus:Brunner_s_Gland Brunner's gland FMA:15060 gland of Brunner FMA:15060 glandula duodenales BTO:0002376 glandula duodenales Brunneri BTO:0002376 the tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO] the BTO class refers to a generic villous UBERON:0007607 BTO:0003121 EMAPA:35784 FMA:15072 MA:0001563 NCIT:C33874 TAO:0005125 UMLS:C1519988 ZFA:0005125 enteric villi enteric villous enteric villus intestinal villi villi intestinales villus villus intestinalis (intestinum tenue) uberon intestinal villus layer small intestine villus villi intestinales UBERON:0001213 intestinal villus http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg FMA ZFA the tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold MGI:csmith MGI:rbabiuk MP:0008108 The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO] 2012-08-14 TAO:0005125 TAO ZFIN:curator the BTO class refers to a generic villous BTO UMLS:C1519988 ncithesaurus:Villus enteric villi HP:0011473 enteric villous HP:0011473 enteric villus HP:0011473 intestinal villi ZFA:0005125 villi intestinales villus BTO:0003121 villus intestinalis (intestinum tenue) FMA:15072 small intestine villus MA:0001563 villi intestinales A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002782 EHDAA2:0000819 EHDAA:8712 EMAPA:18642 FMA:15391 MA:0002178 NCIT:C32782 OpenCyc:Mx4rvcV53ZwpEbGdrcN5Y29ycA UMLS:C0226754 VHOG:0001118 uberon lower mesenteric vein vena mesenterica inferior UBERON:0001215 inferior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png FMA/obol A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. UMLS:C0226754 ncithesaurus:Inferior_Mesenteric_Vein lower mesenteric vein BTO:0002782 vena mesenterica inferior The veins that drain blood from the ileum into the superior mesenteric vein. EMAPA:37149 FMA:15405 MA:0002140 NCIT:C53046 UMLS:C1301431 uberon UBERON:0001217 ileal vein FMA Wikipedia The veins that drain blood from the ileum into the superior mesenteric vein. ncithesaurus:Ileal_Vein EMAPA:37149 MA:th UMLS:C1301431 ncithesaurus:Ileal_Vein The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted]. EMAPA:37174 FMA:15406 MA:0002181 OpenCyc:Mx4rvywYIpwpEbGdrcN5Y29ycA vena colica media (intermedia) uberon vena colica media UBERON:0001218 middle colic vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted]. EMAPA:37174 MA:th vena colica media An ureter that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37373 FMA:15571 MA:0001685 NCIT:C49327 UMLS:C0227682 uberon UBERON:0001222 right ureter An ureter that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37373 MA:th UMLS:C0227682 ncithesaurus:Right_Ureter An ureter that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37372 FMA:15572 MA:0001684 NCIT:C49324 UMLS:C0227683 uberon UBERON:0001223 left ureter An ureter that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37372 MA:th UMLS:C0227683 ncithesaurus:Left_Ureter A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. CALOHA:TS-2230 EMAPA:17948 FMA:15575 GAID:426 MA:0000374 MESH:D007682 NCIT:C12887 UMLS:C0227666 galen:RenalPelvis kidney pelvis pelvis of ureter uberon p. renallis pyelum UBERON:0001224 In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter renal pelvis Illu:kidney2.jpg MA FMA A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. MP:0004194 UMLS:C0227666 ncithesaurus:Renal_Pelvis p. renallis pyelum MP:0004194 Outer cortical portion of the kidney, between the renal capsule and the renal medulla. In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP] BTO:0001166 CALOHA:TS-0503 EMAPA:17952 FMA:15581 GAID:424 MA:0000372 MESH:D007672 NCIT:C12739 UMLS:C0022655 galen:CortexOfKidney cortex renalis kidney cortex renal cortex uberon UBERON:0001225 cortex of kidney Illu:kidney.jpg FMA Outer cortical portion of the kidney, between the renal capsule and the renal medulla. UMLS:C0022655 ncithesaurus:Renal_Cortex cortex renalis FMA:15581 FMA:TA An epithelial tube that is part of the nephron, the functional part of the kidney. note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA UBERON:0004210 renal tubule BTO:0000343 CALOHA:TS-1262 EFO:0003666 EMAPA:27782 EV:0100387 FMA:15627 GAID:433 MA:0000377 MESH:D007684 NCIT:C49274 TAO:0001287 UMLS:C0022674 ZFA:0001287 kidney tubule tubulus renalis uberon uriniferous tubule UBERON:0001231 nephron tubule GO MA ZFA GO checkme An epithelial tube that is part of the nephron, the functional part of the kidney. GO:0072078 note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA MA UMLS:C0022674 ncithesaurus:Renal_Tubule kidney tubule GAID:433 uriniferous tubule MA:0000377 The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient Renal duct that collects the output from renal tubules.[TAO] in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron BTO:0000761 CALOHA:TS-0860 EMAPA:28407 EV:0100391 FMA:15628 GAID:434 MA:0000371 MESH:D007685 TAO:0005294 ZFA:0005294 collecting duct kidney collecting duct renal collecting tubule tubulus renalis arcuatus tubulus renalis colligens uberon arcuate renal tubule collecting duct system collecting tubule junctional tube kidney collecting tubule ureteric tree UBERON:0001232 collecting duct of renal tubule checkme GO The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient GO:0072044 Renal duct that collects the output from renal tubules.[TAO] 2012-08-14 TAO:0005294 TAO ZFIN:curator in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron FMA collecting duct GO:0072044 renal collecting tubule FMA:15628 tubulus renalis arcuatus arcuate renal tubule collecting duct system BTO:0000761 junctional tube ureteric tree EMAPA:28407 An adrenal gland that is in the right side of the abdomen https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, the right adrenal gland is triangular shaped EMAPA:37357 FMA:15629 MA:0000719 NCIT:C49325 UMLS:C0229559 glandula suprarenalis dexter right suprarenal gland uberon UBERON:0001233 right adrenal gland An adrenal gland that is in the right side of the abdomen OBOL:automatic In humans, the right adrenal gland is triangular shaped WP EMAPA:37357 MA:th UMLS:C0229559 ncithesaurus:Right_Adrenal_Gland glandula suprarenalis dexter An adrenal gland that is in the left side of the abdomen https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, the left adrenal gland is semilunar shaped EMAPA:37356 FMA:15630 MA:0000718 NCIT:C49322 UMLS:C0229560 glandula suprarenalis sinister left suprarenal gland uberon UBERON:0001234 left adrenal gland An adrenal gland that is in the left side of the abdomen OBOL:automatic In humans, the left adrenal gland is semilunar shaped WP EMAPA:37356 MA:th UMLS:C0229560 ncithesaurus:Left_Adrenal_Gland glandula suprarenalis sinister the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO AAO:0011009 BTO:0000045 CALOHA:TS-0015 EFO:0000237 EMAPA:18427 EV:0100136 FMA:15632 GAID:447 MA:0000118 MAT:0000494 MESH:D000302 NCIT:C12396 UMLS:C0001613 VHOG:0001481 XAO:0000165 adrenal gland cortex cortex (glandula suprarenalis) cortex of adrenal gland cortex of suprarenal gland suprarenal cortex uberon cortex glandulae suprarenalis suprarenal UBERON:0001235 adrenal cortex http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone ISBN:0-683-40008-8 MGI:llw2 MP:0008288 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001481 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 UMLS:C0001613 ncithesaurus:Adrenal_Cortex cortex glandulae suprarenalis cortex glandulae suprarenalis BTO:0000045 the inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] AAO:0011010 BTO:0000049 CALOHA:TS-0018 EFO:0000852 EMAPA:18428 EV:0100137 FMA:15633 GAID:451 MA:0000119 MAT:0000495 MESH:D019439 NCIT:C12397 UMLS:C0001629 VHOG:0001378 XAO:0000166 adrenal gland medulla medulla (glandula suprarenalis) medulla glandulae suprarenalis medulla of adrenal gland medulla of suprarenal gland suprarenal medulla uberon adrenal central medulla chromaffin cells medulla of glandula suprarenalis UBERON:0001236 adrenal medulla http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png Wikipedia the inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine MESH:A06.407.071.265 MGI:llw2 MP:0008289 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001378 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 UMLS:C0001629 ncithesaurus:Adrenal_Medulla medulla glandulae suprarenalis FMA:15633 FMA:TA medulla of adrenal gland OBOL:automatic medulla of glandula suprarenalis BTO:0000049 Lamina propria that is part_of the small intestine. EMAPA:35779 FMA:15651 MA:0001554 NCIT:C49297 UMLS:C1711325 lamina propria mucosa of small bowel lamina propria mucosa of small intestine lamina propria mucosae of small bowel lamina propria mucosae of small intestine lamina propria of mucosa of small intestine lamina propria of small bowel small bowel lamina propria small bowel lamina propria mucosa small bowel lamina propria mucosae small intestine lamina propria small intestine lamina propria mucosa small intestine lamina propria mucosae uberon UBERON:0001238 lamina propria of small intestine Lamina propria that is part_of the small intestine. GOC:Obol UMLS:C1711325 ncithesaurus:Small_Intestinal_Lamina_Propria lamina propria mucosa of small bowel OBOL:automatic lamina propria mucosa of small intestine OBOL:automatic lamina propria mucosae of small bowel OBOL:automatic lamina propria of small bowel OBOL:automatic small bowel lamina propria OBOL:automatic small bowel lamina propria mucosa OBOL:automatic small bowel lamina propria mucosae OBOL:automatic small intestine lamina propria mucosa OBOL:automatic small intestine lamina propria mucosae OBOL:automatic Mucosal layer that lines the intestine. BTO:0000642 EMAPA:35440 FMA:15695 GAID:296 MA:0001537 MESH:A03.492.411.369 NCIT:C49241 UMLS:C0021839 bowel mucosa bowel mucosa of organ bowel mucous membrane bowel organ mucosa intestine mucosa intestine mucosa of organ intestine mucous membrane intestine organ mucosa mucosa of bowel mucosa of intestine mucosa of organ of bowel mucosa of organ of intestine mucous membrane of bowel mucous membrane of intestine organ mucosa of bowel organ mucosa of intestine tunica mucosa intestini uberon UBERON:0001242 intestinal mucosa Mucosal layer that lines the intestine. UBERON:cjm UMLS:C0021839 ncithesaurus:Intestinal_Mucosa bowel mucosa OBOL:automatic bowel mucosa of organ OBOL:automatic bowel mucous membrane OBOL:automatic bowel organ mucosa OBOL:automatic intestine mucosa of organ OBOL:automatic intestine mucous membrane OBOL:automatic intestine organ mucosa OBOL:automatic mucosa of bowel OBOL:automatic mucosa of organ of bowel OBOL:automatic mucosa of organ of intestine OBOL:automatic mucous membrane of bowel OBOL:automatic mucous membrane of intestine OBOL:automatic organ mucosa of bowel OBOL:automatic organ mucosa of intestine OBOL:automatic A serous membrane that is part of a wall of intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37619 FMA:15701 MA:0001538 anatomical wall of bowel serosa anatomical wall of bowel serous membrane anatomical wall of intestine serosa anatomical wall of intestine serous membrane bowel anatomical wall serosa bowel anatomical wall serous membrane bowel wall serosa bowel wall serous membrane intestinal serosa intestinal wall serosa intestinal wall serous membrane intestine anatomical wall serosa intestine anatomical wall serous membrane intestine serosa intestine wall serosa intestine wall serous membrane serosa of anatomical wall of bowel serosa of anatomical wall of intestine serosa of bowel anatomical wall serosa of bowel wall serosa of intestinal wall serosa of intestine anatomical wall serosa of intestine wall serosa of wall of bowel serosa of wall of intestine serous membrane of anatomical wall of bowel serous membrane of anatomical wall of intestine serous membrane of bowel anatomical wall serous membrane of bowel wall serous membrane of intestinal wall serous membrane of intestine anatomical wall serous membrane of intestine wall serous membrane of wall of bowel serous membrane of wall of intestine visceral peritoneum of intestine wall of bowel serosa wall of bowel serous membrane wall of intestine serosa wall of intestine serous membrane uberon UBERON:0001243 serosa of intestine A serous membrane that is part of a wall of intestine [Automatically generated definition]. OBOL:automatic EMAPA:37619 MA:th anatomical wall of bowel serosa OBOL:automatic anatomical wall of bowel serous membrane OBOL:automatic anatomical wall of intestine serosa OBOL:automatic anatomical wall of intestine serous membrane OBOL:automatic bowel anatomical wall serosa OBOL:automatic bowel anatomical wall serous membrane OBOL:automatic bowel wall serosa OBOL:automatic bowel wall serous membrane OBOL:automatic intestinal wall serosa OBOL:automatic intestinal wall serous membrane OBOL:automatic intestine anatomical wall serosa OBOL:automatic intestine anatomical wall serous membrane OBOL:automatic intestine wall serosa OBOL:automatic intestine wall serous membrane OBOL:automatic serosa of anatomical wall of bowel OBOL:automatic serosa of anatomical wall of intestine OBOL:automatic serosa of bowel anatomical wall OBOL:automatic serosa of bowel wall OBOL:automatic serosa of intestinal wall OBOL:automatic serosa of intestine anatomical wall OBOL:automatic serosa of intestine wall OBOL:automatic serosa of wall of bowel OBOL:automatic serosa of wall of intestine OBOL:automatic serous membrane of anatomical wall of bowel OBOL:automatic serous membrane of anatomical wall of intestine OBOL:automatic serous membrane of bowel anatomical wall OBOL:automatic serous membrane of bowel wall OBOL:automatic serous membrane of intestinal wall OBOL:automatic serous membrane of intestine anatomical wall OBOL:automatic serous membrane of intestine wall OBOL:automatic serous membrane of wall of bowel OBOL:automatic serous membrane of wall of intestine OBOL:automatic wall of bowel serosa OBOL:automatic wall of bowel serous membrane OBOL:automatic wall of intestine serosa OBOL:automatic wall of intestine serous membrane OBOL:automatic Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. anal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html BTO:0001680 CALOHA:TS-2005 EV:0100082 FBbt:00003148 FMA:15711 GAID:312 MA:0000331 MESH:A03.492.411.495.767.288 NCIT:C43362 OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA TADS:0000066 TGMA:0001279 UMLS:C0003461 WBbt:0005364 galen:Anus anal opening anal orifice opening of terminal part of digestive tract uberon proctodeum UBERON:0001245 anus http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. ZFIN:curator UMLS:C0003461 ncithesaurus:Anus The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad. FMA:15767 MA:0002668 NCIT:C32827 UMLS:C0227515 interlobular ductule uberon UBERON:0001246 interlobular bile duct MA-part-of FMA FMA MA MP The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad. MP:0009500 UMLS:C0227515 ncithesaurus:Interlobular_Bile_Duct interlobular ductule MP:0009500 A ligament that attaches the liver to the anterior body wall. It is a broad and thin antero-posterior peritoneal fold, falciform in shape, its base being directed downward and backward and its apex upward and backward. It is a remnant of the ventral mesentery of the fetus. It is situated in an antero-posterior plane but lies obliquely, so that one surface faces forward and is in contact with the peritoneum behind the right rectus and the diaphragm, while the other is directed backward and is in contact with the left lobe of the liver. It is attached by its left margin to the under surface of the diaphragm and the posterior surface of the sheath of the right Rectus as low down as the umbilicus; by its right margin it extends from the notch on the anterior margin of the liver, as far back as the posterior surface. It is composed of two layers of peritoneum closely united together. Its base or free edge contains between its layers the round ligament and the paraumbilical veins[WP]. in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament EHDAA2:0000499 EHDAA:4856 EMAPA:18288 FMA:15823 MA:0001622 NCIT:C32582 UMLS:C0230240 VHOG:0000355 falciform ligament of liver ligamentum falciforme (hepatis) ligamentum falciforme hepatis uberon UBERON:0001247 falciform ligament MA A ligament that attaches the liver to the anterior body wall. It is a broad and thin antero-posterior peritoneal fold, falciform in shape, its base being directed downward and backward and its apex upward and backward. It is a remnant of the ventral mesentery of the fetus. It is situated in an antero-posterior plane but lies obliquely, so that one surface faces forward and is in contact with the peritoneum behind the right rectus and the diaphragm, while the other is directed backward and is in contact with the left lobe of the liver. It is attached by its left margin to the under surface of the diaphragm and the posterior surface of the sheath of the right Rectus as low down as the umbilicus; by its right margin it extends from the notch on the anterior margin of the liver, as far back as the posterior surface. It is composed of two layers of peritoneum closely united together. Its base or free edge contains between its layers the round ligament and the paraumbilical veins[WP]. in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament FMA UMLS:C0230240 ncithesaurus:Falciform_Ligament ligamentum falciforme hepatis FMA:15823 FMA:TA An adventitia that is part of a ureter. EMAPA:28114 FMA:15892 MA:0002652 external adventitia of ureter tunica adventitia (ureter) tunica adventitia ureteris ureter adventitia ureteral adventitia uberon UBERON:0001252 adventitia of ureter An adventitia that is part of a ureter. OBOL:automatic tunica adventitia (ureter) FMA:15892 FMA:TA tunica adventitia ureteris FMA:15892 FMA:TA A lamina propria that is part of a ureter [Automatically generated definition]. EMAPA:28841 FMA:15896 MA:0002653 lamina propria mucosa of ureter lamina propria mucosae of ureter ureter lamina propria ureter lamina propria mucosa ureter lamina propria mucosae uberon UBERON:0001253 lamina propria of ureter true A lamina propria that is part of a ureter [Automatically generated definition]. OBOL:automatic lamina propria mucosa of ureter OBOL:automatic lamina propria mucosae of ureter OBOL:automatic ureter lamina propria mucosa OBOL:automatic ureter lamina propria mucosae OBOL:automatic urinary bladder distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] vesical The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454] bladder AAO:0000623 BTO:0001418 CALOHA:TS-1090 EFO:0000290 EHDAA2:0000174 EHDAA:9328 EMAPA:18321 EV:0100098 FMA:15900 GAID:0000004 MA:0000380 MAT:0000122 MESH:A05.810.161 MIAA:0000122 NCIT:C12414 OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA UMLS:C0005682 VHOG:0000740 XAO:0000154 galen:UrinaryBladder vesica urinaria uberon urocyst vesica UBERON:0001255 urinary bladder Urinary:system.svg BTO FMA upper part of UG sinus distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. MGI:anna A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000740 VHOG Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] 2012-06-20 AAO:0000623 AAO AAO:BJB In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] 2012-09-17 VHOG:0000740 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78 bladder EHDAA2:0000174 UMLS:C0005682 ncithesaurus:Bladder vesica urinaria urocyst vesica BTO:0001418 An anatomical wall that lines the insider of a urinary bladder. BTO:0001462 EMAPA:35175 FMA:15902 MA:0002493 NCIT:C48941 UMLS:C0458421 anatomical wall of bladder anatomical wall of urinary bladder bladder anatomical wall bladder wall urinary bladder anatomical wall urinary bladder wall wall of bladder uberon UBERON:0001256 wall of urinary bladder An anatomical wall that lines the insider of a urinary bladder. UMLS:C0458421 ncithesaurus:Bladder_Wall anatomical wall of bladder OBOL:automatic anatomical wall of urinary bladder OBOL:automatic bladder anatomical wall OBOL:automatic bladder wall OBOL:automatic urinary bladder anatomical wall OBOL:automatic wall of bladder OBOL:automatic The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]. EMAPA:36078 FMA:15912 MA:0002491 NCIT:C12336 UMLS:C0227716 galen:UrinaryBladderNeck bladder neck cervix vesicae collum vesicae neck of bladder urinary bladder neck vesical neck uberon cervix vesicae urinariae UBERON:0001258 neck of urinary bladder http://upload.wikimedia.org/wikipedia/commons/6/63/Gray1156.png The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]. MP:anna UMLS:C0227716 ncithesaurus:Bladder_Neck cervix vesicae FMA:15912 FMA:TA collum vesicae FMA:15912 FMA:TA cervix vesicae urinariae the mucous membrane lining the urinary bladder EFO:0000293 EMAPA:35897 FMA:15928 MA:0001692 NCIT:C32205 UMLS:C0227691 galen:MucousMembraneOfUrinaryBladder bladder mucosa bladder mucous membrane bladder organ mucosa mucosa of bladder mucous membrane of bladder mucous membrane of urinary bladder tunica mucosa (vesica urinaria) tunica mucosa vesicae tunica mucosa vesicae urinariae urinary bladder mucosa urinary bladder mucous membrane uberon UBERON:0001259 mucosa of urinary bladder the mucous membrane lining the urinary bladder MGI:anna MP:0011766 UMLS:C0227691 ncithesaurus:Bladder_Mucosa bladder mucous membrane OBOL:automatic bladder organ mucosa OBOL:automatic mucosa of bladder OBOL:automatic tunica mucosa (vesica urinaria) FMA:15928 FMA:TA tunica mucosa vesicae FMA:15928 FMA:TA tunica mucosa vesicae urinariae MP:MP urinary bladder mucous membrane OBOL:automatic A serous membrane that is part of a urinary bladder [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:28661 FMA:15932 MA:0001696 bladder serosa bladder serous membrane serosa of bladder serous coat of bladder serous coat of urinary bladder serous membrane of bladder serous membrane of urinary bladder tunica serosa (vesica urinaria) tunica serosa vesicae urinary bladder serosa urinary bladder serous membrane visceral peritoneum of urinary bladder uberon UBERON:0001260 serosa of urinary bladder A serous membrane that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic bladder serous membrane OBOL:automatic serous membrane of bladder OBOL:automatic serous membrane of urinary bladder OBOL:automatic tunica serosa (vesica urinaria) FMA:15932 FMA:TA tunica serosa vesicae FMA:15932 FMA:TA urinary bladder serous membrane OBOL:automatic A lamina propria that is part of a urinary bladder [Automatically generated definition]. Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue EMAPA:30088 FMA:15935 MA:0001695 NCIT:C48940 UMLS:C1706967 bladder lamina propria bladder lamina propria mucosa bladder lamina propria mucosae lamina propria mucosa of bladder lamina propria mucosa of urinary bladder lamina propria mucosae of bladder lamina propria mucosae of urinary bladder lamina propria of bladder urinary bladder lamina propria urinary bladder lamina propria mucosa urinary bladder lamina propria mucosae uberon UBERON:0001261 lamina propria of urinary bladder A lamina propria that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic UMLS:C1706967 ncithesaurus:Bladder_Lamina_Propria bladder lamina propria OBOL:automatic bladder lamina propria mucosa OBOL:automatic bladder lamina propria mucosae OBOL:automatic lamina propria mucosa of bladder OBOL:automatic lamina propria mucosa of urinary bladder OBOL:automatic lamina propria mucosae of bladder OBOL:automatic lamina propria mucosae of urinary bladder OBOL:automatic lamina propria of bladder OBOL:automatic urinary bladder lamina propria mucosa OBOL:automatic urinary bladder lamina propria mucosae OBOL:automatic An anatomical wall that is part of a intestine [Automatically generated definition]. we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different BTO:0000647 EMAPA:35444 FMA:15949 MA:0001525 MA:0002693 NCIT:C49478 UMLS:C1708548 anatomical wall of bowel anatomical wall of intestine bowel anatomical wall bowel wall intestinal wall intestine anatomical wall intestine wall wall of bowel uberon bowel wall UBERON:0001262 wall of intestine An anatomical wall that is part of a intestine [Automatically generated definition]. OBOL:automatic UMLS:C1708548 ncithesaurus:Intestinal_Wall_Tissue anatomical wall of bowel OBOL:automatic anatomical wall of intestine OBOL:automatic bowel anatomical wall OBOL:automatic bowel wall OBOL:automatic intestine anatomical wall OBOL:automatic wall of bowel OBOL:automatic bowel wall MA:0001525 The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. EMAPA:35651 FMA:16011 MA:0002417 NCIT:C49268 UMLS:C0227578 acinus pancreaticus pancreas acinus uberon pancreatic acinar pancreatic acini UBERON:0001263 pancreatic acinus FMA The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. MP:0009145 UMLS:C0227578 ncithesaurus:Pancreatic_Acinus acinus pancreaticus FMA:16011 pancreatic acinar TEMP:MP pancreatic acini pancreas An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. pancreas http://langual.org Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] pancreatic As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans AAO:0010112 BTO:0000988 CALOHA:TS-0736 EFO:0000855 EHDAA2:0001367 EHDAA:6893 EMAPA:17503 EV:0100092 FMA:7198 GAID:334 MA:0000120 MAT:0000075 MESH:D010179 MIAA:0000075 NCIT:C12393 OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA TAO:0000140 UMLS:C0030274 VHOG:0000050 XAO:0000136 ZFA:0000140 galen:Pancreas http://www.langual.org/langual_thesaurus.asp?termid=C0204 uberon UBERON:0001264 pancreas https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png Wikipedia Wikipedia An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. GO:0031016 Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] 2012-06-20 AAO:0010112 AAO AAO:BJB In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] 2012-09-17 VHOG:0000050 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans UMLS:C0030274 ncithesaurus:Pancreas A trabecula that is part of a spleen. EMAPA:35808 FMA:16027 MA:0000758 NCIT:C33607 UMLS:C0229688 spleen trabeculum splenic trabecula uberon UBERON:0001265 trabecula of spleen FMA A trabecula that is part of a spleen. OBOL:automatic UMLS:C0229688 ncithesaurus:Splenic_Trabecula Transudate contained in the peritoneal cavity. BTO:0001031 EMAPA:35683 FMA:16515 MA:0002531 ncithesaurus:Peritoneal_Fluid uberon UBERON:0001268 peritoneal fluid FMA Transudate contained in the peritoneal cavity. FMA:16515 The acetabulum is a concave surface of the pelvis. The head of the femur meets with the pelvis at the acetabulum, forming the hip joint. There are three bones of the os coxae (hip bone) that come together to form the acetabulum. Contributing a little more than two-fifths of the structure is the ischium, which provides lower and side boundaries to the acetabulum. The ilium forms the upper boundary, providing a little less than two-fifths of the structure of the acetabulum. The rest is formed by the pubis, near the midline. It is bounded by a prominent uneven rim, which is thick and strong above, and serves for the attachment of the acetabular labrum, which reduces its opening, and deepens the surface for formation of the hip joint. At the lower part of the acetabulum is the acetabular notch, which is continuous with a circular depression, the acetabular fossa, at the bottom of the cavity of the acetabulum. The rest of the acetabulum is formed by a curved, crescent-moon shaped surface, the lunate surface, where the joint is made with the head of the femur. Its counterpart in the pectoral girdle is the glenoid fossa.[WP,unvetted]. Cavity for the articulation of the proximal bone of the hind limb.[AAO] During the transformation from the osteolepiform fins to tetrapod limbs, the appendages and girdles underwent a number of radical changes. The pelvic girdle became a weight-bearing structure by evolution of an ischium, a full mesio-ventral contact between the two sides of the girdle, an ilium, and a contact between the vertebral column and the girdle through a sacral rib. Fore- and hindlimbs shifted laterally by reorientation of the glenoid and the acetabulum.[well established][VHOG] In reptiles and in birds, the acetabula are deep sockets. whilst WP defines this as a surface, MA treats it as a bone. There are other FMA classes that may be better suited to representing the surface. AAO:0000770 EHDAA:10661 EMAPA:18346 FMA:16579 GAID:206 MA:0001335 MESH:A02.835.232.611.108 NCIT:C32042 OpenCyc:Mx4rwJlP9ZwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001427 UMLS:C0000962 VHOG:0000974 acetabular region acetabulum uberon UBERON:0001269 acetabular part of hip bone http://upload.wikimedia.org/wikipedia/commons/2/29/Illu_pelvic_girdle.jpg FMA Phenoscape FMA The acetabulum is a concave surface of the pelvis. The head of the femur meets with the pelvis at the acetabulum, forming the hip joint. There are three bones of the os coxae (hip bone) that come together to form the acetabulum. Contributing a little more than two-fifths of the structure is the ischium, which provides lower and side boundaries to the acetabulum. The ilium forms the upper boundary, providing a little less than two-fifths of the structure of the acetabulum. The rest is formed by the pubis, near the midline. It is bounded by a prominent uneven rim, which is thick and strong above, and serves for the attachment of the acetabular labrum, which reduces its opening, and deepens the surface for formation of the hip joint. At the lower part of the acetabulum is the acetabular notch, which is continuous with a circular depression, the acetabular fossa, at the bottom of the cavity of the acetabulum. The rest of the acetabulum is formed by a curved, crescent-moon shaped surface, the lunate surface, where the joint is made with the head of the femur. Its counterpart in the pectoral girdle is the glenoid fossa.[WP,unvetted]. Cavity for the articulation of the proximal bone of the hind limb.[AAO] 2012-06-20 AAO:0000770 AAO AAO:LAP During the transformation from the osteolepiform fins to tetrapod limbs, the appendages and girdles underwent a number of radical changes. The pelvic girdle became a weight-bearing structure by evolution of an ischium, a full mesio-ventral contact between the two sides of the girdle, an ilium, and a contact between the vertebral column and the girdle through a sacral rib. Fore- and hindlimbs shifted laterally by reorientation of the glenoid and the acetabulum.[well established][VHOG] 2012-09-17 VHOG:0000974 VHOG DOI:10.1038/nature04119 Boisvert CA, The pelvic fin and girdle of Panderichthys and the origin of tetrapod locomotion. Nature (2005) In reptiles and in birds, the acetabula are deep sockets. WP whilst WP defines this as a surface, MA treats it as a bone. There are other FMA classes that may be better suited to representing the surface. MA UMLS:C0000962 ncithesaurus:Acetabulum acetabular region VHOG:0000974 acetabulum MA:0001335 The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] EMAPA:37862 FMA:16581 NCIT:C33291 UMLS:C0684083 VSAO:0000304 uberon girdle - pelvic pelvic girdle UBERON:0001271 pelvic girdle region The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. FMA:16581 FMA:23217 UBERONREF:0000003 Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] 2012-08-14 VSAO:0000304 VSAO EMAPA:37862 MA:th UMLS:C0684083 ncithesaurus:Pelvic_Girdle pelvic girdle A fused bone consisting of the ilium, ischium and and pubis. Together with the sacrum and coccyx, it comprises the pelvis. [WP,modified]. currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra. bone of pelvic girdle innominate FMA:16585 GAID:205 MESH:A02.835.232.611 coxal bone hip bone innominate bone os coxa os coxae pelvic bone uberon basipterygium os innominatum UBERON:0001272 innominate bone http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray341.png FMA FMA A fused bone consisting of the ilium, ischium and and pubis. Together with the sacrum and coccyx, it comprises the pelvis. [WP,modified]. The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column WP in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra. FMA bone of pelvic girdle FMA:16585 coxal bone FMA:16585 hip bone FMA:16585 innominate bone FMA:16585 os coxa os coxae FMA:16585 FMA:TA pelvic bone FMA:16585 os innominatum Paired endochondral bone that is the dorsal-most of the pelvic bones, offering attachment areas for gluteal muscles on its main surface [PHENOSCAPE:ad]. Paired, rodlike endochondral bones that constitute the anterior pelvic girdle.[AAO] iliac All reptiles have an ilium except snakes, although some snake species have a tiny bone which is considered to be an ilium this is_a hip bone in MA. AAO:0000772 CALOHA:TS-2200 EFO:0003049 EMAPA:18726 FMA:16589 GAID:207 MA:0001336 MESH:A02.835.232.611.434 NCIT:C32765 OpenCyc:Mx4rvhwFJ5wpEbGdrcN5Y29ycA UMLS:C0020889 galen:Ilium iliac bone ilium bone os iliacum os ilii os ilium uberon illium UBERON:0001273 ilium FMA cjm Paired endochondral bone that is the dorsal-most of the pelvic bones, offering attachment areas for gluteal muscles on its main surface [PHENOSCAPE:ad]. PHENOSCAPE:ad Wikipedia Paired, rodlike endochondral bones that constitute the anterior pelvic girdle.[AAO] 2012-06-20 AAO:0000772 AAO AAO:LAP All reptiles have an ilium except snakes, although some snake species have a tiny bone which is considered to be an ilium WP this is_a hip bone in MA. MA UMLS:C0020889 ncithesaurus:Ilium iliac bone EMAPA:18726 os ilium FMA:16589 FMA:TA The epithelial layer of the stomach . in FMA this is classified as simple columnar, MA divides this into squamous and glandular BTO:0000500 CALOHA:TS-2068 EHDAA2:0001918 EMAPA:17023 FMA:17091 MA:0001610 VHOG:0001433 epithelial tissue of stomach epithelial tissue of ventriculus epithelium of ventriculus stomach epithelial tissue stomach epithelium ventriculus epithelial tissue ventriculus epithelium uberon gastric epithelium UBERON:0001276 epithelium of stomach The epithelial layer of the stomach . MP:0000471 in FMA this is classified as simple columnar, MA divides this into squamous and glandular FMA epithelial tissue of stomach OBOL:automatic epithelial tissue of ventriculus OBOL:automatic epithelium of ventriculus OBOL:automatic stomach epithelial tissue OBOL:automatic stomach epithelium OBOL:automatic ventriculus epithelial tissue OBOL:automatic ventriculus epithelium OBOL:automatic gastric epithelium BTO:0000500 Epithelial layer that lines the intestine. Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] BTO:0000781 EMAPA:32873 FMA:17229 MA:0001536 NCIT:C49240 TAO:0005124 UMLS:C0226890 ZFA:0005124 bowel epithelial tissue bowel epithelium epithelial tissue of bowel epithelial tissue of intestine epithelium of bowel epithelium of intestine intestine epithelial tissue villous epithelium uberon intestine epithelium UBERON:0001277 intestinal epithelium Epithelial layer that lines the intestine. UBERON:cjm Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] 2012-08-14 TAO:0005124 TAO ZFIN:curator UMLS:C0226890 ncithesaurus:Intestinal_Epithelium bowel epithelial tissue OBOL:automatic bowel epithelium OBOL:automatic epithelial tissue of bowel OBOL:automatic epithelial tissue of intestine OBOL:automatic epithelium of bowel OBOL:automatic epithelium of intestine OBOL:automatic intestine epithelial tissue OBOL:automatic villous epithelium ZFA:0005124 An epithelium that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2105 EMAPA:35466 FMA:17301 MA:0001545 epithelial tissue of large intestine large intestinal epithelium large intestine epithelial tissue large intestine epithelium uberon UBERON:0001278 epithelium of large intestine An epithelium that is part of a large intestine [Automatically generated definition]. OBOL:automatic epithelial tissue of large intestine OBOL:automatic large intestine epithelial tissue OBOL:automatic A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver. FMA:17523 MA:0002499 NCIT:C33342 UMLS:C0227514 trias hepatica uberon trias hepatica UBERON:0001279 portal triad Portal:triad.JPG A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel ISBN:0-683-40008-8 MGI:csmith MP:0008993 UMLS:C0227514 ncithesaurus:Portal_Triad trias hepatica The functional units of the liver including the lobules. the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG] UBERON:0003223 AAO:0010405 EHDAA2:0001004 EHDAA:2201 EMAPA:17203 FMA:17540 MA:0000366 NCIT:C32735 VHOG:0000539 XAO:0000454 hepatic parenchyma liver parenchyme parenchyma of liver uberon hepatic parenchyme UBERON:0001280 liver parenchyma XAO The functional units of the liver including the lobules. MP:0008986 the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG] 2012-09-17 VHOG:0000539 VHOG DOI:10.1002/ar.20524 Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007) hepatic parenchyma FMA:17540 liver parenchyme XAO:0000454 parenchyma of liver FMA:17540 hepatic parenchyme VHOG:0000539 Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers. (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] UBERON:0003275 EHDAA2:0000999 EMAPA:17365 FMA:17543 MA:0000367 NCIT:C32733 TAO:0005091 UMLS:C0227523 VHOG:0000708 ZFA:0005091 liver hepatic sinusoids liver sinusoid liver sinusoidal blood vessel sinusoid of liver sinusoidal blood vessel of liver vas capillare sinusoideum vas sinusoideum uberon hepatic sinusoids UBERON:0001281 hepatic sinusoid Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers. ZFIN:curator (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] 2012-09-17 VHOG:0000708 VHOG DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) UMLS:C0227523 ncithesaurus:Hepatic_Sinusoid liver hepatic sinusoids EHDAA2:0000999 liver sinusoidal blood vessel OBOL:automatic sinusoid of liver OBOL:automatic sinusoidal blood vessel of liver OBOL:automatic vas sinusoideum the tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct) FMA:17545 MA:0002669 NCIT:C32255 UMLS:C0227517 canal of Herring cholangiole ductus interlobularis bilifer uberon canal of Hering canals of Hering duct of Herring intrahepatic bile ductule UBERON:0001282 intralobular bile duct FMA FMA FMA the tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule MGI:csmith MP:0009499 UMLS:C0227517 ncithesaurus:Canal_of_Hering canal of Herring FMA:17545 cholangiole FMA:17545 ductus interlobularis bilifer FMA:17545 FMA:TA canals of Hering duct of Herring intrahepatic bile ductule The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP] kidney terms require review for cross-vertebrate compatibility and developmental relationships. Functional unit of the kidney that filters waste.[TAO] In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) BTO:0000924 CALOHA:TS-1312 EMAPA:28491 EMAPA:35592 EV:0100384 FMA:17640 GAID:428 MA:0000375 MESH:D009399 NCIT:C13048 TAO:0002153 UMLS:C0027713 ZFA:0005282 mature nephron uberon nephroneum tubulus renalis UBERON:0001285 nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png FMA Bgee:AN The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP] Functional unit of the kidney that filters waste.[TAO] 2012-08-14 TAO:0002153 TAO ZFIN:curator In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) GO UMLS:C0027713 ncithesaurus:Nephron mature nephron EMAPA:28491 nephroneum tubulus renalis the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy The mucous membrane lining the uterus. [TFD][VHOG] The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG] endometrial Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead in FMA this is subdivided into basal and outer BTO:0001422 CALOHA:TS-0276 EFO:0000980 EMAPA:29917 EV:0100115 FMA:17742 GAID:377 MA:0000390 MAT:0000319 MESH:D004717 MIAA:0000319 NCIT:C12313 UMLS:C0014180 VHOG:0001285 tunica mucosa (endometrium) tunica mucosa uteri uterine endometrium uberon uterine mucosa uterine mucous membrane UBERON:0001295 endometrium Illu:cervix.jpg FMA the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy MESH:A05.360.319.679.490 MGI:smb MP:0004896 The mucous membrane lining the uterus. [TFD][VHOG] 2012-09-17 VHOG:0001285 VHOG The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG] 2012-09-17 VHOG:0001285 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144 in FMA this is subdivided into basal and outer FMA UMLS:C0014180 ncithesaurus:Endometrium tunica mucosa (endometrium) FMA:17742 tunica mucosa uteri uterine endometrium BTO:0001422 uterine mucous membrane BTO:0001422 Outer serosa layer of the uterus. TODO - check for parallel structure with peritoneum EMAPA:37792 FMA:17744 MA:0001729 NCIT:C33298 UMLS:C0227824 perimetrium serous coat of uterus serous membrane of uterus tunica serosa (perimetrium) tunica serosa uteri uterine serosa uterus serosa uterus serous membrane visceral peritoneum of uterus uberon UBERON:0001297 serosa of uterus Illu:cervix.jpg Outer serosa layer of the uterus. EMAPA:37792 MA:th UMLS:C0227824 ncithesaurus:Perimetrium perimetrium serous coat of uterus serous membrane of uterus OBOL:automatic tunica serosa uteri FMA:17744 FMA:TA uterus serous membrane OBOL:automatic the conic expansion of the corpus spongiosum that forms the head of the penis glans BTO:0003118 EMAPA:18988 EV:0100108 FMA:18247 GAID:0000012 MA:0002726 NCIT:C12324 OpenCyc:Mx4rvdCpE5wpEbGdrcN5Y29ycA UMLS:C0227948 VHOG:0001475 uberon balanus coronal sulcus UBERON:0001299 glans penis Male:anatomy.png http://upload.wikimedia.org/wikipedia/commons/1/13/Anteriorglanspenis.jpg Bgee:AN the conic expansion of the corpus spongiosum that forms the head of the penis MGI:anna MP:0009102 glans EV:0100108 UMLS:C0227948 ncithesaurus:Glans_Penis balanus BTO:0003118 coronal sulcus the external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus. scrotal In elephants the testes remain in the abdomen In hedgehogs the testes remain in the inguinal canal In humans and some other mammals, the base of the scrotum becomes covered with pubic hair at puberty In marsupials, the scrotum is not homologous to the eutherian scrotum, and development is under the control of X-linked genes, not androgens In marsupials, the scrotum is positioned in the caudal area of the abdomen, in the same position as the pouch in females. It has been suggested that the pouch and marsupial scrotum are sexual homologs, but it is more likely they arise from different primordia in the same morphogenetic field The scrotum of marsupials is not homologous with the scrotum of mammals[ISBN:113945742X] BTO:0003098 CALOHA:TS-2341 EMAPA:19296 FMA:18252 GAID:393 MA:0000409 MESH:D012611 NCIT:C12785 OpenCyc:Mx4rwUC_upwpEbGdrcN5Y29ycA UMLS:C0036471 galen:Scrotum uberon UBERON:0001300 scrotum http://upload.wikimedia.org/wikipedia/commons/a/a6/Scrotum_warm_and_cold.jpg http://upload.wikimedia.org/wikipedia/en/thumb/3/3e/HairedHumanScrotum.png/200px-HairedHumanScrotum.png Wikipedia the external sac of skin that encloses the testes. It is an extension of the abdomen, and in placentals is located between the penis and anus. ISBN:0-683-40008-8 MP:0002669 In elephants the testes remain in the abdomen PMC1570914 NCBITaxon:9780 In hedgehogs the testes remain in the inguinal canal PMC1570914 NCBITaxon:9363 In humans and some other mammals, the base of the scrotum becomes covered with pubic hair at puberty NCBITaxon:9606 In marsupials, the scrotum is not homologous to the eutherian scrotum, and development is under the control of X-linked genes, not androgens NCBITaxon:9263 In marsupials, the scrotum is positioned in the caudal area of the abdomen, in the same position as the pouch in females. It has been suggested that the pouch and marsupial scrotum are sexual homologs, but it is more likely they arise from different primordia in the same morphogenetic field ISBN:113945742X NCBITaxon:9263 UMLS:C0036471 ncithesaurus:Scrotum the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens Kardong has epididymis in elasmobranch epididymal A similar, but probably non-homologous, structure is found in cartilaginous fishes Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells. BTO:0000408 CALOHA:TS-0285 EFO:0000982 EMAPA:19290 EV:0100103 FMA:18255 GAID:397 MA:0000397 MAT:0000130 MESH:A05.360.444.849.286 MIAA:0000130 NCIT:C12328 UMLS:C0014533 VHOG:0001265 galen:Epididymis uberon Nebenhoden@de UBERON:0001301 epididymis http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg FMA Wikipedia the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens MGI:pvb MP:0002631 A similar, but probably non-homologous, structure is found in cartilaginous fishes WP UMLS:C0014533 ncithesaurus:Epididymis Nebenhoden@de BTO:0000408 A fallopian tube that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern non-functional in monotremes[ISBN:978-0226870137] EMAPA:37369 FMA:18483 MA:0001717 NCIT:C33475 UMLS:C0227900 right fallopian tube right oviduct uberon UBERON:0001302 right uterine tube A fallopian tube that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37369 MA:th UMLS:C0227900 ncithesaurus:Right_Fallopian_Tube A fallopian tube that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37368 FMA:18484 MA:0001716 NCIT:C32959 UMLS:C0227902 left fallopian tube left oviduct uberon UBERON:0001303 left uterine tube A fallopian tube that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37368 MA:th UMLS:C0227902 ncithesaurus:Left_Fallopian_Tube layer of simple cuboidal cells covering surface of ovary[WP]. BTO:0004483 EHDAA:8126 EMAPA:17963 FMA:18629 MA:0001711 NCIT:C61518 RETIRED_EHDAA2:0001361 UMLS:C0227875 VHOG:0000630 epithelium superficiale (ovarium) germinal epithelium (female) ovarian surface epithelium ovary germinal epithelium surface epithelium of ovary uberon female coelomic epithelium ovary surface epithelium UBERON:0001304 Controversial - see article. Requires expert input. Also check BTO placement germinal epithelium of ovary layer of simple cuboidal cells covering surface of ovary[WP]. UMLS:C0227875 ncithesaurus:Ovarian_Surface_Epithelium germinal epithelium (female) ovarian surface epithelium BTO:0004483 female coelomic epithelium EMAPA:17384 ovary surface epithelium EMAPA:17963 A capsule that surrounds a female gonad. EMAPA:35626 FMA:18662 MA:0001706 NCIT:C49265 UMLS:C0227877 ovarian capsule ovary capsule uberon UBERON:0001307 capsule of ovary A capsule that surrounds a female gonad. OBOL:automatic UMLS:C0227877 ncithesaurus:Ovarian_Capsule The external iliac artery is a large artery in the pelvic region that carries blood to the lower limb. The external iliac artery is a paired artery, meaning there is one on each side of the body: a right external iliac artery and left external iliac artery. The external iliac artery is accompanied by the external iliac vein, which is located posterior to the artery. [WP,unvetted]. BTO:0004666 EHDAA2:0000463 EHDAA:4337 EMAPA:17614 FMA:18805 MA:0001973 NCIT:C32558 OpenCyc:Mx4rvkh47pwpEbGdrcN5Y29ycA UMLS:C0226398 galen:ExternalIliacArtery uberon arteria iliaca externa UBERON:0001308 external iliac artery http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray539.png MA The external iliac artery is a large artery in the pelvic region that carries blood to the lower limb. The external iliac artery is a paired artery, meaning there is one on each side of the body: a right external iliac artery and left external iliac artery. The external iliac artery is accompanied by the external iliac vein, which is located posterior to the artery. [WP,unvetted]. UMLS:C0226398 ncithesaurus:External_Iliac_Artery arteria iliaca externa The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted]. todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships BTO:0000841 CALOHA:TS-1077 EHDAA:1026 EHDAA:410 EMAPA:16331 EMAPA:16372 FMA:18820 GAID:516 MA:0002072 MESH:D014469 NCIT:C33827 OpenCyc:Mx4rCWdhMGWbEd2AAABQjYGu0g RETIRED_EHDAA2:0002106 UMLS:C0041632 uberon a. umbilicalis UBERON:0001310 umbilical artery https://github.com/obophenotype/uberon/issues/328 http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted]. UMLS:C0041632 ncithesaurus:Umbilical_Artery a. umbilicalis An artery that supplies blood to the upper urinary bladder. The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP] EMAPA:37123 FMA:18839 MA:0002080 NCIT:C52686 UMLS:C0226376 arteria vesicali superior arteria vesicalis superior uberon arteriae vesicales superiores UBERON:0001312 superior vesical artery https://upload.wikimedia.org/wikipedia/commons/0/02/Internal_iliac_branches.PNG An artery that supplies blood to the upper urinary bladder. EMAPA:37123 MA:th UMLS:C0226376 ncithesaurus:Superior_Vesical_Artery arteria vesicali superior arteria vesicalis superior arteriae vesicales superiores A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted]. EHDAA2:0000874 EMAPA:37148 FMA:18884 MA:0002139 MA:0002145 NCIT:C32847 UMLS:C0226764 VHOG:0000749 galen:InternalIliacVein uberon hypogastric vein v. hypogastrica v. iliaca interna UBERON:0001317 internal iliac vein http://upload.wikimedia.org/wikipedia/commons/c/cb/Internaliliacv.png MA A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted]. EMAPA:37148 MA:th UMLS:C0226764 ncithesaurus:Internal_Iliac_Vein hypogastric vein MA:0002139 v. hypogastrica v. iliaca interna One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified]. EMAPA:37796 FMA:18899 MA:0002251 vagina vein vein of vagina uberon UBERON:0001319 vaginal vein http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png FMA/obol One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified]. EMAPA:37796 MA:th vagina vein OBOL:automatic vein of vagina OBOL:automatic Muscle (organ) which is a part of the pelvis. Examples: levator ani, EMAPA:18184 EMAPA:37481 FMA:19086 MA:0000534 muscle organ of pelvis pelvic muscle pelvis muscle pelvis muscle organ uberon UBERON:0001325 muscle of pelvis FMAdef MA Muscle (organ) which is a part of the pelvis. Examples: levator ani, FMA:19086 EMAPA:37481 MA:th muscle organ of pelvis OBOL:automatic pelvic muscle FMA:19086 pelvis muscle organ OBOL:automatic A portion of a prostate that forms a lobe. Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue BTO:0000548 EMAPA:35712 FMA:19570 MA:0001738 NCIT:C52726 UMLS:C0227970 lobe of prostate gland prostate gland lobe prostatic lobe uberon UBERON:0001328 lobe of prostate A portion of a prostate that forms a lobe. Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue UMLS:C0227970 ncithesaurus:Prostate_Gland_Lobe The pampiniform plexus is a network of many small veins found in the male spermatic cord. It is formed by the union of multiple spermatic veins from the back of the testis and tributaries from the epididymis. The veins of the plexus ascend along the cord in front of the ductus deferens. Below the subcutaneous inguinal ring they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins. These again unite to form a single vein, the testicular vein, which opens on the right side into the inferior vena cava, at an acute angle, and on the left side into the left renal vein, at a right angle. The pampinoform plexus forms the chief mass of the cord. In addition to its function in venous return from the testes, the pampiniform plexus also plays a role in the temperature regulation of the testes. It acts as a heat exchanger, cooling blood in adjacent arteries. An abnormal enlargement of the pampiniform plexus is a medical condition called varicocele. [WP,unvetted]. EMAPA:37385 FMA:19607 MA:0001866 pampiniform venous plexus plexus of veins of fascia of prostate plexus venosus pampiniformis venous plexus of fascia of prostate venous plexus of fascia of prostate gland uberon UBERON:0001330 pampiniform plexus http://upload.wikimedia.org/wikipedia/commons/a/af/Gray1147.png The pampiniform plexus is a network of many small veins found in the male spermatic cord. It is formed by the union of multiple spermatic veins from the back of the testis and tributaries from the epididymis. The veins of the plexus ascend along the cord in front of the ductus deferens. Below the subcutaneous inguinal ring they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins. These again unite to form a single vein, the testicular vein, which opens on the right side into the inferior vena cava, at an acute angle, and on the left side into the left renal vein, at a right angle. The pampinoform plexus forms the chief mass of the cord. In addition to its function in venous return from the testes, the pampiniform plexus also plays a role in the temperature regulation of the testes. It acts as a heat exchanger, cooling blood in adjacent arteries. An abnormal enlargement of the pampiniform plexus is a medical condition called varicocele. [WP,unvetted]. EMAPA:37385 MA:th plexus venosus pampiniformis FMA:19607 FMA:TA A zone of skin that is part of a penis [Automatically generated definition]. EMAPA:35675 FMA:19638 MA:0002727 penile skin penis skin penis zone of skin zone of skin of penis uberon UBERON:0001331 skin of penis A zone of skin that is part of a penis [Automatically generated definition]. OBOL:automatic penile skin FMA:19638 penis zone of skin OBOL:automatic zone of skin of penis OBOL:automatic A retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect. prepuce preputium BTO:0001113 CALOHA:TS-0383 EFO:0001664 EMAPA:18989 EV:0100109 FMA:19639 MA:0000407 NCIT:C33049 OpenCyc:Mx4rvVjlTZwpEbGdrcN5Y29ycA UMLS:C0227952 penile prepuce prepuce of male preputium penis uberon foreskin praeputium prepucium UBERON:0001332 prepuce of penis Foreskin:CloseupV2.jpg http://upload.wikimedia.org/wikipedia/en/thumb/c/cc/Foreskin2.jpg/200px-Foreskin2.jpg A retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect. prepuce MA:0000407 preputium HP:0100587 UMLS:C0227952 ncithesaurus:Male_Prepuce penile prepuce FMA:19639 prepuce of male EMAPA:18989 preputium penis FMA:19639 FMA:TA foreskin FMA:19639 praeputium prepucium A urethra that is part of a male reproductive system. BTO:0004089 EMAPA:18692 FMA:19668 MA:0002640 NCIT:C33050 UMLS:C0458452 uberon UBERON:0001333 male urethra Female:anatomy.png A urethra that is part of a male reproductive system. UMLS:C0458452 ncithesaurus:Male_Urethra A urethra that is part of a female reproductive system. BTO:0004088 EMAPA:28747 FMA:19669 MA:0002637 NCIT:C32591 UMLS:C0458485 uberon urethra feminina urethra muliebris UBERON:0001334 female urethra Female:anatomy.png A urethra that is part of a female reproductive system. UMLS:C0458485 ncithesaurus:Female_Urethra urethra feminina BTO:0004088 urethra muliebris BTO:0004088 Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine NCIT:C12339 paraurethral gland belongs here EMAPA:37784 FMA:19683 MA:0001688 gland of urethra urethra gland urethra gland (male or female) urethral mucuous gland uberon UBERON:0001338 urethral gland MP Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine MP:anna NCIT:C12339 paraurethral gland belongs here NCIT EMAPA:37784 MA:th gland of urethra OBOL:automatic The tubules in the testes where spermatogenesis occurs. Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO] One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG] Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG] AAO:0010399 BTO:0001235 CALOHA:TS-1239 EFO:0001404 EMAPA:18685 EMAPA:31476 EV:0100380 FMA:19825 GAID:400 MA:0000412 MAT:0000503 MESH:D012671 NCIT:C13047 NCIT:C34293 UMLS:C0036630 UMLS:C1519236 VHOG:0001363 XAO:0003088 seminiferous cord seminiferous tubule testis - seminiferous tubule tubuli seminiferi uberon tubuli seminiferi UBERON:0001343 seminiferous tubule of testis http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg http://upload.wikimedia.org/wikipedia/commons/6/6a/Gray1145.png Wikipedia The tubules in the testes where spermatogenesis occurs. ISBN:0-683-40008-8 MGI:csmith MP:0002216 Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO] 2012-06-20 AAO:0010399 AAO AAO:BJB One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG] 2012-09-17 VHOG:0001363 VHOG Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG] 2012-09-17 VHOG:0001363 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 and Figure 21-28 UMLS:C0036630 ncithesaurus:Seminiferous_Tubule UMLS:C1519236 ncithesaurus:Seminiferous_Cord seminiferous cord EMAPA:18685 tubuli seminiferi The epithelial layer of the vagina. FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous) BTO:0000422 CALOHA:TS-1325 EMAPA:30991 FMA:19978 MA:0001730 NCIT:C49313 UMLS:C0920840 epithelial tissue of vagina vagina epithelial tissue vagina epithelium vaginal epithelium uberon epithelium, vaginal UBERON:0001344 epithelium of vagina The epithelial layer of the vagina. MP:0001140 FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous) FMA UMLS:C0920840 ncithesaurus:Vaginal_Epithelium epithelial tissue of vagina OBOL:automatic vagina epithelial tissue OBOL:automatic epithelium, vaginal BTO:0000422 The upper dilated end of the nasolacrimal duct that is lodged in a deep groove formed by the lacrimal bone and frontal process of the maxilla; it connects the lacrimal canaliculi, which drain tears from the eye's surface, and the nasolacrimal duct, which conveys this fluid into the nasal cavity; like the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue. FMA:20289 MA:0001298 NCIT:C32909 UMLS:C0229289 lachrymal sac lacrymal sac saccus lacrimalis uberon UBERON:0001351 lacrimal sac http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png The upper dilated end of the nasolacrimal duct that is lodged in a deep groove formed by the lacrimal bone and frontal process of the maxilla; it connects the lacrimal canaliculi, which drain tears from the eye's surface, and the nasolacrimal duct, which conveys this fluid into the nasal cavity; like the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue. MGI:anna UMLS:C0229289 ncithesaurus:Lacrimal_Sac saccus lacrimalis A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter. consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct. tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469] subdivision of head in FMA. EHDAA2:0000460 EHDAA:8975 EMAPA:17588 EV:0100356 FMA:61734 GAID:864 MA:0000260 MESH:D004424 NCIT:C12498 OpenCyc:Mx4rvli-nZwpEbGdrcN5Y29ycA UMLS:C0013444 VHOG:0000977 galen:ExternalAuditoryMeatus auditory canal ear canal external acoustic tube external auditory canal external auditory tube uberon auditory meatus external auditory meatus UBERON:0001352 external acoustic meatus FMA EHDAA2 A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter. subdivision of head in FMA. FMA UMLS:C0013444 ncithesaurus:External_Acoustic_Meatus ear canal external acoustic tube FMA:61734 external auditory tube FMA:61734 auditory meatus EHDAA2:0000460 The anus and surrounding regions. Encompasses both internal and external regions, where present Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 EHDAA2:0000122 EHDAA:2931 EMAPA:16831 MA:0000329 MAT:0000042 MIAA:0000042 NCIT:C32069 UMLS:C0230120 VHOG:0000395 WBbt:0006919 uberon posterior posterior end of organism UBERON:0001353 anal region https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png cjm The anus and surrounding regions. Encompasses both internal and external regions, where present Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000395 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0230120 ncithesaurus:Anal_Region The profunda femoris artery (also known as the deep femoral artery, or the deep artery of the thigh) is a branch of the femoral artery that, as its name suggests, travels more deeply (posteriorly) than the rest of the femoral artery. [WP,unvetted]. EMAPA:37216 FMA:20741 MA:0002027 NCIT:C32436 UMLS:C0226455 arteria profunda femoris profunda femoris artery uberon UBERON:0001355 deep femoral artery http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray548.png The profunda femoris artery (also known as the deep femoral artery, or the deep artery of the thigh) is a branch of the femoral artery that, as its name suggests, travels more deeply (posteriorly) than the rest of the femoral artery. [WP,unvetted]. EMAPA:37216 MA:th UMLS:C0226455 ncithesaurus:Deep_Femoral_Artery The medial circumflex femoral artery (internal circumflex artery, medial femoral circumflex artery) is an artery in the upper thigh that helps supply blood to the neck of the femur. [WP,unvetted]. EMAPA:37670 FMA:20799 MA:0001996 medial femoral circumflex artery uberon arteria circumflexa femoris medialis UBERON:0001356 medial circumflex femoral artery http://upload.wikimedia.org/wikipedia/commons/c/c5/Circumflex_femoral_arteries.png FMA The medial circumflex femoral artery (internal circumflex artery, medial femoral circumflex artery) is an artery in the upper thigh that helps supply blood to the neck of the femur. [WP,unvetted]. EMAPA:37670 MA:th arteria circumflexa femoris medialis A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6] Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO] In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG] EHDAA2 models this as developing from CP, which is wrong the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. BIRNLEX:1798 BTO:0000237 CALOHA:TS-0130 EFO:0000329 EHDAA2:0004441 ENVO:02000029 EV:0100311 FMA:20935 GAID:1181 MA:0002503 MAT:0000499 MESH:A12.207.268 NCIT:C12692 TAO:0002184 UMLS:C0007806 VHOG:0001278 ZFA:0001626 CSF cerebral spinal fluid uberon liquor cerebrospinalis spinal fluid UBERON:0001359 cerebrospinal fluid Wikipedia EHDAA2 see notes EHDAA2 A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO] 2012-08-14 TAO:0002184 TAO ZFIN:curator In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG] 2012-09-17 VHOG:0001278 VHOG DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005) EHDAA2 models this as developing from CP, which is wrong EHDAA2 the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. FMA UMLS:C0007806 BIRNLEX:1798 UMLS:C0007806 ncithesaurus:Cerebrospinal_Fluid cerebral spinal fluid ZFA:0001626 liquor cerebrospinalis spinal fluid BTO:0000237 The outer layer of peritoneum that is attached to the abdominal and pelvic walls. Peritoneum attached to the abdominal wall.[AAO] UBERON:0004459 AAO:0010816 EMAPA:16591 FMA:21451 TAO:0005131 VHOG:0001527 ZFA:0005131 parietal serous membrane of peritoneum uberon peritoneal cavity lining UBERON:0001366 parietal peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png The outer layer of peritoneum that is attached to the abdominal and pelvic walls. Peritoneum attached to the abdominal wall.[AAO] 2012-06-20 AAO:0010816 AAO AAO:JMG parietal serous membrane of peritoneum UBERON:cjm A muscle that is part of the region of the hindlimb between the pelvis and ankle. see notes on UBERON:0000978 for possible confusion over the term 'leg'. UBERON:0003270 BTO:0000722 EHDAA:8291 EMAPA:19144 EMAPA:19318 MA:0000672 RETIRED_EHDAA2:0000974 leg muscle leg muscle organ leg skeletal muscle leg skeletal muscle tissue muscle of hindlimb zeugopod or stylopod muscle of thigh or crus muscle of upper or lower hindlimb segment muscle of upper/lower leg muscle organ of leg skeletal muscle of leg uberon UBERON:0001383 muscle of leg prolog A muscle that is part of the region of the hindlimb between the pelvis and ankle. leg muscle organ OBOL:automatic leg skeletal muscle OBOL:automatic leg skeletal muscle tissue OBOL:automatic muscle of hindlimb zeugopod or stylopod OBOL:automatic muscle of thigh or crus OBOL:automatic muscle of upper or lower hindlimb segment OBOL:automatic muscle organ of leg OBOL:automatic skeletal muscle of leg OBOL:automatic A zone of skin that is part of a pelvis [Automatically generated definition]. EMAPA:37282 FMA:22984 MA:0000546 pelvic skin pelvis skin pelvis zone of skin zone of skin of pelvis uberon UBERON:0001415 skin of pelvis A zone of skin that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37282 MA:th pelvis zone of skin OBOL:automatic zone of skin of pelvis OBOL:automatic A zone of skin that is part of an abdomen [Automatically generated definition]. EFO:0000214 FMA:22988 FMA:23000 MA:0000523 NCIT:C52758 UMLS:C0222166 abdomen skin abdomen zone of skin abdominal skin skin of abdomen proper zone of skin of abdomen uberon UBERON:0001416 skin of abdomen A zone of skin that is part of an abdomen [Automatically generated definition]. OBOL:automatic UMLS:C0222166 ncithesaurus:Abdominal_Skin abdomen zone of skin OBOL:automatic skin of abdomen proper FMA:22988 zone of skin of abdomen OBOL:automatic A zone of skin that is part of a neck [Automatically generated definition]. EMAPA:37277 FMA:23021 FMA:23022 MA:0000590 NCIT:C52756 UMLS:C0205030 neck (volume) zone of skin neck skin neck zone of skin zone of skin of neck zone of skin of neck (volume) uberon UBERON:0001417 skin of neck A zone of skin that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37277 MA:th UMLS:C0205030 ncithesaurus:Neck_Skin neck (volume) zone of skin OBOL:automatic neck zone of skin OBOL:automatic zone of skin of neck OBOL:automatic zone of skin of neck (volume) OBOL:automatic A zone of skin that is part of a thorax [Automatically generated definition]. EMAPA:37765 FMA:23028 FMA:23029 MA:0000564 thoracic skin thorax skin thorax zone of skin zone of skin of thorax uberon upper body skin UBERON:0001418 skin of thorax A zone of skin that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37765 MA:th thorax zone of skin OBOL:automatic zone of skin of thorax OBOL:automatic A zone of skin that is part of a limb [Automatically generated definition]. EMAPA:32726 FMA:23100 MA:0000694 NCIT:C53276 UMLS:C1282135 limb skin limb zone of skin zone of skin of limb uberon UBERON:0001419 skin of limb A zone of skin that is part of a limb [Automatically generated definition]. OBOL:automatic UMLS:C1282135 ncithesaurus:Skin_of_the_Extremity limb zone of skin OBOL:automatic zone of skin of limb OBOL:automatic An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO] Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO] EMAPA:37856 FMA:23217 VSAO:0000305 galen:ShoulderGirdle cingulum membri superioris girdle - pectoral cingulum membri superioris shoulder girdle upper limb girdle uberon pectoral girdle pectoral region UBERON:0001421 pectoral girdle region An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. FMA:23217 UBERONREF:0000003 An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO] 2012-08-14 VSAO:0000305 VSAO Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO] 2012-09-06 VSAO:0000305 VSAO Curator EMAPA:37856 MA:th cingulum membri superioris FMA:23217 FMA:TA cingulum membri superioris FMA:TA shoulder girdle FMA:23217 upper limb girdle FMA:23217 A lymphatic vessel that is part of a face [Automatically generated definition]. FMA:233946 TAO:0005108 ZFA:0005108 buccal lymphatic vessel face lymph vessel face lymphatic vessel lymph vessel of face lymphatic vessel of face uberon FL UBERON:0001422 facial lymphatic vessel A lymphatic vessel that is part of a face [Automatically generated definition]. OBOL:automatic face lymph vessel OBOL:automatic face lymphatic vessel OBOL:automatic lymph vessel of face OBOL:automatic lymphatic vessel of face OBOL:automatic FMA:234865 TAO:0005107 ZFA:0005107 uberon PL UBERON:0001425 pectoral lymphatic vessel PL Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] System that provides physical support to the organism.[AAO] By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] skeletal GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 EFO:0000806 EHDAA2:0003168 EMAPA:35773 FMA:23881 MA:0000018 NCIT:C12788 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA TAO:0000434 UMLS:C0037253 VHOG:0001254 VSAO:0000027 XAO:0003060 ZFA:0000434 skeleton system set of all bones and joints uberon Skelettsystem UBERON:0001434 skeletal system https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. GO_REF:0000034 VSAO:0000027 Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] 2012-08-14 TAO:0000434 TAO TAO:wd Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] 2012-08-14 VSAO:0000027 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 System that provides physical support to the organism.[AAO] 2012-06-20 AAO:0000566 AAO AAO:LAP By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] 2012-09-17 VHOG:0001254 VHOG DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates GO UMLS:C0037253 ncithesaurus:Skeletal_System set of all bones and joints Skelettsystem BTO:0001486 A bone that is part of the carpal skeleton. Examples: scaphoid, lunate, capitate[cjm]. In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist. EMAPA:25056 FMA:23889 GAID:179 MA:0000296 MESH:A02.835.232.087.144 NCIT:C12688 UMLS:C0007285 galen:CarpalBone bone of carpus carpal carpal skeleton bone uberon carpus bone UBERON:0001435 carpal bone http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg A bone that is part of the carpal skeleton. Examples: scaphoid, lunate, capitate[cjm]. In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist. UMLS:C0007285 ncithesaurus:Carpal_Bone carpal PHENOSCAPE:ad carpus bone EMAPA:25056 A phalanx that is part of a forelimb autopod[Automatically generated definition]. Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the four digits of the manus. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the manus, in a medial to lateral sequence, is 2-2-3-3.[AAO] AAO:0000947 EMAPA:32650 FMA:23914 MA:0000306 NCIT:C52771 UMLS:C0223792 digitus manus phalanx finger phalanx hand digit phalanx hand phalanx manual phalanx phalanx of digit of hand phalanx of digitus manus phalanx of finger phalanx of fore digit phalanx of hand phalanx of hand digit phalanx of manual digit digital bone of manus uberon bone of finger phalanges of fore digit UBERON:0001436 phalanx of manus A phalanx that is part of a forelimb autopod[Automatically generated definition]. Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the four digits of the manus. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the manus, in a medial to lateral sequence, is 2-2-3-3.[AAO] 2012-06-20 AAO:0000947 AAO AAO:LAP UMLS:C0223792 ncithesaurus:Hand_Phalanx digitus manus phalanx OBOL:automatic finger phalanx OBOL:automatic hand digit phalanx OBOL:automatic hand phalanx MA:0000306 phalanx of digit of hand OBOL:automatic phalanx of digitus manus OBOL:automatic phalanx of finger FMA:23914 phalanx of hand digit OBOL:automatic digital bone of manus OBOL:automatic bone of finger FMA:23914 phalanges of fore digit AAO:0000947 The head of a long bone that articulates with a neighboring skeletal element and is separated from the shaft by the epiphyseal plate until bone growth stops. At that time, the plate disappears and the head and shaft are united[MESH,modified]. Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO] Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur. epiphyseal epiphysial AAO:0000742 BTO:0000413 EMAPA:35508 FMA:24012 MA:0001362 MESH:D004838 NCIT:C32529 NCIT:C52722 UMLS:C1708734 bone epiphysis end of long bone epiphyses long bone epiphysis uberon UBERON:0001437 epiphysis http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg The head of a long bone that articulates with a neighboring skeletal element and is separated from the shaft by the epiphyseal plate until bone growth stops. At that time, the plate disappears and the head and shaft are united[MESH,modified]. MESH:A02.835.232.251 Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO] 2012-06-20 AAO:0000742 AAO AAO:Pugener_2002 Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur. FMA:24012 UMLS:C1708734 ncithesaurus:Long_Bone_Epiphysis epiphyses Zone of long bone that is between the epiphysis and diaphysis. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA] todo - decide - adjacent to or containing epiphyseal plate? AO Notes: FMA the metaphysis is part of the diaphysis, but not in MA. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA] EMAPA:35509 FMA:24014 MA:0001363 NCIT:C52723 UMLS:C0222671 diaphyseal end of long bone long bone metaphysis metaphyses uberon UBERON:0001438 metaphysis Zone of long bone that is between the epiphysis and diaphysis. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA] FMA:24014 Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA] FMA:24014 UMLS:C0222671 ncithesaurus:Metaphysis metaphyses The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle TODO - find a home for: FMA:24139 ! skeleton of upper limb Skeletal structure of the paired, anterior appendages.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] AAO:0000202 EHDAA2:0002222 EMAPA:32623 FMA:24142 VHOG:0001256 VSAO:0000151 XAO:0003061 bones of upper limb fore limb skeleton forelimb skeleton free upper limb skeleton ossa membri superioris pectoral limb skeleton set of bones of upper limb skeleton of forelimb skeleton of free upper limb skeleton of pectoral limb skeleton of upper limb upper limb skeleton wing skeleton uberon UBERON:0001440 forelimb skeleton FMA The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle Skeletal structure of the paired, anterior appendages.[AAO] 2012-06-20 AAO:0000202 AAO AAO:LAP relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0000202 AAO Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001256 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 forelimb skeleton VHOG:0001256 free upper limb skeleton FMA:24142 ossa membri superioris FMA:24139 FMA:TA skeleton of free upper limb FMA:24142 skeleton of upper limb FMA:24139 upper limb skeleton EHDAA2:0002222 wing skeleton NCBITaxon:8782 OBOL:automatic Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. Skeletal structure of the paired, posterior appendages.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] AAO:0000217 EHDAA2:0002226 EMAPA:32633 FMA:24144 OpenCyc:Mx4rvZcKkZwpEbGdrcN5Y29ycA VHOG:0001255 VSAO:0000152 XAO:0003062 bones of lower limb free lower limb skeleton hind limb skeleton hind-limb skeleton hindlimb skeleton lower limb skeleton ossa membri inferioris set of bones of lower limb skeleton of free lower limb skeleton of lower limb uberon UBERON:0001441 TOOD - find a home for: FMA:24140 hindlimb skeleton FMA Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. Skeletal structure of the paired, posterior appendages.[AAO] 2012-06-20 AAO:0000217 AAO AAO:LAP relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0000217 AAO Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001255 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 free lower limb skeleton FMA:24144 hind limb skeleton XAO:0003062 hind-limb skeleton VSAO:0000152 hindlimb skeleton VHOG:0001255 ossa membri inferioris FMA:24140 FMA:TA skeleton of free lower limb FMA:24144 skeleton of lower limb FMA:24140 Subdivision of skeleton that is the collection of all skeletal elements in a manus, which is the distal section of the anterior forelimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the wrist, palm, and fingers)[Phenoscape]. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EHDAA2:0002227 EMAPA:32643 FMA:24159 OpenCyc:Mx4rvdHPJJwpEbGdrcN5Y29ycA VSAO:0005020 anterior autopodium skeleton bones of hand fore autopod skeleton forelimb autopod skeleton hand region skeleton hand skeleton manual skeleton manus skeleton ossa manus set of bones of hand skeleton of hand uberon anterior autopodium manus UBERON:0001442 here 'manus' includes both the wrist region, metatarsal region and acropodial region skeleton of manus EHDAA2 lexical Subdivision of skeleton that is the collection of all skeletal elements in a manus, which is the distal section of the anterior forelimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the wrist, palm, and fingers)[Phenoscape]. PHENOSCAPE:MAH bones of hand FMA:24159 hand region skeleton EHDAA2:0002227 hand skeleton FMA:24159 ossa manus FMA:24159 FMA:TA set of bones of hand FMA:24159 skeleton of hand FMA:24159 anterior autopodium VSAO:0005020 VSAO:NI manus VSAO:0005020 VSAO:NI Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]. FMA:24216 present in FMA1, but gone in subsequent versions pectoral thoracic BTO:0001368 CALOHA:TS-1039 EFO:0000965 EMAPA:37232 EV:0100010 FMA:9576 GAID:91 MA:0000031 MAT:0000295 MESH:A01.911 MIAA:0000295 NCIT:C12799 NCIT:C25389 OpenCyc:Mx4rvVikFZwpEbGdrcN5Y29ycA UMLS:C0817096 UMLS:C1527391 galen:Chest galen:Thorax anterolateral part of thorax front of thorax pectus ventral part of thoracic region uberon thoracic body wall thorax UBERON:0001443 chest http://upload.wikimedia.org/wikipedia/commons/d/db/Chest.jpg FMA-modified FMA MA Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]. FMA:9576 EMAPA:37232 MA:th UMLS:C0817096 ncithesaurus:Thorax UMLS:C1527391 ncithesaurus:Chest pectus FMA:24816 FMA:TA thoracic body wall MA:0000031 thorax thorax FMA:9576 FMA:24218 XAO:0000040 head subdivision uberon head region region of head UBERON:0001444 subdivision of head Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape]. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EHDAA2:0002228 FMA:24222 VSAO:0005021 foot region skeleton foot skeleton pedal skeleton pes skeleton posterior autopodium skeleton set of bones of foot skeleton of foot uberon pes posterior autopodium UBERON:0001445 here 'pes' includes both the ankle region, metatarsals and acropodial region skeleton of pes EHDAA2 lexical Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape]. PHENOSCAPE:MAH foot region skeleton EHDAA2:0002228 foot skeleton FMA:24222 set of bones of foot FMA:24222 skeleton of foot FMA:24222 pes VSAO:0005021 VSAO:NI posterior autopodium VSAO:0005021 VSAO:NI A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia. In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment BTO:0002343 EMAPA:25072 FMA:24491 GAID:194 MA:0000297 MESH:A02.835.232.300.710 NCIT:C12796 UMLS:C0039316 galen:TarsalBone ankle bone bone of ankle bone of tarsal skeleton bone of tarsus ossa tarsalia ossa tarsi uberon bony tarsus hind mesopodium tarsal tarsus osseus UBERON:0001447 tarsal bone Ankle:en.svg A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia. In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment UMLS:C0039316 ncithesaurus:Tarsal_Bone ankle bone FMA:24491 bone of ankle FMA:24491 bone of tarsal skeleton bone of tarsus FMA:24491 ossa tarsalia FMA:71339 FMA:TA ossa tarsi FMA:71339 FMA:TA bony tarsus BTO:0002343 hind mesopodium AAO:0000220 tarsal BTO:0002343 tarsus osseus BTO:0002343 The metatarsus or metatarsal bones are a group of five long bones in the pes located between the tarsal bones of the hind- and mid-pes and the phalanges of the toes. Lacking individual names, the metatarsal bones are numbered from the medial side (side of big toe): the first, second, third, fourth, and fifth metatarsal. The metatarsals are analogous to the metacarpal bones of the manus. [WP,unvetted]. BTO:0002347 EMAPA:32940 EMAPA:36159 FMA:24492 GAID:193 MA:0000303 MESH:A02.835.232.300.492 NCIT:C12752 UMLS:C0025584 galen:Metatarsal metatarsal uberon ossa metatarsalia ossa metatarsi UBERON:0001448 metatarsal bone http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png true The metatarsus or metatarsal bones are a group of five long bones in the pes located between the tarsal bones of the hind- and mid-pes and the phalanges of the toes. Lacking individual names, the metatarsal bones are numbered from the medial side (side of big toe): the first, second, third, fourth, and fifth metatarsal. The metatarsals are analogous to the metacarpal bones of the manus. [WP,unvetted]. UMLS:C0025584 ncithesaurus:Metatarsal_Bone ossa metatarsalia BTO:0002347 ossa metatarsi BTO:0002347 A phalanx that is part of a hindlimb autopod[Automatically generated definition]. Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO] UBERON:0004272 digital bone of pes AAO:0000930 EMAPA:32941 FMA:24493 MA:0000305 NCIT:C52772 UMLS:C0584876 ncithesaurus:Phalanx_of_the_Foot digitus pedis phalanx foot digit phalanx foot phalanx pedal phalanx phalanx of digit of foot phalanx of digitus pedis phalanx of foot digit phalanx of hind digit phalanx of pes phalanx of toe toe phalanx uberon bone of toe phalanges of hind digit UBERON:0001449 phalanx of pes A phalanx that is part of a hindlimb autopod[Automatically generated definition]. Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO] 2012-06-20 AAO:0000930 AAO AAO:LAP digital bone of pes OBOL:automatic UMLS:C0584876 ncithesaurus:Foot_Phalanx digitus pedis phalanx OBOL:automatic foot digit phalanx OBOL:automatic foot phalanx MA:0000305 phalanx of digit of foot OBOL:automatic phalanx of digitus pedis OBOL:automatic phalanx of foot digit OBOL:automatic phalanx of toe FMA:24493 toe phalanx OBOL:automatic bone of toe FMA:24493 phalanges of hind digit AAO:0000930 A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. The area that extends from the median ocellus to the oral foramen[HAO]. facial The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) BTO:0003369 CALOHA:TS-2216 EMAPA:32763 FMA:24728 GAID:64 HAO:0000316 MA:0002473 MESH:D005145 NCIT:C13071 OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA UMLS:C0015450 galen:Face uberon facia/facies visage UBERON:0001456 face http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. FMA:24728 The area that extends from the median ocellus to the oral foramen[HAO]. HAO:0000316 NCBITaxon:7399 The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf UMLS:C0015450 ncithesaurus:Face facia/facies visage BTO:0003369 A zone of skin that is part of a lip [Automatically generated definition]. EMAPA:37643 FMA:24764 MA:0001579 NCIT:C12291 UMLS:C0222101 lip skin lip zone of skin zone of skin of lip uberon skin of lips UBERON:0001458 skin of lip A zone of skin that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37643 MA:th UMLS:C0222101 ncithesaurus:Skin_of_the_Lip lip zone of skin OBOL:automatic zone of skin of lip OBOL:automatic skin of lips A zone of skin that is part of a external ear [Automatically generated definition]. EMAPA:35301 FMA:24775 MA:0001233 NCIT:C49481 UMLS:C0222110 auricular region of head zone of skin auricular region zone of skin ear skin external ear skin external ear zone of skin outer ear zone of skin zone of skin of auricular region zone of skin of auricular region of head zone of skin of external ear zone of skin of outer ear uberon UBERON:0001459 skin of external ear A zone of skin that is part of a external ear [Automatically generated definition]. OBOL:automatic UMLS:C0222110 ncithesaurus:Ear_Skin auricular region of head zone of skin OBOL:automatic auricular region zone of skin OBOL:automatic external ear zone of skin OBOL:automatic outer ear zone of skin OBOL:automatic zone of skin of auricular region OBOL:automatic zone of skin of auricular region of head OBOL:automatic zone of skin of external ear OBOL:automatic zone of skin of outer ear OBOL:automatic The part of the forelimb extending from the shoulder to the autopod[cjm]. currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand this class refers to the combination of the stylopod and zeugopod of a forelimb. Sometimes (cf FMA), 'arm' denotes the stylopod only; sometimes (cf MA), 'arm' denotes the part of the forelimb covering both (i.e. shoulder to hand). Also note distinction between arm and forelimb: hand is part of forelimb, but not part of arm Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] BTO:0001435 CALOHA:TS-2204 EFO:0001410 EHDAA2:0000140 EHDAA:4164 EHDAA:6210 EHDAA:8275 EMAPA:17413 GAID:52 MA:0000033 MESH:A01.378.800 MESH:D001132 OpenCyc:Mx4rvVjp5ZwpEbGdrcN5Y29ycA VHOG:0000339 uberon brachium upper extremity UBERON:0001460 arm http://upload.wikimedia.org/wikipedia/commons/e/ee/Upperarm.jpg The part of the forelimb extending from the shoulder to the autopod[cjm]. Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000339 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 brachium upper extremity MESH:A01.378.800 The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific]. cubital Naming conventions for pod terms under discussion within phenoscape group CALOHA:TS-2222 EFO:0003069 EHDAA2:0000429 EHDAA:4166 EHDAA:6212 EMAPA:17414 FMA:24901 GAID:54 MA:0000036 MESH:D004550 OpenCyc:Mx4rvVjjNZwpEbGdrcN5Y29ycA VHOG:0000340 galen:Elbow cubital region elbow limb segment elbow region uberon articulatio cubiti UBERON:0001461 elbow Elbow:coude.JPG EHDAA2 The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific]. articulatio cubiti 1st (preaxial) digit of the manus[Wikipedia]. Not present in Anurans (Phenotype RCN Oct 2012) This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit). digitus 1 digitus I digitus primus digitus primus [I] AAO:0010639 EHDAA2:0000511 EMAPA:17429 FMA:24938 GAID:58 MA:0000454 MESH:D013933 NCIT:C52834 OpenCyc:Mx4rvVjVbpwpEbGdrcN5Y29ycA UMLS:C0040067 digit 1 of fore-paw digit 1 of manus finger 1 first digit of hand fore digit I fore limb digit 1 hand digit 1 manual digit 1 manual digit I pollex alula forelimb dewclaw hand digit 1 thumb uberon first finger UBERON:0001463 manual digit 1 Thumbs:up.jpg http://upload.wikimedia.org/wikipedia/commons/6/64/Thumb-up.jpg 1st (preaxial) digit of the manus[Wikipedia]. PMCID:PMC2553264 This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit). NCBITaxon:8782 UBERON:0012260 PhenoscapeRCN digitus I digitus primus UMLS:C0040067 ncithesaurus:Hand_Digit_1 digit 1 of fore-paw EMAPA:17429 finger 1 EHDAA2:0000511 fore digit I AAO:0010639 fore limb digit 1 OBOL:accepted hand digit 1 MA:0000454 manual digit I pollex alula forelimb dewclaw hand digit 1 NCBITaxon:9606 OBOL:accepted thumb first finger EMAPA:17429 The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified]. The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] coxal See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint BTO:0001457 CALOHA:TS-2226 EFO:0001929 EHDAA2:0000783 EHDAA:5153 EHDAA:6178 EMAPA:17490 FMA:24964 GAID:47 MA:0000045 MESH:D006615 NCIT:C64193 OpenCyc:Mx4rvVjhy5wpEbGdrcN5Y29ycA UMLS:C0019552 VHOG:0000346 galen:Hip hip region regio coxae uberon coxa UBERON:0001464 hip http://upload.wikimedia.org/wikipedia/commons/9/9f/Hip.jpg FMA-modified The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified]. The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] 2012-09-17 VHOG:0000346 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333 See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint BTO UMLS:C0019552 ncithesaurus:Hip hip region FMA:24964 regio coxae FMA:24964 coxa A digit that is part of a pes (foot). UBERON:0000027 AAO:0000888 BTO:0002348 EMAPA:32649 FMA:25046 GAID:44 MA:0000048 NCIT:C33788 OpenCyc:Mx4rvVjCHZwpEbGdrcN5Y29ycA UMLS:C0040357 XAO:0003035 galen:Toe digit of foot digit of terminal segment of lower limb digiti pedis digitus pedis foot digit hind digit hind_digit hindlimb digit pedal digit (phalangeal portion) plus soft tissue pes digit toe uberon digiti pedis digitipedis UBERON:0001466 pedal digit http://upload.wikimedia.org/wikipedia/commons/5/5e/Toes.jpg PHENOSCAPE:ni A digit that is part of a pes (foot). UMLS:C0040357 ncithesaurus:Toe digit of terminal segment of lower limb OBOL:automatic digiti pedis FMA:70664 FMA:TA foot digit MA:0000048 hind digit XAO:0003035 hind_digit AAO:0000888 pedal digit (phalangeal portion) plus soft tissue toe FMA:25046 digiti pedis digitipedis BTO:0002348 A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle). (...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG] In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone CALOHA:TS-2229 EFO:0003068 EHDAA2:0001834 EHDAA:4180 EHDAA:6228 EMAPA:17421 FMA:25202 GAID:60 MA:0000038 MESH:D012782 NCIT:C25203 OpenCyc:Mx4rvViCM5wpEbGdrcN5Y29ycA UMLS:C0037004 VHOG:0000342 galen:Shoulder shoulder region uberon articulatio humeri UBERON:0001467 shoulder http://upload.wikimedia.org/wikipedia/commons/9/90/Shoulderjoint.PNG FMA-modified A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle). (...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG] 2012-09-17 VHOG:0000342 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332 In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone FMA UMLS:C0037004 ncithesaurus:Shoulder articulatio humeri 2 2 The joint between adjacent vertebral bodies. May be composed of the nucleus pulposus, annular ligament, and the anterior and posterior longitudinal ligaments. FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra vertebral joint EMAPA:37622 FMA:25511 MA:0001514 NCIT:C49577 UMLS:C1182940 inter-centrum joint inter-vertebral joint intervertebral symphysis joint of vertebral body uberon UBERON:0001468 intervertebral joint FMA FMA connects successive pairs of centra The joint between adjacent vertebral bodies. May be composed of the nucleus pulposus, annular ligament, and the anterior and posterior longitudinal ligaments. FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra FMA EMAPA:37622 MA:th UMLS:C1182940 ncithesaurus:Vertebral_Joint intervertebral symphysis FMA:25511 joint of vertebral body FMA:25511 The glenohumeral joint, commonly known as the shoulder joint, is a multiaxial synovial ball and socket joint and involves articulation between the glenoid fossa of the scapula (shoulder blade) and the head of the humerus (upper arm bone). [WP,unvetted]. note that in this ontology 'glenoid fossa' is a cavity (consistent with FMA) - consider adding a class for the surface of the scapula that is adjacent to this cavity, and making a more explicit connects relationship in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle joint of shoulder shoulder joint EMAPA:19105 FMA:25912 GAID:269 MA:0000459 MESH:D012785 NCIT:C33548 OpenCyc:Mx4rwP32BZwpEbGdrcN5Y29ycA UMLS:C0037009 VHOG:0001002 galen:ShoulderJoint articulatio humeri humeral joint uberon humeroscapular joint UBERON:0001470 glenohumeral joint http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray327.png FMA The glenohumeral joint, commonly known as the shoulder joint, is a multiaxial synovial ball and socket joint and involves articulation between the glenoid fossa of the scapula (shoulder blade) and the head of the humerus (upper arm bone). [WP,unvetted]. in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle FMA joint of shoulder OBOL:automatic shoulder joint MA:0000459 UMLS:C0037009 ncithesaurus:Shoulder_Joint articulatio humeri FMA:25912 FMA:TA humeral joint FMA:25912 humeroscapular joint the loose fold of skin that covers the penis EV:0100109 FMA:27648 MA:0001744 VHOG:0001342 foreskin of penis penis foreskin preputial skin uberon UBERON:0001471 skin of prepuce of penis the loose fold of skin that covers the penis MP:0003553 NCBI:matt The vaginal plexuses are placed at the sides of the vagina; they communicate with the uterine, vesical, and hemorrhoidal plexuses, and are drained by the vaginal veins, one on either side, into the hypogastric veins. [WP,unvetted]. EMAPA:37801 FMA:29713 MA:0002257 venous vaginal plexus uberon plexus venosus vaginalis UBERON:0001472 vaginal venous plexus http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png The vaginal plexuses are placed at the sides of the vagina; they communicate with the uterine, vesical, and hemorrhoidal plexuses, and are drained by the vaginal veins, one on either side, into the hypogastric veins. [WP,unvetted]. EMAPA:37801 MA:th plexus venosus vaginalis A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]. A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] A vessel that contains or conveys lymph.[AAO] Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] AAO:0011005 BTO:0000752 CALOHA:TS-2102 EFO:0000873 EMAPA:35532 FMA:30315 MA:0000138 MAT:0000443 NCIT:C33038 OpenCyc:Mx4rwA1fYZwpEbGdrcN5Y29ycA TAO:0005105 UMLS:C0229889 VHOG:0001249 XAO:0000375 lymph vessel uberon vas lymphaticum UBERON:0001473 lymphatic vessel http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]. BTO:0000752 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] 2012-08-14 TAO:0005105 TAO ZFIN:curator A vessel that contains or conveys lymph.[AAO] 2012-06-20 AAO:0011005 AAO AAO:EJS Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] 2012-09-17 VHOG:0001249 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627 UMLS:C0229889 ncithesaurus:Lymphatic_Vessel vas lymphaticum Skeletal element that is composed of bone tissue. Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] Skeletal element that is composed of bone tissue.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] AAO:0000047 AEO:0000082 BTO:0000140 CALOHA:TS-0088 EFO:0000298 EHDAA2:0003082 EMAPA:32782 ENVO:00002039 EV:0100140 FMA:30317 FMA:5018 GAID:92 MA:0001459 MAT:0000299 MIAA:0000299 NCIT:C12366 OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA TAO:0001514 UMLS:C0262950 VHOG:0001190 VSAO:0000057 XAO:0000169 ZFA:0001514 galen:Bone bone bone organ uberon bone bones UBERON:0001474 bone element VSAO-modified Skeletal element that is composed of bone tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000057 Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] 2012-06-20 AAO:0000047 AAO AAO:LAP Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] 2012-08-14 TAO:0001514 TAO ZFIN:curator Skeletal element that is composed of bone tissue.[VSAO] 2012-08-14 VSAO:0000057 VSAO PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000047 AAO The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] 2012-09-17 VHOG:0001190 VHOG DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) UMLS:C0262950 ncithesaurus:Bone bone organ FMA:5018 bone AEO:0000082 BTO:0000140 MA:0001459 VHOG:0001190 bones ZFA:0001514 A carpal bone that proximally_connected_to a forelimb zeugopod skeleton. EMAPA:36164 FMA:33302 MA:0002557 uberon UBERON:0001480 proximal carpal bone A carpal bone that proximally_connected_to a forelimb zeugopod skeleton. OBOL:automatic Any muscle organ that is part of a shoulder [Automatically generated definition]. EMAPA:36154 FMA:33531 MA:0000633 muscle organ of shoulder shoulder muscle shoulder muscle organ uberon UBERON:0001482 muscle of shoulder prolog Any muscle organ that is part of a shoulder [Automatically generated definition]. OBOL:automatic muscle organ of shoulder OBOL:automatic shoulder muscle organ OBOL:automatic A zone of skin that is part of a shoulder region. in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon EMAPA:18059 FMA:34830 MA:0000635 shoulder skin shoulder zone of skin zone of skin of shoulder uberon UBERON:0001483 skin of shoulder A zone of skin that is part of a shoulder region. UBERONREF:0000003 in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon MA shoulder zone of skin OBOL:automatic zone of skin of shoulder OBOL:automatic An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita EMAPA:37621 FMA:34836 GAID:263 MA:0001519 MESH:D017746 NCIT:C32259 NCIT:C84388 UMLS:C0206207 galen:JointCapsule capsula articularis fibrous capsule of joint joint capsule joint fibrous capsule uberon capsulae articulares UBERON:0001484 articular capsule http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita ncit EMAPA:37621 MA:th UMLS:C0206207 ncithesaurus:Joint_Capsule capsula articularis FMA:34836 FMA:TA capsulae articulares A synovial joint that connects the femur to the acetbulum of the innominate bone. BTO:0001502 EMAPA:19136 FMA:35178 GAID:262 MA:0000470 MESH:D006621 NCIT:C32742 OpenCyc:Mx4rwP32b5wpEbGdrcN5Y29ycA UMLS:C0019558 VHOG:0001001 galen:HipJoint articulatio coxofemoralis femoro-iliac joint uberon coxal articulation UBERON:0001486 hip joint FMA FMA definitional A synovial joint that connects the femur to the acetbulum of the innominate bone. UMLS:C0019558 ncithesaurus:Hip_Joint articulatio coxofemoralis FMA:35178 coxal articulation A skeletal joint that is part of a pes [Automatically generated definition]. TODO check FMA - use the set class for now EMAPA:32949 FMA:35194 GAID:256 MA:0000464 MESH:D033023 articulationes pedis foot joint hind limb autopod joint joint of pes joint of terminal segment of free lower limb joints of foot pedal joint uberon UBERON:0001487 pes joint A skeletal joint that is part of a pes [Automatically generated definition]. OBOL:automatic articulationes pedis FMA:71349 FMA:TA hind limb autopod joint OBOL:automatic joint of terminal segment of free lower limb OBOL:automatic joints of foot FMA:71349 A joint that connects the hindlimb autopod and zeugopod skeletons. todo - accurately represent different types of ankle joint BTO:0004706 EMAPA:35126 FMA:35195 GAID:257 MA:0000463 MESH:D000843 NCIT:C32078 OpenCyc:Mx4rvwiy35wpEbGdrcN5Y29ycA UMLS:C0003087 galen:AnkleJoint gambrel hock hock joint talotibial joint uberon mortise joint talocrural articulation talocrural joint UBERON:0001488 ankle joint Ankle:en.svg A joint that connects the hindlimb autopod and zeugopod skeletons. MESH:A02.835.583.378.062 UMLS:C0003087 ncithesaurus:Ankle_Joint gambrel hock hock joint talotibial joint mortise joint BTO:0004706 talocrural articulation talocrural joint A skeletal joint that is part of a manus (hand) [Automatically generated definition]. TODO check FMA - use the set class for now EMAPA:32641 MA:0000452 articulationes manus hand joint joint of hand joint of manus joint of terminal segment of free upper limb manual joint uberon UBERON:0001489 manus joint A skeletal joint that is part of a manus (hand) [Automatically generated definition]. OBOL:automatic articulationes manus FMA:71345 FMA:TA joint of terminal segment of free upper limb OBOL:automatic A joint that connects the forelimb zeugopod and stylopod skeletons[Obol]. In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis EMAPA:19102 FMA:35289 GAID:253 MA:0000451 MESH:D004551 NCIT:C32497 UMLS:C0013770 VHOG:0000997 galen:ElbowJoint articulatio cubiti cubital region joint joint of cubital region joint of elbow uberon UBERON:0001490 elbow joint definitional A joint that connects the forelimb zeugopod and stylopod skeletons[Obol]. In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis HP UMLS:C0013770 ncithesaurus:Elbow_Joint articulatio cubiti cubital region joint OBOL:automatic joint of cubital region OBOL:automatic joint of elbow OBOL:automatic A joint connecting the forelimb zeugopod skeleton with the carpal skeleton. in FMA this includes radio-carpal and radio-ulnar *ligaments* EMAPA:19205 FMA:321842 GAID:274 MA:0000460 MESH:A02.835.583.959 NCIT:C33894 OpenCyc:Mx4rvZD2PJwpEbGdrcN5Y29ycA UMLS:C1322271 galen:WristJoint carpal region joint joint of carpal region joint of wrist radiocarpal joint uberon UBERON:0001491 wrist joint Human:wrist.png A joint connecting the forelimb zeugopod skeleton with the carpal skeleton. in FMA this includes radio-carpal and radio-ulnar *ligaments* FMA UMLS:C1322271 ncithesaurus:Wrist_Joint carpal region joint OBOL:automatic joint of carpal region OBOL:automatic radiocarpal joint FMA:35291 Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. UBERON:0003271 EHDAA:8326 EMAPA:18184 EMAPA:18185 FMA:37367 MA:0000537 RETIRED_EHDAA2:0001430 girdle-pelvic muscle organ muscle organ of girdle-pelvic muscle organ of pelvic girdle muscle organ of pelvic girdle bone pelvic girdle muscle pelvic girdle muscle organ pelvic girdle skeletal muscle uberon UBERON:0001497 muscle of pelvic girdle Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. MA girdle-pelvic muscle organ OBOL:automatic muscle organ of girdle-pelvic OBOL:automatic muscle organ of pelvic girdle OBOL:automatic muscle organ of pelvic girdle bone OBOL:automatic pelvic girdle muscle organ OBOL:automatic pelvic girdle skeletal muscle EMAPA:18185 Any muscle organ that is part of a pes [Automatically generated definition]. BTO:0000477 EMAPA:36160 FMA:37369 MA:0000652 foot muscle foot muscle organ muscle of foot muscle organ of foot uberon UBERON:0001498 muscle of pes prolog Any muscle organ that is part of a pes [Automatically generated definition]. OBOL:automatic foot muscle organ OBOL:automatic muscle of foot FMA:37369 muscle organ of foot OBOL:automatic A muscle organ that is part of an arm [Automatically generated definition]. See notes on UBERON:0001460 for possible terminological confusion over term 'arm'. MA uses this consistent with uberon (forelimb muscle is subdivided into shoulder, arm and hand) UBERON:0003272 EHDAA:8277 EMAPA:36053 MA:0000594 RETIRED_EHDAA2:0000142 arm muscle arm skeletal muscle arm skeletal muscle tissue muscle of upper arm or lower arm upper arm / lower arm muscle uberon arm muscle system UBERON:0001499 muscle of arm A muscle organ that is part of an arm [Automatically generated definition]. OBOL:automatic arm muscle MA:0000594 arm skeletal muscle OBOL:automatic arm skeletal muscle tissue OBOL:automatic muscle of upper arm or lower arm upper arm / lower arm muscle arm muscle system EHDAA2:0000141 Any muscle organ that is part of a manus [Automatically generated definition]. EMAPA:32644 FMA:37372 MA:0000628 hand muscle manus muscle manus muscle organ muscle of hand muscle organ of manus uberon UBERON:0001500 muscle of manus prolog Any muscle organ that is part of a manus [Automatically generated definition]. OBOL:automatic hand muscle MA:0000628 manus muscle organ OBOL:automatic muscle of hand FMA:37372 muscle organ of manus OBOL:automatic A zone of skin that is part of a leg [Automatically generated definition]. EMAPA:18156 EMAPA:18159 EMAPA:37352 FMA:37828 MA:0000674 NCIT:C52749 UMLS:C0222279 leg skin leg zone of skin zone of skin of leg uberon UBERON:0001511 skin of leg A zone of skin that is part of a leg [Automatically generated definition]. OBOL:automatic EMAPA:37352 MA:th UMLS:C0222279 ncithesaurus:Leg_Skin leg zone of skin OBOL:automatic zone of skin of leg OBOL:automatic A zone of skin that is part of an ankle [Automatically generated definition]. EMAPA:37353 FMA:37831 MA:0000641 NCIT:C52751 UMLS:C0222286 ankle skin ankle zone of skin tarsal region skin zone of skin of ankle uberon UBERON:0001512 skin of ankle A zone of skin that is part of an ankle [Automatically generated definition]. OBOL:automatic EMAPA:37353 MA:th UMLS:C0222286 ncithesaurus:Ankle_Skin ankle zone of skin OBOL:automatic tarsal region skin zone of skin of ankle OBOL:automatic A zone of skin that is part of a pes [Automatically generated definition]. EMAPA:18504 FMA:37834 MA:0000654 NCIT:C52750 UMLS:C0222289 foot skin skin of foot skin of hind-paw uberon UBERON:0001513 skin of pes MA A zone of skin that is part of a pes [Automatically generated definition]. OBOL:automatic UMLS:C0222289 ncithesaurus:Foot_Skin skin of foot FMA:37834 skin of hind-paw EMAPA:18504 The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. results from fusion of left and right dorsal aortae EMAPA:18606 FMA:3784 MA:0002571 NCIT:C32455 OpenCyc:Mx4rv4EE35wpEbGdrcN5Y29ycA UMLS:C0011666 pars descendens aortae uberon aorta descendens pars descendens aortae UBERON:0001514 descending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA Wikipedia The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. GO:0035906 UMLS:C0011666 ncithesaurus:Descending_Aorta pars descendens aortae FMA:3784 aorta descendens aorta descendens pars descendens aortae the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest BTO:0000157 EFO:0002525 EMAPA:18603 FMA:3786 GAID:471 MA:0002569 MESH:D001013 NCIT:C33766 OpenCyc:Mx4rveb9TpwpEbGdrcN5Y29ycA UMLS:C1522460 galen:ThoracicAorta aorta thoracica thoracic part of aorta uberon aorta thoracalis pars thoracica aortae UBERON:0001515 thoracic aorta http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png FMA the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest MP:0010468 UMLS:C1522460 ncithesaurus:Thoracic_Aorta aorta thoracica FMA:3786 FMA:TA aorta thoracalis pars thoracica aortae Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates BTO:0002976 EFO:0002524 EMAPA:17856 FMA:3789 GAID:470 MA:0000474 MESH:D001012 NCIT:C32038 OpenCyc:Mx4rvYhWCZwpEbGdrcN5Y29ycA UMLS:C0003484 galen:AbdominalAorta abdominal part of aorta descending abdominal aorta pars abdominalis aortae uberon abdominal part of aorta aorta abdominalis pars abdominalis aortae UBERON:0001516 abdominal aorta http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png FMA Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. BTO:0002976 UMLS:C0003484 ncithesaurus:Abdominal_Aorta abdominal part of aorta FMA:3789 descending abdominal aorta FMA:3789 pars abdominalis aortae FMA:3789 abdominal part of aorta BTO:0002976 aorta abdominalis aorta abdominalis BTO:0002976 pars abdominalis aortae pars abdominalis aortae BTO:0002976 A zone of skin that is part of a elbow [Automatically generated definition]. UBERON:0003399 EMAPA:18051 FMA:38250 MA:0000610 NCIT:C52755 UMLS:C0222213 cubital region zone of skin elbow skin elbow zone of skin zone of skin of cubital region zone of skin of elbow uberon UBERON:0001517 skin of elbow A zone of skin that is part of a elbow [Automatically generated definition]. OBOL:automatic UMLS:C0222213 ncithesaurus:Elbow_Skin cubital region zone of skin OBOL:automatic elbow zone of skin OBOL:automatic zone of skin of cubital region OBOL:automatic zone of skin of elbow OBOL:automatic A zone of skin that is part of a wrist [Automatically generated definition]. EMAPA:37351 FMA:38280 MA:0000638 NCIT:C52752 UMLS:C0222223 carpal region zone of skin wrist skin wrist zone of skin zone of skin of carpal region zone of skin of wrist uberon UBERON:0001518 skin of wrist A zone of skin that is part of a wrist [Automatically generated definition]. OBOL:automatic EMAPA:37351 MA:th UMLS:C0222223 ncithesaurus:Wrist_Skin carpal region zone of skin OBOL:automatic wrist zone of skin OBOL:automatic zone of skin of carpal region OBOL:automatic zone of skin of wrist OBOL:automatic A zone of skin that is part of a manus [Automatically generated definition]. EMAPA:18486 FMA:38295 MA:0000630 NCIT:C52753 UMLS:C0222224 hand skin manus skin skin of hand skin of fore-paw uberon UBERON:0001519 skin of manus A zone of skin that is part of a manus [Automatically generated definition]. OBOL:automatic UMLS:C0222224 ncithesaurus:Hand_Skin hand skin MA:0000630 skin of hand FMA:38295 skin of fore-paw EMAPA:18486 A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery' This class represents the adult and developing structures' in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae carotid artery CALOHA:TS-0116 EHDAA2:0000217 EHDAA:7331 EMAPA:17855 FMA:3939 GAID:479 MA:0001926 MESH:D017536 NCIT:C32352 UMLS:C0162859 VHOG:0000272 carotid artery system common carotid artery trunk of common carotid tree uberon a. carotis communis UBERON:0001530 common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA Wikipedia A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. carotid artery FMA:3939 UMLS:C0162859 ncithesaurus:Common_Carotid_Artery carotid artery system EHDAA2:0000217 common carotid artery FMA:3939 trunk of common carotid tree FMA:3939 a. carotis communis The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk. placement of the MA class here is not strictly correct, as the MA class does not include the branches EMAPA:35749 FMA:3941 MA:0001928 NCIT:C33473 OpenCyc:Mx4rtW9-AqgEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvg7rcJwpEbGdrcN5Y29ycA UMLS:C0226086 right common carotid artery trunk of right common carotid tree uberon right common carotid artery UBERON:0001531 right common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk. UBERON:cjm UMLS:C0226086 ncithesaurus:Right_Common_Carotid_Artery right common carotid artery MA:0001928 trunk of right common carotid tree FMA:3941 right common carotid artery FMA:3941 A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP] Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG] One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO] AAO:0010219 AAO:0011054 BTO:0004697 EFO:0001952 EHDAA2:0000873 EHDAA:408 EHDAA:6389 EMAPA:16328 FMA:3947 GAID:481 MA:0001930 MESH:D002343 NCIT:C32836 OpenCyc:Mx4rvYx8KZwpEbGdrcN5Y29ycA TAO:0005081 UMLS:C0007276 VHOG:0000267 XAO:0000366 ZFA:0005081 cranial carotid artery internal carotid uberon ICA arteria carotis interna UBERON:0001532 internal carotid artery http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png MA cjm FMA A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP] MGI:anna Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG] 2012-09-17 VHOG:0000267 VHOG One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO] 2012-06-20 AAO:0011054 AAO UMLS:C0007276 ncithesaurus:Internal_Carotid_Artery cranial carotid artery ZFA:0005081 internal carotid AAO:0010219 ICA arteria carotis interna One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO) Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO] In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP] The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO] AAO:0010232 EHDAA2:0001933 EHDAA:4357 EMAPA:17617 FMA:3951 GAID:511 MA:0002045 MESH:D013348 NCIT:C33643 OpenCyc:Mx4rvp8u1JwpEbGdrcN5Y29ycA TAO:0005086 UMLS:C0038530 XAO:0000365 ZFA:0005086 arteria subclavia arterial tree of upper limb pectoral artery subclavian arterial tree uberon PA arteria subclavia UBERON:0001533 subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg EHDAA2 EHDAA2 One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta ISBN:0073040584 Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO] 2012-06-20 AAO:0010232 AAO AAO:BJB In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP] The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO] 2012-08-14 TAO:0005086 TAO ZFIN:curator UMLS:C0038530 ncithesaurus:Subclavian_Artery arteria subclavia XAO:0000365 PA arteria subclavia The subclavian artery that supplies the right pectoral appendage in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery proximal part arises from right 4th aortic arch in humans EHDAA2:0004514 EMAPA:37384 FMA:3953 MA:0002047 NCIT:C33490 OpenCyc:Mx4rtW7hwqgEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvp8u1JwpEbGdrcN5Y29ycA UMLS:C0226261 arteria subclavia dextra uberon UBERON:0001534 right subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg The subclavian artery that supplies the right pectoral appendage EMAPA:37384 MA:th UMLS:C0226261 ncithesaurus:Right_Subclavian_Artery arteria subclavia dextra FMA:3953 FMA:TA The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax. placement of the MA class here is not strictly correct, as the MA class does not include the branches EMAPA:35491 FMA:4058 MA:0001927 NCIT:C32956 OpenCyc:Mx4rdz4xcLVIEduAAAAOpmP6tw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvg7rcJwpEbGdrcN5Y29ycA UMLS:C0226087 left common carotid artery trunk of left common carotid tree uberon left common carotid artery UBERON:0001536 left common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax. UBERON:cjm UMLS:C0226087 ncithesaurus:Left_Common_Carotid_Artery left common carotid artery MA:0001927 trunk of left common carotid tree FMA:4058 left common carotid artery FMA:4058 The dorsal metatarsal veins are veins which drain the metatarsus of the foot. [WP,unvetted]. EMAPA:37143 FMA:44377 MA:0002105 NCIT:C52689 UMLS:C0835053 metatarsal vein uberon venae metatarsales dorsales UBERON:0001549 dorsal metatarsal vein The dorsal metatarsal veins are veins which drain the metatarsus of the foot. [WP,unvetted]. EMAPA:37143 MA:th UMLS:C0835053 ncithesaurus:Dorsal_Metatarsal_Vein venae metatarsales dorsales A zone of skin that is part of a hip region. in MA this isa hindlimb skin EMAPA:18148 FMA:45282 MA:0000658 hip region zone of skin hip skin hip zone of skin regio coxae zone of skin zone of skin of hip zone of skin of hip region zone of skin of regio coxae uberon UBERON:0001554 skin of hip A zone of skin that is part of a hip region. UBERONREF:0000003 in MA this isa hindlimb skin MA hip region zone of skin OBOL:automatic hip zone of skin OBOL:automatic regio coxae zone of skin OBOL:automatic zone of skin of hip OBOL:automatic zone of skin of hip region OBOL:automatic zone of skin of regio coxae OBOL:automatic A tube extending from the mouth to the anus. The alimentary or digestive tract, and associated organs.[TAO] The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] FMA also has a term 'gastrointestinal tract', but this includes the liver. we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 BTO:0000511 BTO:0000545 EHDAA2:0000726 EHDAA:518 EMAPA:16247 FBbt:00003125 FMA:45615 MA:0000917 NCIT:C34082 OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA TAO:0000112 TGMA:0001819 UMLS:C0017189 VHOG:0000309 WBbt:0005743 ZFA:0000112 galen:AlimentaryTract digestive tube enteric tract alimentary canal alimentary tract uberon digestive canal gut tube UBERON:0001555 digestive tract NCBIBook:NBK10107 A tube extending from the mouth to the anus. A tube extending from the mouth to the anus. The alimentary or digestive tract, and associated organs.[TAO] 2012-08-14 TAO:0000112 TAO ZFIN:curator The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000309 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 FMA also has a term 'gastrointestinal tract', but this includes the liver. FMA we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 MA UMLS:C0017189 ncithesaurus:Gastrointestinal_Tract enteric tract ZFA:0000112 digestive canal BTO:0000058 Subdivision of urinary system which consists of the urinary bladder and the urethra. FMA:45659 MA:0002636 galen:LowerUrinaryTract uberon UBERON:0001556 lower urinary tract Subdivision of urinary system which consists of the urinary bladder and the urethra. FMA:45659 upper respiratory tract The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] EHDAA2:0002136 EMAPA:17669 FMA:45661 MA:0000442 OpenCyc:Mx4rtT2HwgJMEdyAAADggVbxzQ VHOG:0000406 uberon UBERON:0001557 upper respiratory tract http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] FMA The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] EHDAA2:0001036 EMAPA:16738 FMA:45662 MA:0000435 OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g VHOG:0000382 lower respiratory system uberon UBERON:0001558 lower respiratory tract http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] FMA:45733 organ neck uberon UBERON:0001560 neck of organ FMA A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. Surface structure that includes the scales, skin, and muscles that are located ventral and posterior to the eye.[TAO] buccal In many animals the inside of the cheek is lined with mucous membrane covered with stratified squamous epithelium and supplied with secretions from buccal glands. BTO:0001754 EMAPA:37451 FMA:46476 GAID:65 MA:0002475 MESH:D002610 NCIT:C13070 OpenCyc:Mx4rvVi5WZwpEbGdrcN5Y29ycA TAO:0002113 UMLS:C0007966 galen:Cheek uberon buccae jowl UBERON:0001567 cheek Chica:cachetona.jpg FMA-abduced-lr A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. Surface structure that includes the scales, skin, and muscles that are located ventral and posterior to the eye.[TAO] 2012-08-14 TAO:0002113 TAO TAO:wd EMAPA:37451 MA:th UMLS:C0007966 ncithesaurus:Cheek buccae jowl The muscles associated with the larynx. BTO:0001626 EMAPA:35473 FMA:46562 GAID:144 MA:0001768 MESH:D007821 NCIT:C32934 UMLS:C0023054 laryngeal muscle larynx muscle larynx muscle organ muscle organ of larynx musculi laryngeales uberon UBERON:0001568 muscle of larynx prolog The muscles associated with the larynx. MP:0002263 UMLS:C0023054 ncithesaurus:Laryngeal_Muscle larynx muscle organ OBOL:automatic muscle organ of larynx OBOL:automatic Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG] Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO] see Intrinsic Tongue.[FEED] relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians. AAO:0010660 EHDAA2:0000704 EHDAA:9150 EMAPA:18276 FMA:46690 MA:0002307 NCIT:C52928 UMLS:C0224194 VHOG:0000847 genioglossus m. genioglossus musculus genioglossus uberon UBERON:0001571 genioglossus muscle http://upload.wikimedia.org/wikipedia/commons/7/7e/Genioglossus.png FMA EHDAA2 Wikipedia Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. VHOG:0000847 Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG] 2012-09-17 VHOG:0000847 VHOG Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO] 2012-06-20 AAO:0010660 AAO AAO:BMZ see Intrinsic Tongue.[FEED] 2012-07-02 FEED http://www.feedexp.org relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] 2012-06-20 AAO:0010660 AAO The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0000847 VHOG DOI:10.1002/dvdy.20587, DOI:10.1186/1471-213X-8-24 Table 7 Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians. AAO:0010660 UMLS:C0224194 ncithesaurus:Genioglossus A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII Makes up part of the tongue in frogs and salamanders.[AAO] The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED] relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] AAO:0010663 EMAPA:18277 FMA:46691 MA:0002317 MFMO_0000064 NCIT:C53161 UMLS:C0224196 hyoglossus m. hyoglossus uberon UBERON:0001572 hyoglossus muscle http://upload.wikimedia.org/wikipedia/commons/7/7e/Hyoglossus.png FMA lingual process in horse dbpedia A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII FEED:rd Makes up part of the tongue in frogs and salamanders.[AAO] 2012-06-20 AAO:0010663 AAO AAO:BMZ The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED] 2012-07-02 FEED http://www.feedexp.org relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO] 2012-06-20 AAO:0010663 AAO UMLS:C0224196 ncithesaurus:Hyoglossus_Muscle hyoglossus A muscle organ that attaches the tongue to some other structure. The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus. EHDAA2:0002063 EHDAA:9148 EMAPA:18275 FMA:46699 MA:0002296 VHOG:0000825 extrinsic lingual muscle extrinsic tongue muscle uberon UBERON:0001575 extrinsic muscle of tongue true check palatoglossus Wikipedia A muscle organ that attaches the tongue to some other structure. The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0000825 VHOG DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005) main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement WP All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus. WP The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII. The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED] The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone EHDAA2:0002064 EHDAA:9152 EMAPA:18280 FMA:46701 MA:0002327 VHOG:0000748 intrinsic lingual muscle intrinsic tongue muscle uberon UBERON:0001576 intrinsic muscle of tongue true FEED Wikipedia EHDAA2 The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII. The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED] 2012-07-02 FEED http://www.feedexp.org The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG] 2012-09-17 VHOG:0000748 VHOG DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005) The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone WP A muscle innervated by a facial nerve. FMA:46751 GAID:143 MA:0003160 MESH:D005152 MFMO:0000005 NCIT:C13073 UMLS:C0015460 XAO:0001013 face muscle face muscle organ facial muscle facial muscle proper facial nerve innervated muscle facial nerve muscle muscle of face muscle organ of face uberon cranial-facial muscle cranio-facial muscle craniofacial muscle mimetic muscles muscle of facil expression muscles of facial expression musculi faciei UBERON:0001577 facial muscle http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png FEED Wikipedia A muscle innervated by a facial nerve. FEED:rd UMLS:C0015460 ncithesaurus:Facial_Muscle face muscle FMA:46751 face muscle organ OBOL:automatic facial muscle FMA:46751 facial muscle XAO:0001013 facial nerve innervated muscle muscle of face FMA:46751 muscle organ of face OBOL:automatic cranial-facial muscle EMAPA:25133 cranio-facial muscle EMAPA:25133 craniofacial muscle EMAPA:25133 mimetic muscles muscle of facil expression muscles of facial expression musculi faciei The subclavian artery that supplies the left pectoral appendage in humans, branches off the arch of aorta arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans EMAPA:37100 FMA:4694 MA:0002046 NCIT:C32972 OpenCyc:Mx4rtW7hw6gEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvp8u1JwpEbGdrcN5Y29ycA UMLS:C0226262 arteria subclavia (sinistra) uberon UBERON:0001584 left subclavian artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg The subclavian artery that supplies the left pectoral appendage EMAPA:37100 MA:th UMLS:C0226262 ncithesaurus:Left_Subclavian_Artery arteria subclavia (sinistra) FMA:4694 FMA:TA A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green). BTO:0002683 EHDAA2:0001962 EHDAA:8726 EMAPA:18417 FMA:4720 GAID:549 MA:0000481 MESH:D014683 NCIT:C12816 UMLS:C0042459 VHOG:0001195 galen:SuperiorVenaCava superior caval vein superior vena cava uberon cranial vena cava precava vena cava superior vena maxima UBERON:0001585 anterior vena cava http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png lexical A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart. Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] 2012-09-17 VHOG:0001195 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 UMLS:C0042459 ncithesaurus:Superior_Vena_Cava superior caval vein superior vena cava FMA:4720 cranial vena cava VHOG:0001195 vena cava superior vena cava superior BTO:0002683 vena maxima One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] AAO:0010236 EHDAA2:0000877 EHDAA:5407 EMAPA:17620 FMA:4724 MA:0002157 NCIT:C32849 OpenCyc:Mx4rvqdb95wpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000878 UMLS:C0226550 XAO:0000382 galen:InternalJugularVein internal jugular internal jugular venous tree uberon vena jugularis interna UBERON:0001586 internal jugular vein http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] 2012-06-20 AAO:0010236 AAO AAO:BJB UMLS:C0226550 ncithesaurus:Internal_Jugular_Vein internal jugular EHDAA2:0000877 vena jugularis interna A vein that drains blood from the thymus. EMAPA:36325 FMA:4747 MA:0002246 NCIT:C53143 UMLS:C0226698 thymic tributary of brachiocephalic vein vena thymica uberon venae thymicae UBERON:0001591 thymic vein A vein that drains blood from the thymus. UMLS:C0226698 ncithesaurus:Thymic_Vein vena thymica venae thymicae The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted]. EMAPA:36284 FMA:4749 MA:0002088 NCIT:C53031 UMLS:C0226650 bronchial venous tree uberon UBERON:0001592 bronchial vein The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted]. UMLS:C0226650 ncithesaurus:Bronchial_Vein A congregation of multiple veins. EMAPA:36327 FMA:4767 MA:0000069 venous network uberon plexus venosus rete venosum UBERON:0001593 venous plexus http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png A congregation of multiple veins. plexus venosus rete venosum The muscle that stabilizes the stapes bone. The stapedius emerges from a pinpoint foramen in the apex of the pyramidal eminence (a hollow, cone-shaped prominence in the posterior wall of the tympanic cavity), and inserts into the neck of the stapes. [WP,unvetted]. The depressor mandibulae of tetrapods, which opens the jaws, is the homologue of the levator operculi and epihyoidean. In mammals, the depressor mandibulae evolves into the stapedius (...).[well established][VHOG] EHDAA:9029 EMAPA:18586 FMA:49027 GAID:164 MA:0001220 MESH:D013198 NCIT:C33611 UMLS:C0038151 VHOG:0000813 stapedius uberon musculus stapedius UBERON:0001599 stapedius muscle http://upload.wikimedia.org/wikipedia/commons/6/65/Musculusstapedius.png neck of stapes dbpedia The muscle that stabilizes the stapes bone. The stapedius emerges from a pinpoint foramen in the apex of the pyramidal eminence (a hollow, cone-shaped prominence in the posterior wall of the tympanic cavity), and inserts into the neck of the stapes. [WP,unvetted]. The depressor mandibulae of tetrapods, which opens the jaws, is the homologue of the levator operculi and epihyoidean. In mammals, the depressor mandibulae evolves into the stapedius (...).[well established][VHOG] 2012-09-17 VHOG:0000813 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.398 UMLS:C0038151 ncithesaurus:Stapedius_Muscle stapedius EHDAA2:0001909 musculus stapedius The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 EMAPA:35240 FMA:49151 MA:0001269 NCIT:C32315 UMLS:C0559230 musculus ciliarus uberon Bowman`s muscles ciliaris musculus ciliaris UBERON:0001605 ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png MA FMA FMA The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. UMLS:C0559230 ncithesaurus:Ciliary_Muscle musculus ciliarus BTO:0000654 Bowman`s muscles BTO:0000654 ciliaris musculus ciliaris . revisit this, see issue #331 The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP] in aves, stromal mesenchymal cells may migrate to the iris and become skeletal EMAPA:35448 FMA:49154 MA:0001287 iris muscle iris muscle organ muscle organ of iris uberon UBERON:0001606 muscle of iris FMA . iris muscle organ OBOL:automatic muscle organ of iris OBOL:automatic A sphincter muscle that is part of the iris. In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted] WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure constricts iris BTO:0000656 EMAPA:35788 FMA:49157 MA:0001289 NCIT:C33586 UMLS:C0229189 M. sphincter pupillae iris sphincter muscle musculus sphincter pupillae sphincter muscle of pupil uberon circular fibers constrictor pupillae iris constrictor iris constrictor muscle iris sphincter m. sphincter pupillae pupillary constrictor muscle pupillary sphincter pupillary sphincter muscle sphincter pupillae sphincter pupillae muscle spincter pupillae UBERON:0001607 sphincter pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png BTO ISBN:0781772214 encircles iris dbpedia encircles iris dbpedia dbpedia A sphincter muscle that is part of the iris. UMLS:C0229189 ncithesaurus:Sphincter_Pupillae_Muscle iris sphincter muscle BTO:0000656 musculus sphincter pupillae BTO:0000656 sphincter muscle of pupil BTO:0000656 circular fibers constrictor pupillae iris constrictor muscle iris sphincter m. sphincter pupillae pupillary constrictor muscle pupillary sphincter pupillary sphincter muscle sphincter pupillae sphincter pupillae muscle spincter pupillae A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted]. It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina BTO:0001371 EMAPA:35286 FMA:49158 MA:0001288 NCIT:C32463 UMLS:C0229190 dilator muscle of pupil dilator of pupil dilator pupillae dilator pupillae muscle iris dilator muscle musculus dilatator pupillae pupillary dilator muscle radial muscle of iris uberon dilator pupillae muscle iris dilator musculus dilatator pupillae musculus dilator pupillae pupil dilator pupil dilator muscle pupillary dilator pupillary muscle radial muscle radiating fibers UBERON:0001608 dilatator pupillae http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png BTO ISBN:0781772214 outer margins of iris dbpedia inner margins of iris dbpedia dbpedia A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted]. UMLS:C0229190 ncithesaurus:Dilator_Pupillae_Muscle dilator pupillae muscle iris dilator muscle BTO:0001371 musculus dilatator pupillae FMA:49158 FMA:TA pupillary dilator muscle radial muscle of iris dilator pupillae muscle BTO:0001371 iris dilator musculus dilatator pupillae musculus dilator pupillae BTO:0001371 pupil dilator pupil dilator muscle pupillary dilator pupillary muscle radial muscle radiating fibers The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP]. Part of the external carotid which supplies blood to the tongue.[AAO] relationship loss: part_of external carotid (AAO:0010218)[AAO] AAO:0010492 EMAPA:36324 FMA:49526 MA:0001992 NCIT:C52961 OpenCyc:Mx4rvfqDCZwpEbGdrcN5Y29ycA UMLS:C0226104 lingual branch of external carotid artery uberon arteria lingualis UBERON:0001610 lingual artery Lingual:artery.PNG FMA-abduced-lr The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP]. Part of the external carotid which supplies blood to the tongue.[AAO] 2012-06-20 AAO:0010492 AAO AAO:BJB relationship loss: part_of external carotid (AAO:0010218)[AAO] 2012-06-20 AAO:0010492 AAO UMLS:C0226104 ncithesaurus:Lingual_Artery arteria lingualis A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. EMAPA:19213 FMA:49549 MA:0001950 NCIT:C32578 OpenCyc:Mx4rwCt95ZwpEbGdrcN5Y29ycA UMLS:C0226109 uberon arteria maxillaris externa external maxillary artery UBERON:0001612 facial artery http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. UMLS:C0226109 ncithesaurus:Facial_Artery arteria maxillaris externa An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries EHDAA2:0001069 EHDAA:7357 EMAPA:17311 FMA:49675 GAID:498 MA:0001919 MESH:D008438 NCIT:C34205 OpenCyc:Mx4rwDDJ45wpEbGdrcN5Y29ycA UMLS:C0024949 uberon arteria maxillaris internal maxillary artery UBERON:0001616 maxillary artery http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries UMLS:C0024949 ncithesaurus:Maxillary_Artery arteria maxillaris The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified]. Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO] relationship loss: part_of internal carotid (AAO:0010219)[AAO] AAO:0010497 EHDAA2:0001300 EHDAA:7363 EMAPA:17007 FMA:49868 GAID:503 MA:0002011 MESH:D009880 NCIT:C33216 OpenCyc:Mx4rvcCxpJwpEbGdrcN5Y29ycA UMLS:C0029078 XAO:0000368 uberon arteria ophthalmica opthalmic artery UBERON:0001619 ophthalmic artery http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified]. Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO] 2012-06-20 AAO:0010497 AAO AAO:BJB relationship loss: part_of internal carotid (AAO:0010219)[AAO] 2012-06-20 AAO:0010497 AAO UMLS:C0029078 ncithesaurus:Opthalmic_Artery arteria ophthalmica opthalmic artery The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted]. EMAPA:37094 FMA:49927 MA:0001988 NCIT:C52948 UMLS:C0226171 uberon a. lacrimalis UBERON:0001622 lacrimal artery http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png FMA The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted]. EMAPA:37094 MA:th UMLS:C0226171 ncithesaurus:Lacrimal_Artery a. lacrimalis One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery. An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO] todo - verify ZFA link: An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery EHDAA2:0004518 EHDAA:3352 EMAPA:18600 FMA:50084 MA:0002023 NCIT:C33357 OpenCyc:Mx4rwDDlqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001487 TAO:0005001 UMLS:C0149559 ZFA:0005001 caudal communicating segment posterior communicating segment of the basilar artery uberon PCA PCS arteria cerebri communicans posterior UBERON:0001628 posterior communicating artery http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg FMA-abduced-lr FMA ZFA One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery. An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005001 TAO ZFIN:curator UMLS:C0149559 ncithesaurus:Posterior_Communicating_Artery caudal communicating segment ZFA:0005001 posterior communicating segment of the basilar artery ZFA:0005001 arteria cerebri communicans posterior Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Portion of tissue composed of contractile fibers.[TAO] It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] muscular muscle AAO:0011066 EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 GAID:131 MA:0000015 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA TAO:0005145 VHOG:0001245 XAO:0000172 ZFA:0005145 galen:Muscle uberon UBERON:0001630 muscle organ Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 Portion of tissue composed of contractile fibers.[TAO] 2012-08-14 TAO:0005145 TAO ZFIN:curator It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] 2012-09-17 VHOG:0001245 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 muscle ZFA:0005145 EMAPA:37474 MA:th An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] arterial AAO:0010211 AEO:0000208 BTO:0000573 CALOHA:TS-0054 EFO:0000814 EHDAA2:0000143 EHDAA2:0003253 EMAPA:35147 EV:0100026 FMA:50720 GAID:468 MA:0000064 MAT:0000034 MESH:D001158 MIAA:0000034 NCIT:C12372 OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA TAO:0000005 UMLS:C0003842 VHOG:0001251 XAO:0000114 ZFA:0000005 galen:Artery arterial subtree arterial tree organ part arteries uberon arterial system arterial vessel UBERON:0001637 artery An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. AEO:JB Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] 2012-06-20 AAO:0010211 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001251 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) UMLS:C0003842 ncithesaurus:Artery arteries TAO:0000005 Any of the tubular branching vessels that carry blood from the capillaries toward the heart. TODO - check with MA - vein vs venous blood vessel Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] venous venous subtree venous vessel AAO:0010212 AEO:0000209 BTO:0000234 CALOHA:TS-1108 EFO:0000816 EHDAA2:0003254 EMAPA:35906 EV:0100031 FMA:50723 GAID:492 MA:0000067 MAT:0000037 MESH:D014680 MIAA:0000037 NCIT:C12814 OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA TAO:0000082 UMLS:C0042449 VHOG:0001743 XAO:0000115 ZFA:0000082 galen:Vein venous tree organ part uberon vascular element vena venae UBERON:0001638 vein http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg Any of the tubular branching vessels that carry blood from the capillaries toward the heart. Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] 2012-06-20 AAO:0010212 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001743 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) UMLS:C0042449 ncithesaurus:Vein vascular element EMAPA:th vena venae VHOG:0001743 The first major branch of the abdominal aorta. EHDAA2:0004519 EMAPA:35202 FMA:50737 GAID:483 MA:0001931 MESH:D002445 NCIT:C52846 UMLS:C0007569 celiac tree coeliac artery uberon arteria coeliaca arteria cœliaca celiac trunk coeliac axis coeliac trunck coeliac trunk truncus coeliacus truncus cœliacus UBERON:0001640 dorsal aorta in Kardong celiac artery http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png ISBN:0073040584 ISBN:0073040584 ISBN:0073040584 ISBN:0073040584 The first major branch of the abdominal aorta. UMLS:C0007569 ncithesaurus:Coeliac_Artery coeliac artery arteria coeliaca arteria cœliaca celiac trunk coeliac axis coeliac trunck coeliac trunk truncus coeliacus truncus coeliacus truncus cœliacus Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls 5n AAO:0010470 BAMS:5n BAMS:Vn BAMS:nV BIRNLEX:869 BM:VN BTO:0001072 EFO:0001402 EHDAA2:0002084 EHDAA:3738 EMAPA:17576 FMA:50866 GAID:726 HBA:9322 MA:0001100 MBA:901 MESH:D014276 MFMO:0000093 NCIT:C12806 OpenCyc:Mx4rwMF8CJwpEbGdrcN5Y29ycA TAO:0000697 UMLS:C0040996 VHOG:0000704 XAO:0003092 ZFA:0000697 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=549 fifth cranial nerve nervus trigeminus nervus trigeminus [v] trigeminal V trigeminal nerve [V] trigeminal nerve tree trigeminal v nerve uberon CN-V cranial nerve V nerve V nervus trigeminus trigeminus UBERON:0001645 trigeminal nerve Gray778:Trigeminal.png Wikipedia Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). ISBN:0471209627 Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] 2012-06-20 AAO:0010470 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000704 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls ISBN:0471888893 5n BIRNLEX:869 NIFSTD:NeuroNames_abbrevSource UMLS:C0040996 BIRNLEX:869 UMLS:C0040996 ncithesaurus:Trigeminal_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=549 BIRNLEX:869 nervus trigeminus nervus trigeminus [v] FMA:50866 FMA:TA trigeminal V EHDAA2:0002084 nerve V NeuroNames:549 nervus trigeminus BTO:0001072 trigeminus BTO:0001072 Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches). Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 7n AAO:0010472 BAMS:7n BAMS:VIIn BAMS:Viin BAMS:nVII BIRNLEX:827 BM:Pons-VIIN EHDAA2:0000489 EHDAA:3729 EMAPA:17796 FMA:50868 GAID:719 HBA:9328 MA:0001091 MBA:798 MESH:D005154 NCIT:C12714 OpenCyc:Mx4rvthgEpwpEbGdrcN5Y29ycA TAO:0000664 UMLS:C0015462 VHOG:0000706 XAO:0003094 ZFA:0000664 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=551 branchiomeric cranial nerve face nerve facial VII facial VII nerve facial nerve [VII] facial nerve tree nerve of face nervus facialis nervus facialis [vii] seventh cranial nerve uberon CN-VII cranial nerve VII facial nerve or its root facial nerve/root nerve VII nervus facialis UBERON:0001647 facial nerve http://upload.wikimedia.org/wikipedia/commons/1/1f/Cranial_nerve_VII.svg ZFA Wikipedia Wikipedia Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches). ISBN:0471209627 Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO] 2012-06-20 AAO:0010472 AAO AAO:DSM We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000706 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 7n BIRNLEX:827 NIFSTD:NeuroNames_abbrevSource UMLS:C0015462 BIRNLEX:827 UMLS:C0015462 ncithesaurus:Facial_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=551 BIRNLEX:827 face nerve OBOL:automatic facial VII EHDAA2:0000489 nerve of face OBOL:automatic nervus facialis ZFA:0000664 nervus facialis [vii] FMA:50868 FMA:TA facial nerve or its root BAMS:7n facial nerve/root BAMS:7n nerve VII NeuroNames:551 nervus facialis Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 9n AAO:0010474 BAMS:9n BAMS:IXn BIRNLEX:899 BTO:0004979 EHDAA2:0000709 EHDAA:3733 EMAPA:17268 FMA:50870 GAID:827 HBA:9334 MA:0001093 MBA:808 MESH:D005930 NCIT:C12723 OpenCyc:Mx4rwIr5X5wpEbGdrcN5Y29ycA TAO:0000668 UMLS:C0017679 UMLS:C1305752 VHOG:0000701 XAO:0003096 ZFA:0000668 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=701 glossopharyngeal IX glossopharyngeal IX nerve glossopharyngeal nerve [IX] glossopharyngeal nerve tree nervus glossopharyngeus nervus glossopharyngeus [ix] ninth cranial nerve uberon CN-IX cranial nerve IX nerve IX nervus glossopharyngeus UBERON:0001649 glossopharyngeal nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png motor Wikipedia Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). ISBN:0471209627 Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO] 2012-06-20 AAO:0010474 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000701 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 9n BIRNLEX:899 NIFSTD:NeuroNames_abbrevSource UMLS:C0017679 BIRNLEX:899 UMLS:C0017679 ncithesaurus:Glossopharyngeal_Nerve UMLS:C1305752 BIRNLEX:899 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=701 BIRNLEX:899 glossopharyngeal IX EHDAA2:0000709 nervus glossopharyngeus ZFA:0000668 nervus glossopharyngeus [ix] FMA:50870 FMA:TA CN-IX nerve IX NeuroNames:701 nervus glossopharyngeus Cranial nerve that innervates the muscles of the tongue. Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO] Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves 12n AAO:0010477 BAMS:12n BAMS:XIIn BAMS:nXII BIRNLEX:820 BTO:0003386 EHDAA2:0000798 EHDAA:2859 EMAPA:17269 FMA:50871 GAID:828 HBA:9343 MA:0001094 MBA:813 MESH:D007002 NCIT:C12732 OpenCyc:Mx4rv9eWA5wpEbGdrcN5Y29ycA UMLS:C0020614 VHOG:0000693 XAO:0004215 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=704 cranial nerve XII hypoglossal XII hypoglossal XII nerve hypoglossal nerve [XII] hypoglossal nerve tree nervus hypoglossus [xii] twelfth cranial nerve uberon CN-XII hypoglossal nerve/ root nerve XII nervi hypoglossalis nervus hypoglossus UBERON:0001650 hypoglossal nerve http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png Cranial nerve that innervates the muscles of the tongue. ISBN:080184780X VHOG:0000693 Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000693 VHOG In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis ISBN:080184780X Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO] 2012-06-20 AAO:0010477 AAO AAO:EJS Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] 2012-09-17 VHOG:0000693 VHOG 12n BIRNLEX:820 NIFSTD:NeuroNames_abbrevSource UMLS:C0020614 BIRNLEX:820 UMLS:C0020614 ncithesaurus:Hypoglossal_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=704 BIRNLEX:820 cranial nerve XII BIRNLEX:820 hypoglossal XII EHDAA2:0000798 nervus hypoglossus [xii] FMA:50871 FMA:TA CN-XII VHOG:0000693 hypoglossal nerve/ root BAMS:12n nerve XII NeuroNames:704 nervi hypoglossalis NeuroNames:704 nervus hypoglossus The pulmonary artery that supplies the right lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37378 FMA:50872 MA:0002500 NCIT:C33489 UMLS:C0923924 galen:RightPulmonaryArtery right main pulmonary artery right pulmonary arterial tree uberon arteria pulmonalis dextra UBERON:0001651 right pulmonary artery Alveoli:diagram.png http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png The pulmonary artery that supplies the right lung. UBERON:cjm EMAPA:37378 MA:th UMLS:C0923924 ncithesaurus:Right_Pulmonary_Artery arteria pulmonalis dextra The pulmonary artery that supplies the left lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37097 FMA:50873 MA:0002032 NCIT:C32971 UMLS:C0923925 galen:LeftPulmonaryArtery left main pulmonary artery left pulmonary arterial tree uberon arteria pulmonalis sinistra UBERON:0001652 left pulmonary artery Alveoli:diagram.png http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png The pulmonary artery that supplies the left lung. UBERON:cjm EMAPA:37097 MA:th UMLS:C0923925 ncithesaurus:Left_Pulmonary_Artery arteria pulmonalis sinistra The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] MA and NCITA also has 'anterior facial vein' AAO:0010513 EMAPA:19220 FMA:50874 MA:0002115 NCIT:C32579 OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA UMLS:C0226532 face vein vein of face uberon anterior facial vein vena facialis anterior UBERON:0001653 facial vein http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png FMA The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] 2012-06-20 AAO:0010513 AAO AAO:BJB MA and NCITA also has 'anterior facial vein' MA UMLS:C0226532 ncithesaurus:Facial_Vein face vein OBOL:automatic vein of face OBOL:automatic anterior facial vein vena facialis anterior The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted]. EMAPA:37140 FMA:50981 GAID:530 MA:0002096 MESH:D002550 NCIT:C53037 UMLS:C0007797 XAO:0004160 uberon venae cerebri venae encephali UBERON:0001663 cerebral vein http://upload.wikimedia.org/wikipedia/commons/9/9f/Gray568.png The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted]. EMAPA:37140 MA:th UMLS:C0007797 ncithesaurus:Cerebral_Vein venae cerebri venae encephali A vein that drains the cerebellum. EMAPA:37139 FMA:51227 MA:0002093 NCIT:C53032 UMLS:C0226601 cerebellum vein epencephalon-1 vein vein of cerebellum vein of epencephalon-1 uberon UBERON:0001668 cerebellar vein A vein that drains the cerebellum. EMAPA:37139 MA:th UMLS:C0226601 ncithesaurus:Cerebellar_Vein cerebellum vein OBOL:automatic epencephalon-1 vein OBOL:automatic vein of cerebellum OBOL:automatic vein of epencephalon-1 OBOL:automatic The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks) A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. AAO:0011107 BAMS:5Gn BAMS:GV BTO:0001231 EFO:0000903 EHDAA2:0002085 EHDAA:2113 EMAPA:16797 FMA:52618 GAID:725 MA:0001080 MAT:0000511 MESH:D012668 NCIT:C62642 TAO:0000295 UMLS:C0040995 VHOG:0000694 XAO:0000427 XAO:0000428 ZFA:0000295 5th ganglion Gasserian ganglion fifth ganglion ganglion of trigeminal complex semilunar ganglion trigeminal V ganglion fused trigeminal ganglion uberon Gasser's ganglion Gasserian ganglia gV ganglion of trigeminal nerve ganglion semilunare ganglion trigeminale trigeminal ganglia trigeminus ganglion UBERON:0001675 trigeminal ganglion http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png ncithesaurus Bgee:AN The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000295 TAO ZFIN:curator In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. XAO:0004093 UMLS:C0040995 ncithesaurus:Trigeminal_Ganglion 5th ganglion ZFA:0000295 Gasserian ganglion fifth ganglion ZFA:0000295 ganglion of trigeminal complex semilunar ganglion ISBN:0471888893 trigeminal V ganglion MA:0001080 fused trigeminal ganglion NCBITaxon:32524 Gasser's ganglion BTO:0001231 Gasserian ganglia ganglion of trigeminal nerve BTO:0001231 ganglion semilunare ganglion trigeminale ganglion trigeminale BTO:0001231 trigeminal ganglia the bone at the lower, posterior part of the skull formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII fusion of basi-, exo- and supra-occipitals (and maybe tabular) EMAPA:25112 FMA:52735 GAID:227 MA:0001468 MESH:D009777 NCIT:C12757 OpenCyc:Mx4rwQtsiZwpEbGdrcN5Y29ycA UMLS:C0028784 uberon occipital complex occipital squama os occipitale UBERON:0001676 occipital bone http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png FMA FMA basi paired exo and supra occipital bones MA-modified interparietal (postparietal) the bone at the lower, posterior part of the skull ISBN:0-683-40008-8 MP:0005269 formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII fusion of basi-, exo- and supra-occipitals (and maybe tabular) Kardong UMLS:C0028784 ncithesaurus:Occipital_Bone occipital complex os occipitale the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA EHDAA:6035 EMAPA:17682 FMA:52737 GAID:232 MA:0001476 MESH:D013701 NCIT:C12797 OpenCyc:Mx4rvbkAk5wpEbGdrcN5Y29ycA UMLS:C0039484 VHOG:0000800 uberon os temporale UBERON:0001678 temporal bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg FMA petrosal squamosal plus angular temporal series styloid process the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous ISBN:0-683-40008-8 MP:0005272 fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) chond. The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. [WP] Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA FMA UMLS:C0039484 ncithesaurus:Temporal_Bone os temporale A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified]. Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO] relationship loss: part_of hyoid plate (AAO:0000664)[AAO] The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia. AAO:0000684 EMAPA:18650 FMA:52749 GAID:197 MA:0001484 MESH:D006928 NCIT:C32752 UMLS:C0020417 VHOG:0001325 uberon hyoid hyoid bone hyoideum lingual bone os hyoideum UBERON:0001685 hyoid bone http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png FMA Wikipedia Wikipedia A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified]. Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO] 2012-06-20 AAO:0000684 AAO AAO:LAP relationship loss: part_of hyoid plate (AAO:0000664)[AAO] 2012-06-20 AAO:0000684 AAO The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia. https://github.com/obophenotype/uberon/issues/548 WP UMLS:C0020417 ncithesaurus:Hyoid_Bone hyoid hyoid bone hyoideum lingual bone os hyoideum os hyoideum One of 3 small bones contained within the middle ear space and serve to transmit sounds from the air to the fluid-filled labyrinth. The absence of the auditory ossicles would constitute a moderate-to-severe hearing loss. The term 'ossicles' literally means 'tiny bones' and commonly refers to the auditory ossicles, though the term may refer to any small bone throughout the body. [WP,unvetted]. This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5. The small bones of the middle ear: incus, malleus, and stapes. [TFD][VHOG] Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals.[well established][VHOG] Studies have shown that ear bones in mammal embryos are attached to the dentary, which is part of the jaw. These are ossified portions of cartilage -- called Meckel's cartilage -- that are attached to the jaw. As the embryo develops, the cartilage hardens to form bone. Later in development, the bone structure breaks loose from the jaw and migrates to the inner ear area. The structure is known as the middle ear, and is made up of the incus, stapes, malleus, and tympanic membrane. These correspond to the quadrate, prearticular, articular, and angular structures in the reptile jaw. For this reason, researchers believe the similarity of the results shows that mammals and reptiles have a common ancestry. ossicle AAO:0011015 EHDAA2:0001183 EHDAA:5697 EMAPA:17824 EV:0100360 FMA:52750 MA:0000254 NCIT:C32164 UMLS:C0013450 VHOG:0000461 XAO:0000214 auditory bone middle ear ossicle uberon auditory ossicle ear bone ear ossicle ear ossicles middle ear bone ossicle of ear ossicle of inner ear ossicular chain UBERON:0001686 auditory ossicle bone http://upload.wikimedia.org/wikipedia/commons/b/b0/Illu_auditory_ossicles.jpg One of 3 small bones contained within the middle ear space and serve to transmit sounds from the air to the fluid-filled labyrinth. The absence of the auditory ossicles would constitute a moderate-to-severe hearing loss. The term 'ossicles' literally means 'tiny bones' and commonly refers to the auditory ossicles, though the term may refer to any small bone throughout the body. [WP,unvetted]. The small bones of the middle ear: incus, malleus, and stapes. [TFD][VHOG] 2012-09-17 VHOG:0000461 VHOG Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals.[well established][VHOG] 2012-09-17 VHOG:0000461 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.695 Studies have shown that ear bones in mammal embryos are attached to the dentary, which is part of the jaw. These are ossified portions of cartilage -- called Meckel's cartilage -- that are attached to the jaw. As the embryo develops, the cartilage hardens to form bone. Later in development, the bone structure breaks loose from the jaw and migrates to the inner ear area. The structure is known as the middle ear, and is made up of the incus, stapes, malleus, and tympanic membrane. These correspond to the quadrate, prearticular, articular, and angular structures in the reptile jaw. For this reason, researchers believe the similarity of the results shows that mammals and reptiles have a common ancestry. WP ossicle EMAPA:17824 UMLS:C0013450 ncithesaurus:Auditory_Ossicle middle ear ossicle MP:0005105 auditory ossicle MA:0000254 ear bone MA:0000254 ear ossicles ossicular chain The stapes or stirrup is the stirrup-shaped small bone or ossicle in the middle ear which is attached to the incus laterally and to the fenestra ovalis, the 'oval window' medially. The oval window is adjacent to the vestibule of the inner ear. The stapes is the smallest and lightest bone in the human body. The stapes transmits the sound vibrations from the incus to the membrane of the inner ear inside the fenestra ovalis. The stapes is also stabilized by the stapedius muscle, which is innervated by the facial nerve. In non-mammalian vertebrates, the bone homologous to the stapes is usually called the columella; however, in reptiles, either term may be used[WP,unvetted]. This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG] 'This structure [the hyomandibular], on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.' Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) 62:339-357?[VHOG]. As the stapes first develops embryologically from the 6th to 8th week of life, it surrounds the stapedial artery, which supplies the majority of the vasculature of the embryonic head. After that period, the external carotid artery is generated and takes over for the stapedial artery, which subsequently involutes, leaving the stapes with a windowframe-like structure[WP] The stapes develops at the cranial end of the second branchial arch through an independent anlage of the cartilage of this arch. Between the stapedial anlage and the cranial end of the Reichert's cartilage there is a formation called the interhyale, the internal segment of which gives rise to the tendon of the stapedial muscle. The stapedial anlage is a unique formation with two distinct parts: the superior part that will comprise the base and the inferior part that will be crossed by the stapedial artery during embryonic development and will constitute the limbs and the head of the stapes. According to the results, the otic capsule is not involved in formation of the base of the stapes. EMAPA:18585 FMA:52751 GAID:868 MA:0001217 MESH:D013199 NCIT:C33612 OpenCyc:Mx4rv5UnkZwpEbGdrcN5Y29ycA UMLS:C0038152 VHOG:0000688 stirrup uberon columella columella auris columellare interstapediale mediostapediale mesostapediale os columellare os intermedium stapellos stapes stelidium stilus columellare UBERON:0001687 stapes bone http://upload.wikimedia.org/wikipedia/commons/c/c1/Gray918.png DOI:10.1111/j.1469-7580.2006.00524.x classical definition definitional The stapes or stirrup is the stirrup-shaped small bone or ossicle in the middle ear which is attached to the incus laterally and to the fenestra ovalis, the 'oval window' medially. The oval window is adjacent to the vestibule of the inner ear. The stapes is the smallest and lightest bone in the human body. The stapes transmits the sound vibrations from the incus to the membrane of the inner ear inside the fenestra ovalis. The stapes is also stabilized by the stapedius muscle, which is innervated by the facial nerve. In non-mammalian vertebrates, the bone homologous to the stapes is usually called the columella; however, in reptiles, either term may be used[WP,unvetted]. This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG] 2012-09-17 VHOG:0000688 VHOG DOI:10.1017/S0022215100009087 Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) As the stapes first develops embryologically from the 6th to 8th week of life, it surrounds the stapedial artery, which supplies the majority of the vasculature of the embryonic head. After that period, the external carotid artery is generated and takes over for the stapedial artery, which subsequently involutes, leaving the stapes with a windowframe-like structure[WP] The stapes develops at the cranial end of the second branchial arch through an independent anlage of the cartilage of this arch. Between the stapedial anlage and the cranial end of the Reichert's cartilage there is a formation called the interhyale, the internal segment of which gives rise to the tendon of the stapedial muscle. The stapedial anlage is a unique formation with two distinct parts: the superior part that will comprise the base and the inferior part that will be crossed by the stapedial artery during embryonic development and will constitute the limbs and the head of the stapes. According to the results, the otic capsule is not involved in formation of the base of the stapes. UMLS:C0038152 ncithesaurus:Stapes columella columella auris AAO:0000580 columellare AAO:0000580 interstapediale AAO:0000580 mediostapediale AAO:0000580 mesostapediale AAO:0000580 os columellare AAO:0000580 os intermedium AAO:0000580 stapellos stapes AAO:0000580 stelidium AAO:0000580 stilus columellare AAO:0000580 Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. http://langual.org The organ of hearing and of equilibrium. [TFD][VHOG] Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] auricular AAO:0011014 BIRNLEX:1062 BTO:0000368 CALOHA:TS-1165 EFO:0000826 EHDAA2:0000423 EHDAA:502 EMAPA:16193 EV:0100353 FMA:52780 GAID:62 MA:0000236 MAT:0000138 MESH:D004423 MIAA:0000138 NCIT:C12394 OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA UMLS:C0013443 UMLS:C0521421 VHOG:0000330 XAO:0000189 galen:Ear http://www.langual.org/langual_thesaurus.asp?termid=C0311 uberon auditory apparatus auris UBERON:0001690 ear http://upload.wikimedia.org/wikipedia/commons/b/b8/Ear.jpg Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. GO:0042471 The organ of hearing and of equilibrium. [TFD][VHOG] 2012-09-17 VHOG:0000330 VHOG Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] 2012-09-17 VHOG:0000330 VHOG DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005) UMLS:C0013443 BIRNLEX:1062 UMLS:C0013443 ncithesaurus:Ear UMLS:C0521421 BIRNLEX:1062 auris BTO:0000368 Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO]. The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG] in XAO this includes and is only the tympanum auricular region AAO:0011037 BIRNLEX:1705 BTO:0002100 EFO:0004221 EHDAA2:0000462 EHDAA:3786 EMAPA:16991 EV:0100354 FMA:52781 GAID:104 MA:0000258 MAT:0000147 MESH:D004431 MIAA:0000147 NCIT:C12292 OpenCyc:Mx4rwOHtXJwpEbGdrcN5Y29ycA UMLS:C0013453 UMLS:C1269548 VHOG:0000311 XAO:0000190 auricular region of head outer ear uberon auris externa UBERON:0001691 external ear http://upload.wikimedia.org/wikipedia/commons/2/29/Gray907.png Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO]. GO:0042473 The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000311 VHOG Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG] 2012-09-17 VHOG:0000311 VHOG DOI:10.1007/s00359-008-0327-1 Schoffelen RLM, Segenhout JM, Van Dijk P, Mechanics of the exceptional anuran ear. Journal of Comparative Physiology A (2008) in XAO this includes and is only the tympanum XAO UMLS:C0013453 BIRNLEX:1705 UMLS:C0013453 ncithesaurus:External_Ear UMLS:C1269548 BIRNLEX:1705 outer ear MA:0000258 auris externa BTO:0002100 The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted]. The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG] derivative of prootic and opisthotic petrosal EHDAA2:0001452 EMAPA:17683 FMA:52871 GAID:234 MA:0001477 MESH:D010579 NCIT:C32316 UMLS:C1261761 VHOG:0001553 pars petrosa (os temporale) pars petrosa ossis temporalis petromastoid part of temporal bone temporal bone petrous part uberon petrosal bone petrous bone UBERON:0001694 petrous part of temporal bone http://upload.wikimedia.org/wikipedia/commons/9/96/Gray137.png FMA The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted]. The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG] 2012-09-17 VHOG:0001553 VHOG petrosal VHOG:0001553 UMLS:C1261761 ncithesaurus:Ciliary_Process pars petrosa (os temporale) FMA:52871 petromastoid part of temporal bone FMA:52871 petrosal bone FMA:52871 petrous bone FMA:52871 the group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve) resolve facial VII vs geniculate (see EHDAA2) These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] geniculate BAMS:GgVII EFO:0003669 EHDAA2:0000491 EHDAA2:0004623 EHDAA:5567 EHDAA:6644 EMAPA:17569 FMA:53414 GAID:718 MA:0001076 MESH:D005830 NCIT:C12721 TAO:0001291 UMLS:C0017406 VHOG:0000707 ZFA:0001291 facial VII ganglion gVII ganglion genicularum genicular ganglion uberon facial ganglion ganglion geniculi ganglion geniculi nervi facialis geniculate ganglion internal genu UBERON:0001700 geniculate ganglion http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png ncithesaurus EHDAA2:0004623 ZFA EHDAA2:0004623 EHDAA2:0000491 the group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve) ISBN:0-683-40008-8 MP:0001082 These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000707 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) geniculate UMLS:C0017406 ncithesaurus:Geniculate_Ganglion facial VII ganglion MA:0001076 gVII ZFA:0001291 ganglion genicularum FMA:53414 genicular ganglion genicular ganglion FMA:53414 facial ganglion ZFA:0001291 ganglion geniculi ganglion geniculi nervi facialis geniculate ganglion MA:0001076 internal genu The group of neuron cell bodies associated with the ninth cranial nerve. These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] EHDAA2:0000710 EHDAA:2838 EMAPA:16795 FMA:53471 MA:0001077 TAO:0001301 VHOG:0000702 ZFA:0001301 ganglion of glossopharyngeal nerve ganglion of glosspharyngeal nerve glossopharyngeal IX ganglion petrosal ganglion uberon gIX UBERON:0001701 glossopharyngeal ganglion ZFA dorsal EHDAA2 ISBN:0471888893 ZFA ventrolateral EHDAA2 ISBN:0471888893 ZFA The group of neuron cell bodies associated with the ninth cranial nerve. MP:0001096 These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000702 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) ganglion of glosspharyngeal nerve FMA:53471 glossopharyngeal IX ganglion MA:0001077 petrosal ganglion ZFA:0001301 Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] neurocranial It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... AAO:0010153 EHDAA2:0000243 EMAPA:17681 FMA:53672 MA:0000317 TAO:0001580 XAO:0003170 ZFA:0001580 brain box uberon brain case brain pan braincase UBERON:0001703 neurocranium FMA Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. TAO:MAH ZFA:0001580 Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] 2012-08-14 TAO:0001580 TAO TAO:MAH The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. WP It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... MA brain case ZFA:0001580 brain pan braincase ZFA:0001580 An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong. Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO] a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]. Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG] in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures AAO:0000314 BTO:0002096 EHDAA2:0001226 EHDAA:6801 EMAPA:17604 FMA:54378 GAID:350 MA:0000284 MESH:D009296 NCIT:C12424 TAO:0000130 UMLS:C0027423 VHOG:0000271 ZFA:0000130 cavity of nose cavity of olfactory apparatus nasal canal nasal conduit space nasal fossa olfactory chamber cavity uberon cavitas nasalis cavitas nasi cavum nasi nasal pit olfactory cavity olfactory chamber olfactory pit UBERON:0001707 nasal cavity http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg cjm An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO] 2012-06-20 AAO:0000314 AAO AAO:LAP a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]. Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG] 2012-09-17 VHOG:0000271 VHOG DOI:10.1666/0094-8373(2006)032[0109:NCHACC]2.0.CO;2 Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006) in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures HP UMLS:C0027423 ncithesaurus:Nasal_Cavity cavity of olfactory apparatus nasal canal ZFA:0000130 nasal conduit space nasal fossa olfactory chamber cavity cavitas nasalis BTO:0002096 cavitas nasi cavitas nasi BTO:0002096 cavum nasi olfactory chamber olfactory pit ZFA:0000130 Subdivision of skeleton which includes upper and lower jaw skeletons. TODO - move ZFA:0001227 (it is the entire jaw skeleton). Skeletal and cartilage elements of the first pharyngeal arch.[TAO] There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983). in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates AAO:0000988 BTO:0001749 EMAPA:35455 FMA:54396 GAID:214 MA:0001905 MESH:D007568 NCIT:C48821 OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA TAO:0001227 UMLS:C0022359 ZFA:0001227 galen:Jaw jaw jaw cartilage mandibular arch skeleton uberon anterior splanchnocranium jaws mandibular arch oral jaw skeleton pharyngeal arch 1 skeleton visceral arch 1 UBERON:0001708 jaw skeleton cjm Subdivision of skeleton which includes upper and lower jaw skeletons. Skeletal and cartilage elements of the first pharyngeal arch.[TAO] 2012-08-14 TAO:0001227 TAO ZFIN:curator in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates FMA UMLS:C0022359 ncithesaurus:Jaw jaw MA:0001905 jaw cartilage ZFA:0001227 mandibular arch skeleton ZFA:0001227 mandibular arch TAO:0001227 Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] Note isa/partof difference MA/FMA AAO:0000272 EFO:0003660 EHDAA2:0001018 EHDAA:7995 EMAPA:17906 FMA:59398 MESH:D008334 VHOG:0000453 ncithesaurus:Lower_Jaw mandibular part of mouth uberon lower part of mouth mandibular series UBERON:0001710 See notes for jaw w.r.t skeletal element vs subdivision of head lower jaw region http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] 2012-06-20 AAO:0000272 AAO AAO:LAP Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000453 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) Note isa/partof difference MA/FMA MA mandibular part of mouth FMA:59398 the groups of nerve cell bodies associated with the twelve cranial nerves Ganglion which is located in the head.[TAO] UBERON:0003213 UBERON:0026601 BIRNLEX:2597 BTO:0000106 EFO:0000902 EMAPA:16659 FMA:54502 MA:0000213 MA:0000214 MAT:0000200 MIAA:0000200 TAO:0000013 VHOG:0000076 XAO:0000027 ZFA:0000013 cranial ganglion cranial ganglion part of peripheral nervous system cranial ganglion/nerve cranial nerve ganglion cranial neural ganglion cranial neural tree organ ganglion ganglion of cranial nerve ganglion of cranial neural tree organ uberon cranial ganglia head ganglion presumptive cranial ganglia UBERON:0001714 cranial ganglion the groups of nerve cell bodies associated with the twelve cranial nerves ISBN:0-683-40008-8 MGI:csmith MP:0001081 Ganglion which is located in the head.[TAO] 2012-08-14 TAO:0000013 TAO ZFIN:curator cranial ganglion part of peripheral nervous system BIRNLEX:2597 cranial neural tree organ ganglion OBOL:automatic ganglion of cranial nerve FMA:54502 ganglion of cranial neural tree organ OBOL:automatic presumptive cranial ganglia ZFA:0000013 tongue A muscular organ in the floor of the mouth. in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence. tongue http://langual.org A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG] Muscular organ in the floor of the mouth.[FEED] The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586]. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] glossal lingual Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions AAO:0010360 BTO:0001385 CALOHA:TS-1050 EFO:0000833 EHDAA2:0002062 EHDAA:9144 EMAPA:17185 EV:0100058 FMA:54640 GAID:816 MA:0000347 MAT:0000040 MESH:D014059 MIAA:0000040 NCIT:C12422 OpenCyc:Mx4rvVjmJ5wpEbGdrcN5Y29ycA_53KXLq9EdqAAAACs6hnmQ TAO:0005333 UMLS:C0040408 VHOG:0000419 XAO:0000446 ZFA:0005333 http://www.langual.org/langual_thesaurus.asp?termid=C0189 uberon glossus UBERON:0001723 tongue http://upload.wikimedia.org/wikipedia/commons/a/a6/Tongue.agr.jpg GO BTO EHDAA2 FMA ZFA MA anterior 2/3 Wikipedia Wikipedia definitional A muscular organ in the floor of the mouth. FEED:rd A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG] 2012-09-17 VHOG:0000419 VHOG Muscular organ in the floor of the mouth.[FEED] 2012-07-02 FEED http://www.feedexp.org The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586]. GO:0043586 Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000419 VHOG DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002) UMLS:C0040408 ncithesaurus:Tongue glossus The cartilaginous joints of the skull; these include sphenoethmoidal synchondrosis, sphenooccipital synchondrosis, sphenopetrosal synchondrosis, petrooccipital synchondrosis, anterior intraoccipital synchondrosis and posterior intraoccipital synchondrosis. EMAPA:35264 FMA:54816 MA:0001502 uberon UBERON:0001725 cranial synchondrosis FMA The cartilaginous joints of the skull; these include sphenoethmoidal synchondrosis, sphenooccipital synchondrosis, sphenopetrosal synchondrosis, petrooccipital synchondrosis, anterior intraoccipital synchondrosis and posterior intraoccipital synchondrosis. BIRNLEX:4102 EMAPA:32777 FMA:54819 MA:0001593 NCIT:C33258 UMLS:C0226964 UMLS:C1289183 lingual papilla tongue papilla uberon UBERON:0001726 papilla of tongue FMA-modified UMLS:C0226964 BIRNLEX:4102 UMLS:C0226964 ncithesaurus:Papilla_of_the_Tongue UMLS:C1289183 BIRNLEX:4102 A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. A chemoreceptive organ.[AAO] One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish. arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN:1607950324 (todo - request cell terms from CL) AAO:0010573 BIRNLEX:4101 BTO:0000989 CALOHA:TS-1015 EMAPA:35850 FMA:54825 GAID:815 MA:0001591 MESH:A08.800.550.700.120.800 NCIT:C96518 OpenCyc:Mx4rvVjan5wpEbGdrcN5Y29ycA TAO:0001074 UMLS:C0039337 VHOG:0000130 XAO:0000445 ZFA:0001074 tastebud uberon caliculus gustatorius taste buds taste-bud tastebuds UBERON:0001727 taste bud http://upload.wikimedia.org/wikipedia/commons/5/5a/Gray1018.png NIF A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. A chemoreceptive organ.[AAO] 2012-06-20 AAO:0010573 AAO AAO:EJS One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] 2012-09-17 VHOG:0000130 VHOG Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000130 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) UMLS:C0039337 BIRNLEX:4101 UMLS:C0039337 ncithesaurus:Taste_Bud tastebud caliculus gustatorius caliculus gustatorius taste buds taste-bud tastebuds nasopharynx the section of the pharynx that lies above the soft palate The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG] nasopharyngeal In humans - in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane BTO:0000662 CALOHA:TS-0663 EHDAA2:0001239 EHDAA:7086 EMAPA:17670 EV:0100066 FMA:54878 GAID:339 MA:0000443 MAT:0000447 MESH:A03.867.557 NCIT:C12423 OpenCyc:Mx4rwUPoDJwpEbGdrcN5Y29ycA UMLS:C0027442 VHOG:0000375 nasal part of pharynx rhinopharynx uberon Nasenrachenraum epipharynx pars nasalis pharyngis UBERON:0001728 nasopharynx Illu:pharynx.jpg the section of the pharynx that lies above the soft palate MGI:cwg MP:0002251 The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG] 2012-09-17 VHOG:0000375 VHOG UMLS:C0027442 ncithesaurus:Nasopharynx Nasenrachenraum BTO:0000662 epipharynx pars nasalis pharyngis oropharynx the portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis One of the three anatomic divisions of the pharynx that lies posterior to the mouth and is continuous above with the nasopharynx and below with the laryngopharynx. It extends behind the mouth from the soft palate above to the level of the hyoid bone below and contains the palatine and lingual tonsils. [TFD][VHOG] oropharyngeal BTO:0005257 CALOHA:TS-0718 EFO:0001976 EHDAA2:0004082 EMAPA:25094 EV:0100067 FMA:54879 GAID:340 MA:0000351 MAT:0000446 MESH:A03.867.603 NCIT:C12762 OpenCyc:Mx4rwACoxpwpEbGdrcN5Y29ycA UMLS:C0521367 VHOG:0000457 VSAO:0000034 XAO:0004048 oral part of pharynx uberon mesopharynx pars oralis pharyngis UBERON:0001729 oropharynx Illu:pharynx.jpg ISBN:0073040584-table13.1 the portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis MGI:cwg MP:0002252 One of the three anatomic divisions of the pharynx that lies posterior to the mouth and is continuous above with the nasopharynx and below with the laryngopharynx. It extends behind the mouth from the soft palate above to the level of the hyoid bone below and contains the palatine and lingual tonsils. [TFD][VHOG] 2012-09-17 VHOG:0000457 VHOG UMLS:C0521367 ncithesaurus:Oropharynx mesopharynx pars oralis pharyngis A anatomical space that is enclosed by a pharynx. See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship TOODO check AAO:0010435 BSA:0000113 BTO:0002097 EMAPA:18381 FMA:54935 XAO:0000105 lumen of pharynx pharyngeal cavity uberon cavitas pharyngealis cavitas pharyngis UBERON:0001731 cavity of pharynx XAO A anatomical space that is enclosed by a pharynx. OBOL:automatic cavitas pharyngealis cavitas pharyngis BTO:0002097 the lymph tissue in the roof and posterior wall of the nasopharynx BTO:0000777 EV:0100054 FMA:54970 GAID:1288 MA:0000774 MESH:A15.382.520.604.084 NCIT:C33318 UMLS:C0001428 adenoid nasopharyngeal tonsil tonsil of Luschka tonsilla pharyngealis uberon Rachenmandel tonsilla pharyngea UBERON:0001732 pharyngeal tonsil http://upload.wikimedia.org/wikipedia/commons/b/be/Gray994-adenoid.png cjm the lymph tissue in the roof and posterior wall of the nasopharynx MGI:cwg MP:0002384 UMLS:C0001428 ncithesaurus:Pharyngeal_Tonsil tonsilla pharyngealis FMA:54970 FMA:TA Rachenmandel BTO:0000777 tonsilla pharyngea the circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils FMA:55070 MA:0000752 NCIT:C73468 UMLS:C0459892 Waldeyer's ring Waldeyer's tonsillar ring anulus lymphoideus pharyngis oropharyngeal lymphoid tissue pharyngeal lymphatic ring pharyngeal lymphoid ring uberon UBERON:0001735 tonsillar ring the circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils MGI:cwg MP:0002379 UMLS:C0459892 ncithesaurus:Waldeyers_Tonsillar_Ring anulus lymphoideus pharyngis FMA:55070 FMA:TA Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible. Either of two major salivary glands situated in the neck near the lower edge of each side of the mandible and emptying into the submandibular duct. [TFD][VHOG] The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG] In humans, they account for 70% of the salivary volume and weigh about 15 grams. [WP,unvetted] In mouse, multilobed and lobulated, on the ventral midline of the neck in mice, submandibular gland development initiates as a thickening of the oral epithelium; around E12 an initial (single) epithelial bud on a stalk grows into a condensing neural crest-derived mesenchyme; clefts in the epithelium result in 3-5 epithelial buds at E13.5, and branching morphogenesis occurs with continued proliferation, successive rounds of cleft formation, duct elongation, and duct lumen formation, so that by E14 the gland is highly branched (multi-lobed); functional differentiation, with the appearance of proacinar cells and secretory products begins after E15 and continues to birth; acinar differentiation continues postnatally with final differentiation of the granular convoluted tubules at puberty[MGI:anna] The submandibular is the first major salivary gland to develop in the embryo, followed by the neighbouring sublingual and then the parotid.[PMID:17336109] The term submandibular as used in humans, is incorrect due the difference in topography of these structures[http://www.avdc.org] BTO:0001316 CALOHA:TS-0988 EFO:0001387 EMAPA:18812 EV:0100061 FMA:55093 GAID:942 MA:0001589 MESH:D013363 NCIT:C12233 UMLS:C0038556 VHOG:0000364 mandibular gland mandibular salivary gland submandibular salivary gland uberon glandula submandibularis maxillary gland submaxillary gland UBERON:0001736 lobular, sexually dimorphic in mouse submandibular gland http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg FMA-abduced-lr Either of the paired compound tubuloalveolar (aka tubuloacinar) major salivary glands composed of both serous and mucous secretory cells and situated beneath the mandible. MGI:anna Either of two major salivary glands situated in the neck near the lower edge of each side of the mandible and emptying into the submandibular duct. [TFD][VHOG] 2012-09-17 VHOG:0000364 VHOG The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG] 2012-09-17 VHOG:0000364 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.525 In mouse, multilobed and lobulated, on the ventral midline of the neck ISBN:0123813611 UMLS:C0038556 ncithesaurus:Submandibular_Gland mandibular gland mandibular salivary gland glandula submandibularis A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] laryngeal AAO:0000268 BTO:0001208 CALOHA:TS-0532 EFO:0000838 EHDAA2:0004063 EMAPA:18333 EV:0100039 FMA:55097 GAID:108 MA:0000414 MAT:0000187 MESH:D007830 MIAA:0000187 NCIT:C12420 OpenCyc:Mx4rvViOnZwpEbGdrcN5Y29ycA UMLS:C0023078 VHOG:0001279 XAO:0003081 galen:Larynx uberon Kehlkopf@de UBERON:0001737 larynx http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg EHDAA2 A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] 2012-07-02 FEED http://www.feedexp.org Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] 2012-06-20 AAO:0000268 AAO AAO:BJB (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001279 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 UMLS:C0023078 ncithesaurus:Larynx Kehlkopf@de BTO:0001208 The cartilaginous structures that support the larynx. (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] BTO:0003660 EHDAA:8157 EMAPA:18697 FMA:55108 GAID:107 MA:0001758 MESH:A02.165.507 NCIT:C12281 UMLS:C0023050 VHOG:0001550 cartilage of larynx cartilagines laryngeales larynx cartilage uberon UBERON:0001739 laryngeal cartilage The cartilaginous structures that support the larynx. MP:0002256 (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001550 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 UMLS:C0023050 ncithesaurus:Laryngeal_Cartilage cartilage of larynx FMA:55108 cartilagines laryngeales larynx cartilage VHOG:0001550 A ligament that is part of a larynx and connexts the cartilages of the larynx EMAPA:37626 FMA:55131 MA:0001755 NCIT:C32933 UMLS:C0458519 laryngeal ligament larynx ligament uberon UBERON:0001743 ligament of larynx FMA A ligament that is part of a larynx and connexts the cartilages of the larynx EMAPA:37626 MA:th UMLS:C0458519 ncithesaurus:Laryngeal_Ligament larynx ligament MA:0001755 Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]. BTO:0000753 CALOHA:TS-0584 FMA:55220 GAID:342 MA:0002436 MESH:D008221 NCIT:C13049 UMLS:C0024296 galen:LymphoidTissue lymphatic tissue lymphocytic tissue uberon UBERON:0001744 lymphoid tissue FMA Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]. lampreys lack organized lymphoid tissue NCBIBook:NBK27108 UMLS:C0024296 ncithesaurus:Lymphoid_Tissue EMAPA:37767 FMA:55513 MA:0002675 NCIT:C33781 UMLS:C0229575 capsula fibrosa glandulae thyroideae fibrous capsule of thyroid gland thyroid capsule thyroid gland capsule uberon UBERON:0001746 capsule of thyroid gland EMAPA:37767 MA:th UMLS:C0229575 ncithesaurus:Thyroid_Gland_Capsule capsula fibrosa glandulae thyroideae FMA:55513 FMA:TA fibrous capsule of thyroid gland FMA:55513 thyroid gland capsule MA:0002675 A parenchyma that is part of a thyroid follicle [Automatically generated definition]. BTO:0004579 EMAPA:37769 FMA:55515 MA:0000730 parenchyma of thyroid parenchyma of thyroid follicle parenchyma of thyroid gland follicle thyroid follicle parenchyma thyroid gland follicle parenchyma thyroid gland parenchyma thyroid parenchyma uberon parenchyma glandulae thyroideae UBERON:0001747 parenchyma of thyroid gland A parenchyma that is part of a thyroid follicle [Automatically generated definition]. OBOL:automatic EMAPA:37769 MA:th parenchyma of thyroid OBOL:accepted parenchyma of thyroid follicle OBOL:automatic parenchyma of thyroid gland follicle OBOL:automatic thyroid follicle parenchyma OBOL:automatic thyroid gland follicle parenchyma OBOL:automatic thyroid parenchyma OBOL:accepted parenchyma glandulae thyroideae BTO:0004579 The dense and irregular connective tissue capsule surrounding a parathyroid gland. EMAPA:35663 FMA:55566 MA:0002676 NCIT:C33265 UMLS:C0927176 parathyroid gland capsule uberon UBERON:0001748 capsule of parathyroid gland MA The dense and irregular connective tissue capsule surrounding a parathyroid gland. MGI:anna UMLS:C0927176 ncithesaurus:Parathyroid_Gland_Capsule A parenchyma that is part of a parathyroid gland [Automatically generated definition]. EMAPA:35664 FMA:55569 MA:0002677 parathyroid gland parenchyma parathyroid parenchyma parenchyma of parathyroid uberon UBERON:0001749 parenchyma of parathyroid gland A parenchyma that is part of a parathyroid gland [Automatically generated definition]. OBOL:automatic parathyroid parenchyma OBOL:automatic parenchyma of parathyroid OBOL:automatic A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta. TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye EMAPA:35462 FMA:55605 GAID:901 MA:0000274 MESH:D007765 NCIT:C32905 UMLS:C0022903 apparatus lacrimalis lacrymal system uberon lacrimal drainage system nasolacrimal drainage system nasolacrimal system UBERON:0001750 lacrimal apparatus http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png MA HPO:pr ISBN:0781772214 A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta. MGI:anna this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye ncit UMLS:C0022903 ncithesaurus:Lacrimal_Apparatus apparatus lacrimalis lacrymal system MGI:anna lacrimal drainage system nasolacrimal drainage system nasolacrimal system HPO:pr Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular. Mineralized collagen containing substance that forms the tooth structure.[TAO] Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG] dentinal Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP] BTO:0003453 EMAPA:35281 FMA:55628 GAID:1272 MA:0002542 MESH:A14.254.900.280 NCIT:C32453 TAO:0005143 UMLS:C0011429 VHOG:0001589 VSAO:0000069 XAO:0004051 ZFA:0005143 dentin dentine of tooth predentin uberon UBERON:0001751 . dentine VSAO VSAO Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular. GO_REF:0000034 PSPUB:0000170 VSAO:0000069 Mineralized collagen containing substance that forms the tooth structure.[TAO] 2012-08-14 TAO:0005143 TAO ZFIN:curator Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG] 2012-09-17 VHOG:0001589 VHOG DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) UMLS:C0011429 ncithesaurus:Dentin dentin MA:0002542 dentin ZFA:0005143 predentin GO:0070468 The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO]. The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG] AAO:0011065 BIRNLEX:1695 BTO:0002099 CALOHA:TS-2233 EHDAA2:0001181 EHDAA:5693 EMAPA:17000 EV:0100357 FMA:56513 GAID:165 MA:0000253 MAT:0000146 MESH:D004432 MIAA:0000146 NCIT:C12274 OpenCyc:Mx4rvbw1j5wpEbGdrcN5Y29ycA UMLS:C0013455 UMLS:C1268972 VHOG:0000312 XAO:0000191 uberon auris media UBERON:0001756 middle ear The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO]. GO:0042474 The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000312 VHOG The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG] 2012-09-17 VHOG:0000312 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417 UMLS:C0013455 BIRNLEX:1695 UMLS:C0013455 ncithesaurus:Middle_Ear UMLS:C1268972 BIRNLEX:1695 auris media auris media BTO:0002099 The part of the ear that projects from the head, connecting to the external acoustic meatus. The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG] In various species, the pinna can also signal mood and radiate heat The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch). EHDAA2:0001467 EMAPA:17589 EV:0100355 FMA:56580 MA:0000259 NCIT:C32165 OpenCyc:Mx4rvs_VC5wpEbGdrcN5Y29ycA UMLS:C0928075 VHOG:0000460 galen:Auricle auricle auricle of ear auricle of external ear auricula auricula (auris externa) pinna of ear uberon pinnae UBERON:0001757 pinna The part of the ear that projects from the head, connecting to the external acoustic meatus. The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000460 VHOG Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG] 2012-09-17 VHOG:0000460 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.420 UMLS:C0928075 ncithesaurus:Auricle auricula pinnae Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 10n AAO:0010475 BAMS:10n BAMS:Xn BIRNLEX:801 BTO:0003472 EFO:0002549 EMAPA:37797 FMA:5731 GAID:721 HBA:9337 MA:0001106 MBA:917 MESH:D014630 NCIT:C12812 OpenCyc:Mx4rviHk2ZwpEbGdrcN5Y29ycA TAO:0000453 UMLS:C0042276 UMLS:C1305910 VHOG:0000737 XAO:0003097 ZFA:0000453 galen:VagusNerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 nervus vagus [x] tenth cranial nerve vagus vagus X nerve vagus nerve [X] vagus nerve tree uberon CN-X cranial nerve X nerve X nervus vagus pneuomgastric nerve vagal nerve vagus nerve or its root UBERON:0001759 vagus nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png motor Wikipedia Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). ISBN:0471209627 Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] 2012-06-20 AAO:0010475 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000737 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 10n BIRNLEX:801 NIFSTD:NeuroNames_abbrevSource EMAPA:37797 MA:th UMLS:C0042276 BIRNLEX:801 UMLS:C0042276 ncithesaurus:Vagus_Nerve UMLS:C1305910 BIRNLEX:801 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 BIRNLEX:801 nervus vagus [x] FMA:5731 FMA:TA vagus X nerve MA:0001106 nerve X NeuroNames:702 nervus vagus nervus vagus BTO:0003472 pneuomgastric nerve BTO:0003472 vagus nerve or its root BAMS:10n the small curved bones that extends horizontally along the lateral wall of the nasal passage In humans, the turbinates divide the nasal airway into three groove-like air passages -and are responsible for forcing inhaled air to flow in a steady, regular pattern around the largest possible surface of cilia and climate controlling tissue. Turbinals are only ossified in birds and derived synapsids. FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here EHDAA2:0004101 EMAPA:25093 GAID:224 MA:0000286 MESH:D014420 NCIT:C49594 OpenCyc:Mx4rv07bVJwpEbGdrcN5Y29ycA UMLS:C1266928 ossified nasal turbinal ossified nasal turbinate ossified turbinate turbinal bone turbinate bone uberon concha UBERON:0001762 turbinate bone http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray153.png the small curved bones that extends horizontally along the lateral wall of the nasal passage ISBN:0-683-40008-8 MP:0002244 In humans, the turbinates divide the nasal airway into three groove-like air passages -and are responsible for forcing inhaled air to flow in a steady, regular pattern around the largest possible surface of cilia and climate controlling tissue. WP,unvetted FMA considers nasal concha and nasal concha of ethmoid bone to be synonymous. We disambiguate these here FMA UMLS:C1266928 ncithesaurus:Nasal_Turbinate turbinate bone EMAPA:25093 concha EMAPA:25093 A condensation of odontoblasts that forms the part of a tooth germ that gives rise to dentin and pulp in the mature tooth. It lies below a cellular aggregation known as the enamel organ. Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO] Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO] Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG] In humans, the dental papilla appears after 8-10 weeks intra uteral life BTO:0001839 EMAPA:32892 FMA:57662 GAID:1277 MA:0001598 MESH:A14.254.900.720.250 TAO:0005140 VHOG:0001465 VSAO:0000025 XAO:0004045 ZFA:0005140 odontogenic condensation pharyngeal tooth mesenchyme uberon dental papilla dentinal papilla dermal papilla papilla dentis tooth mesenchyme UBERON:0001763 odontogenic papilla http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png ZFA A condensation of odontoblasts that forms the part of a tooth germ that gives rise to dentin and pulp in the mature tooth. It lies below a cellular aggregation known as the enamel organ. ZFA:0005140 Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO] 2012-08-14 VSAO:0000025 VSAO PSPUB:0000170 Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO] 2012-08-14 TAO:0005140 TAO ZFIN:curator Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG] 2012-09-17 VHOG:0001465 VHOG DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011) odontogenic condensation VSAO:0000025 pharyngeal tooth mesenchyme ZFA:0005140 dental papilla MA:0001598 dentinal papilla BTO:0001839 dermal papilla ISBN:0073040584 papilla dentis tooth mesenchyme ZFA:0005140 the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball BTO:0002084 EHDAA2:0000129 EHDAA:9033 EMAPA:18231 FMA:58078 GAID:889 MA:0000262 MESH:D000867 NCIT:C12667 UMLS:C0003151 VHOG:0001431 anterior chamber anterior chamber of eye camera anterior eye anterior chamber uberon camera anterior bulbi camera anterior bulbi oculi camera oculi anterior UBERON:0001766 anterior chamber of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens MESH:A09.371.060.067 MP:0005205 The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] 2012-09-17 VHOG:0001431 VHOG space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball EHDAA2 UMLS:C0003151 ncithesaurus:Anterior_Chamber_of_the_Eye anterior chamber HP:0000593 MP:0010709 camera anterior bulbi BTO:0002084 camera anterior bulbi oculi camera oculi anterior BTO:0002084 the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus uveal CALOHA:TS-2228 EMAPA:35901 FMA:58103 GAID:912 MA:0002480 MESH:D014602 NCIT:C12811 UMLS:C0042160 tunica vasculosa of eyeball uvea uveal tract uberon pars iridica retinae tunica vasculatis oculi tunica vasculosa bulbi vascular layer of eyeball UBERON:0001768 uvea http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png FMA the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. MP:0005197 UMLS:C0042160 ncithesaurus:Uvea tunica vasculosa of eyeball FMA:58103 uvea FMA:58103 uveal tract FMA:58103 pars iridica retinae tunica vasculatis oculi tunica vasculosa bulbi vascular layer of eyeball FMA:58103 the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] iridial The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019] AAO:0010347 BTO:0000653 CALOHA:TS-0491 EFO:0004245 EMAPA:19154 EV:0100345 FMA:58235 GAID:917 MA:0000273 MESH:D007498 NCIT:C12737 OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA TAO:0001238 UMLS:C0022077 VHOG:0000101 XAO:0000185 ZFA:0001238 uberon anterior uvea irides irises UBERON:0001769 iris XAO the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye ISBN:0-683-40008-8 MP:0001322 The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000101 VHOG The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000101 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) UMLS:C0022077 ncithesaurus:Iris irides irises VHOG:0000101 the smooth stratified squamous epithelium that covers the outer surface of the cornea Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals BTO:0000287 CALOHA:TS-0173 EFO:0001917 EHDAA2:0000319 EMAPA:17162 FMA:58263 GAID:895 MA:0001243 MESH:D019573 NCIT:C12928 TAO:0002187 UMLS:C0459875 ZFA:0001683 anterior corneal epithelium cornea epithelial tissue cornea epithelium epithelial tissue of cornea epithelium anterius (cornea) epithelium anterius corneae epithelium corneæ anterior layer epithelium of cornea external epithelium of cornea uberon anterior endothelium of cornea e. anterius corneae endothelium anterius corneae endothelium camerae anterioris bulbi endothelium corneale epithelium posterius corneae UBERON:0001772 corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png ISBN:0781772214 the smooth stratified squamous epithelium that covers the outer surface of the cornea MESH:A09.371.060.217.325 MGI:smb MP:0006000 Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] 2012-08-14 TAO:0002187 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0459875 ncithesaurus:Corneal_Epithelium cornea epithelial tissue OBOL:automatic cornea epithelium OBOL:automatic epithelial tissue of cornea OBOL:automatic epithelium anterius corneae FMA:58263 FMA:TA anterior endothelium of cornea BTO:0000287 e. anterius corneae endothelium anterius corneae BTO:0000287 endothelium camerae anterioris bulbi BTO:0000287 endothelium corneale BTO:0000287 epithelium posterius corneae BTO:0000287 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] scleral in fish, reptiles and monotremes the connective tissue of the sclera is skeletal continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]. AAO:0010354 BTO:0001606 EMAPA:19027 EV:0100342 FMA:58269 GAID:911 MA:0000280 MESH:D012590 NCIT:C12784 OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA UMLS:C0036410 VHOG:0001274 XAO:0000183 ZFA:0005563 uberon scleral capsule UBERON:0001773 Disease notes: implicated in rheumatoid arthritis. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA ISBN:0781772214 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. ZFIN:ZDB-PUB-050701-15 The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] 2012-09-17 VHOG:0001274 VHOG UMLS:C0036410 ncithesaurus:Sclera A skeletal muscle organ that is part of the trunk region. Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'. Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here. AAO:0000611 EMAPA:35888 FMA:58274 MA:0000514 TAO:0000473 XAO:0003230 ZFA:0000473 body musculature muscle of trunk muscle organ of torso muscle organ of trunk torso muscle organ trunk muscle trunk muscle organ trunk musculature uberon UBERON:0001774 skeletal muscle of trunk prolog A skeletal muscle organ that is part of the trunk region. body musculature ZFA:0000473 muscle of trunk FMA:58274 muscle organ of torso OBOL:automatic muscle organ of trunk OBOL:automatic torso muscle organ OBOL:automatic trunk muscle organ OBOL:automatic the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] AAO:0010341 BTO:0000260 CALOHA:TS-0694 EMAPA:19065 EV:0100346 FMA:58295 GAID:916 MA:0000264 MESH:D002924 NCIT:C12345 UMLS:C0008779 VHOG:0000102 XAO:0000186 ocular ciliary body uberon anterior uvea ciliary bodies corpus ciliare UBERON:0001775 ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg ISBN:0781772214 the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes ISBN:0-683-40008-8 MP:0005099 The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000102 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) UMLS:C0008779 ncithesaurus:Ciliary_Body ciliary bodies VHOG:0000102 corpus ciliare corpus ciliare vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA choroidal MP treats posterior uvea and optic choroid as distinct BTO:0001829 CALOHA:TS-2054 EMAPA:19077 EV:0100347 FMA:58298 GAID:913 MA:0000263 MESH:D002829 NCIT:C12344 TAO:0005229 UMLS:C0008520 VHOG:0001568 ZFA:0005229 choroid choroid coat choroidea eye choroid posterior uvea uberon chorioid choroidea optic choroid UBERON:0001776 optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg MA Wikipedia lexical vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. MP treats posterior uvea and optic choroid as distinct MP UMLS:C0008520 ncithesaurus:Choroid choroid MA:0000263 choroid coat choroidea eye choroid VHOG:0001568 posterior uvea chorioid BTO:0001829 choroidea optic choroid ZFA:0005229 the lamellated connective tissue of the cornea between the Bowman and Descemet membranes Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] substantia propria CALOHA:TS-1138 EFO:0002514 EMAPA:17602 FMA:58306 GAID:893 MA:0001245 MESH:D003319 NCIT:C12699 TAO:0002189 UMLS:C0010040 ZFA:0001685 corneal stroma stroma of cornea substantia propria corneae uberon UBERON:0001777 substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png cjm ISBN:0781772214 Wikipedia the lamellated connective tissue of the cornea between the Bowman and Descemet membranes ISBN:0-683-40008-8 MESH:A09.371.060.217.228 MP:0005300 Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] 2012-08-14 TAO:0002189 TAO ZFIN:ZDB-PUB-061010-3 relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] 2012-08-14 TAO:0002189 TAO relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] 2012-08-14 TAO:0002189 TAO UMLS:C0010040 ncithesaurus:Corneal_Stroma corneal stroma MA:0001245 substantia propria corneae FMA:58306 FMA:TA A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 CALOHA:TS-0695 EMAPA:35239 FMA:58464 MA:0001238 NCIT:C32314 UMLS:C0459736 ciliary body epithelium epithelium of ciliary body ocular ciliary epithelium uberon UBERON:0001778 ciliary epithelium FMA MA Wikipedia A double layer covering the ciliary body that produces aqueous humor. UMLS:C0459736 ncithesaurus:Ciliary_Epithelium ciliary body epithelium FMA:58464 epithelium of ciliary body FMA:58464 The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. EMAPA:35451 FMA:58526 MA:0002777 ZFA:0005569 iridial stroma stroma of iris uberon UBERON:0001779 iris stroma http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified] Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] AAO:0011101 BAMS:spin BTO:0000870 EHDAA2:0001898 EMAPA:16989 FMA:5858 GAID:841 MA:0000233 MESH:D013127 NCIT:C12792 OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA UMLS:C0037941 VHOG:0000824 XAO:0003101 backbone nerve nerve of backbone nerve of spinal column nerve of spine nerve of vertebral column spinal column nerve spinal nerve tree spine nerve vertebral column nerve uberon nervi spinales spinal nerves UBERON:0001780 spinal nerve Spinal:nerve.svg the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified] MESH:A08.800.800.720 MP:0001077 Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] 2012-09-17 VHOG:0000824 VHOG UMLS:C0037941 ncithesaurus:Spinal_Nerve backbone nerve OBOL:automatic nerve of backbone OBOL:automatic nerve of spinal column OBOL:automatic nerve of spine OBOL:automatic nerve of vertebral column OBOL:automatic spinal column nerve OBOL:automatic spine nerve OBOL:automatic vertebral column nerve OBOL:automatic nervi spinales spinal nerves BAMS:spin Any of the layers that make up the retina[MP]. MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers AAO:0010353 EMAPA:35742 FMA:58617 MA:0001319 NCIT:C49328 UMLS:C0459649 XAO:0000266 retina layer retina neuronal layer retinal layer retinal neuronal layer uberon UBERON:0001781 layer of retina Any of the layers that make up the retina[MP]. MP:0003727 MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers MA UMLS:C0459649 ncithesaurus:Retina_Layer retina neuronal layer MP:0006069 retinal neuronal layer MP:0006069 Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6 AAO:0000108 BAMS:cran BIRNLEX:1623 BTO:0001104 EHDAA2:0000323 EMAPA:17264 FMA:5865 GAID:802 HBA:9299 MA:0000215 MBA:967 MESH:D003391 NCIT:C12700 OpenCyc:Mx4rvWvJVpwpEbGdrcN5Y29ycA TAO:0000641 UMLS:C0010268 UMLS:C1269897 VHOG:0000279 XAO:0000429 XAO:0003089 ZFA:0000641 cranial neural tree organ uberon cranial nerves nervus cranialis UBERON:0001785 cranial nerve http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] 2012-08-14 TAO:0000641 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] 2012-09-17 VHOG:0000279 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 UMLS:C0010268 BIRNLEX:1623 UMLS:C0010268 ncithesaurus:Cranial_Nerve UMLS:C1269897 BIRNLEX:1623 nervus cranialis A thick watery refractive medium that fills the space between the lens and the cornea[WP]. The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. EHDAA2:0000139 EHDAA:10196 EMAPA:18232 ENVO:02000024 FMA:58819 GAID:890 MA:0001236 MESH:D001082 NCIT:C13190 OpenCyc:Mx4rvdGd-5wpEbGdrcN5Y29ycA UMLS:C0003662 VHOG:0000548 ZFA:0005564 aqueous humor aqueous humour humor aquosus uberon UBERON:0001796 aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA def states A and P located_in in EHDAA2 VHOG A thick watery refractive medium that fills the space between the lens and the cornea[WP]. The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] 2012-09-17 VHOG:0000548 VHOG (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000548 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. FMA UMLS:C0003662 ncithesaurus:Aqueous_Humor aqueous humour EHDAA2:0000139 humor aquosus FMA:58819 FMA:TA vitreous humor A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina portion of vitreous humor BTO:0001451 CALOHA:TS-0308 EMAPA:17837 ENVO:02000032 EV:0100344 FMA:58822 MA:0001286 NCIT:C13323 OpenCyc:Mx4rv7ZIfZwpEbGdrcN5Y29ycA UMLS:C0229096 VHOG:0000795 ZFA:0005561 humor vitreous humor vitreus vitreous whole portion of vitreous humor uberon humoral fluid ocular fluid vitreous fluid vitreous humour UBERON:0001797 vitreous humor http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina MP:0002699 portion of vitreous humor FMA:67388 UMLS:C0229096 ncithesaurus:Vitreous_Humor humor vitreus FMA:58822 FMA:TA vitreous ZFA:0005561 whole portion of vitreous humor FMA:58822 humoral fluid BTO:0001451 ocular fluid BTO:0001451 vitreous fluid BTO:0001451 Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified] distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body CALOHA:TS-0308 FMA:58827 GAID:919 MA:0002462 MESH:A09.371.943 NCIT:C33884 UMLS:C0042905 uberon UBERON:0001798 vitreous body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA neural ectoderm of optic cup ISBN:0781772214 Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified] MP:0002699 UMLS:C0042905 ncithesaurus:Vitreous_Body The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified]. BTO:0002087 EMAPA:37805 FMA:58848 MA:0002461 NCIT:C33885 UMLS:C0229095 camera postrema camera postrema bulbi oculi camera vitrea camera vitrea bulbi postremal chamber postremal chamber of eyeball vitreous chamber uberon UBERON:0001799 vitreous chamber of eyeball The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified]. BTO:0002087 EMAPA:37805 MA:th UMLS:C0229095 ncithesaurus:Vitreous_Chamber camera postrema FMA:58848 camera postrema bulbi oculi FMA:58848 FMA:TA camera postrema bulbi oculi FMA:TA camera vitrea FMA:58848 camera vitrea bulbi FMA:58848 postremal chamber FMA:58848 postremal chamber of eyeball FMA:58848 vitreous chamber FMA:58848 The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. AEO:0001000 BTO:0005630 EMAPA:36596 FMA:5885 MA:0002566 MESH:D017950 NCIT:C13060 UMLS:C0206429 ganglion sensorium uberon UBERON:0001800 sensory ganglion The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. MP:0000960 UMLS:C0206429 ncithesaurus:Sensory_Ganglion ganglion sensorium any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive) EMAPA:36594 FMA:58865 MA:0002484 MESH:D000869 NCIT:C12668 UMLS:C0003153 ZFA:0005566 anterior eye segment anterior segment eye anterior segment of eye anterior segment of the eye eye anterior segment segmentum anterius (bulbus oculi) uberon segmentum anterius bulbi oculi UBERON:0001801 anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png FMA cjm lexical any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive) ISBN:0-683-40008-8 MESH:A09.371.060 MP:0005193 UMLS:C0003153 ncithesaurus:Anterior_Eye_Segment anterior segment eye ZFA:0005566 segmentum anterius bulbi oculi any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive) EMAPA:36595 FMA:58868 MA:0002485 NCIT:C12906 UMLS:C0278450 ZFA:0005567 eye posterior segment posterior eye segment posterior segment eye posterior segment of eye posterior segment of the eye segmentum posterius (bulbus oculi) uberon segmentum posterius bulbi oculi UBERON:0001802 posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA cjm lexical any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive) ISBN:0-683-40008-8 MP:0005195 UMLS:C0278450 ncithesaurus:Posterior_Eye_Segment posterior segment eye ZFA:0005567 segmentum posterius bulbi oculi A layer of epithelial cells that is part of the eye. this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former BTO:0001873 CALOHA:TS-0543 EMAPA:32871 FMA:58871 MA:0001301 TAO:0001326 XAO:0004094 ZFA:0001326 epithelial tissue of eye lens epithelial tissue of lens epithelium lentis epithelium of eye lens eye lens epithelial tissue eye lens epithelium lens epithelial tissue lens epithelium uberon UBERON:0001803 epithelium of lens A layer of epithelial cells that is part of the eye. epithelial tissue of eye lens OBOL:automatic epithelial tissue of lens OBOL:automatic epithelium lentis FMA:58871 FMA:TA epithelium of eye lens OBOL:automatic eye lens epithelial tissue OBOL:automatic eye lens epithelium OBOL:automatic lens epithelial tissue OBOL:automatic the elastic, clear, membrane-like structure, that is outer most layer of the lens The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular EHDAA2:0000977 EMAPA:18237 FMA:58881 MA:0001300 NCIT:C32975 UMLS:C0229232 VHOG:0000550 ZFA:0005574 capsula lentis lens capsule uberon UBERON:0001804 capsule of lens http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png EHDAA2 the elastic, clear, membrane-like structure, that is outer most layer of the lens MGI:smb MP:0003236 The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000550 VHOG (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000550 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular FMA UMLS:C0229232 ncithesaurus:Lens_Capsule capsula lentis ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. AEO:0001001 CALOHA:TS-2340 EMAPA:17157 EMAPA:18221 FMA:5889 MA:0000220 MESH:D005725 NCIT:C12720 UMLS:C0017068 autonomic nervous system ganglion ganglion of autonomic nervous system ganglion of visceral nervous system visceral nervous system ganglion uberon ganglion autonomicum UBERON:0001805 autonomic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. UMLS:C0017068 ncithesaurus:Autonomic_Ganglion autonomic nervous system ganglion OBOL:automatic ganglion of autonomic nervous system OBOL:automatic ganglion of visceral nervous system OBOL:automatic visceral nervous system ganglion OBOL:automatic ganglion autonomicum A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia AAO:0010773 BTO:0001333 CALOHA:TS-0994 EHDAA2:0001969 EMAPA:17157 FMA:5890 MA:0000226 NCIT:C12467 UMLS:C0017071 ganglion of sympathetic nervous system ganglion of sympathetic part of autonomic division of nervous system ganglion sympatheticum sympathetic nervous system ganglion sympathetic part of autonomic division of nervous system ganglion uberon ganglion sympathicum UBERON:0001806 sympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png ISBN:0073040584 A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia MP:0001008 UMLS:C0017071 ncithesaurus:Sympathetic_Ganglion ganglion of sympathetic nervous system OBOL:automatic ganglion of sympathetic part of autonomic division of nervous system OBOL:automatic sympathetic nervous system ganglion OBOL:automatic sympathetic part of autonomic division of nervous system ganglion OBOL:automatic ganglion sympathicum ganglion sympathicum BTO:0001333 Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands. BTO:0001256 EHDAA2:0001400 EMAPA:32813 FMA:5894 MA:0002469 NCIT:C52557 NLXANAT:100303 UMLS:C0017069 uberon ganglion parasympathicum UBERON:0001808 parasympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands. NLXANAT:100303 UMLS:C0017069 ncithesaurus:Parasympathetic_Ganglion ganglion parasympathicum ganglion parasympathicum BTO:0001256 The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]. Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands. The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In humans, they are situated in the upper, outer portion of each orbit Innervation is highly complex and species-specific BTO:0000044 CALOHA:TS-0512 EFO:0001389 EMAPA:35463 EV:0100339 FMA:59101 MA:0001296 NCIT:C12346 UMLS:C0022907 VHOG:0001476 glandula lacrimalis lacrimal-preorbital gland uberon glandula praeorbitalis preorbital gland tear gland UBERON:0001817 lacrimal gland http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]. Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands. FMA:59101 The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland]. UMLS:C0022907 ncithesaurus:Lacrimal_Gland glandula lacrimalis lacrimal-preorbital gland glandula praeorbitalis NCBITaxon:91561 preorbital gland NCBITaxon:91561 tear gland BTO:0000044 any of the coil glands of the skin that secrete sweat TODO - check if all sweat glands are epidermal - see EMAPA:29743 A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG] Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG] In humans a system of apocrine - and merocrine sweat glands is the main method of cooling. Many other mammals rely on panting or other means as a primary source of cooling, but still use sweat glands to aid in body temperature regulation BTO:0001331 CALOHA:TS-0993 EMAPA:35844 EV:0100160 FMA:59152 GAID:943 MA:0000150 MESH:D013545 NCIT:C33712 OpenCyc:Mx4rvVjx15wpEbGdrcN5Y29ycA UMLS:C0038989 VHOG:0001467 uberon glandula sudorifera sudoriferous gland sudoriparous gland UBERON:0001820 sweat gland http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg definitional any of the coil glands of the skin that secrete sweat ISBN:0-683-40008-8 MP:0000674 A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG] 2012-09-17 VHOG:0001467 VHOG Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG] 2012-09-17 VHOG:0001467 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.101 UMLS:C0038989 ncithesaurus:Sweat_Gland glandula sudorifera BTO:0001331 sudoriferous gland BTO:0001331 sudoriparous gland BTO:0001331 A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass. Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG] Sebaceous glands are also limited to mammals.[well established][VHOG] BTO:0001980 CALOHA:TS-2384 EMAPA:35754 EV:0100161 FMA:59160 GAID:900 MA:0002565 MESH:D012627 NCIT:C33519 UMLS:C0036505 VHOG:0001468 uberon glandula sebacea glandula sebaceae sebaceous follicle UBERON:0001821 sebaceous gland http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png Wikipedia definitional A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]. MP:0000647 Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG] 2012-09-17 VHOG:0001468 VHOG Sebaceous glands are also limited to mammals.[well established][VHOG] 2012-09-17 VHOG:0001468 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.102 UMLS:C0036505 ncithesaurus:Sebaceous_Gland glandula sebacea glandula sebaceae BTO:0001980 sebaceous follicle BTO:0001980 One of the cartilage structures in the nose that provide form and support[WP]. CALOHA:TS-0655 EMAPA:37681 FMA:59502 MA:0001883 NCIT:C49593 UMLS:C0225415 cartilage of nose uberon UBERON:0001823 nasal cartilage http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray852.png MA One of the cartilage structures in the nose that provide form and support[WP]. EMAPA:37681 MA:th UMLS:C0225415 ncithesaurus:Nasal_Cartilage The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. EMAPA:18334 FMA:59662 GAID:301 MA:0001766 MESH:D007820 NCIT:C49246 UMLS:C0023053 laryngeal mucosa larynx mucosa larynx mucosa of organ larynx mucous membrane larynx organ mucosa mucosa of organ of larynx mucous membrane of larynx organ mucosa of larynx tunica mucosa laryngis uberon laryngeal mucous membrane UBERON:0001824 mucosa of larynx The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. MP:0002261 UMLS:C0023053 ncithesaurus:Laryngeal_Mucosa larynx mucosa of organ OBOL:automatic larynx mucous membrane OBOL:automatic larynx organ mucosa OBOL:automatic mucosa of organ of larynx OBOL:automatic organ mucosa of larynx OBOL:automatic tunica mucosa laryngis FMA:59662 FMA:TA laryngeal mucous membrane EMAPA:18334 The mucous membrane that lines the nasal cavity[MP]. TODO - check lining vs part of. split olfactory and nasal mucosa? BTO:0000912 CALOHA:TS-0657 EMAPA:36026 FMA:59684 GAID:302 mucosa of nose mucous membrane of nose tunica mucosa nasalis tunica mucosa nasi uberon nasal mucosa UBERON:0001826 nasal cavity mucosa The mucous membrane that lines the nasal cavity[MP]. MP:0002238 mucosa of nose FMA:59684 mucous membrane of nose FMA:59684 tunica mucosa nasi FMA:59684 FMA:TA Aqueous substance secreted by the lacrimal gland. BTO:0001499 CALOHA:TS-1016 EMAPA:36537 ENVO:02000034 FMA:59756 GAID:1173 MA:0002508 MESH:D013666 NCIT:C33739 UMLS:C0039409 galen:Tear galen:Tears lacrimal fluid lacrimal gland secretion lacrimal secretion tear tears uberon tear fluid UBERON:0001827 secretion of lacrimal gland Aqueous substance secreted by the lacrimal gland. UMLS:C0039409 ncithesaurus:Tear tear FMA:59756 tears tear fluid BTO:0001499 One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. There are 3 pairs of major salivary glands in human and mouse FMA:59788 MA:0002478 NCIT:C12999 UMLS:C0930553 galen:MajorSalivaryGland uberon UBERON:0001829 major salivary gland One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. MP:0003792 There are 3 pairs of major salivary glands in human and mouse ISBN:0123813611 UMLS:C0930553 ncithesaurus:Major_Salivary_Gland One of the two fleshy folds which surround the opening of the mouth. Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] labial BTO:0001647 CALOHA:TS-0558 EMAPA:32839 FMA:59816 GAID:76 MA:0000343 MESH:D008046 NCIT:C12220 OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA TAO:0007006 UMLS:C0023759 VHOG:0000677 ZFA:0007006 galen:Lip uberon labia oris lips UBERON:0001833 lip http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg ZFA BTO FMA-implicit VHOG ZFA cjm One of the two fleshy folds which surround the opening of the mouth. Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] 2012-08-14 TAO:0007006 TAO ZFIN:curator UMLS:C0023759 ncithesaurus:Lip labia oris Lip that covers the lower portion of the mouth.[TAO]. Lip that covers the lower portion of the mouth.[TAO] UBERON:0003392 EHDAA2:0001020 EMAPA:17909 FMA:59818 MA:0000921 NCIT:C94572 OpenCyc:Mx4rv842UpwpEbGdrcN5Y29ycA TAO:0002060 UMLS:C0458583 ZFA:0005225 lower jaw lip uberon labium inferius oris UBERON:0001835 lower lip http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg Lip that covers the lower portion of the mouth.[TAO]. TAO:0002060 Lip that covers the lower portion of the mouth.[TAO] 2012-08-14 TAO:0002060 TAO TAO:wd UMLS:C0458583 ncithesaurus:Lower_Lip lower jaw lip labium inferius oris A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. salivary We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin BTO:0001202 CALOHA:TS-0891 EMAPA:36536 ENVO:02000036 FMA:59862 GAID:1167 MA:0002507 MAT:0000444 MESH:D012463 NCIT:C13275 OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA UMLS:C0036087 galen:Saliva salivary gland secretion uberon sailva normalis saliva atomaris saliva molecularis UBERON:0001836 saliva A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. GO:0046541 We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin GO UMLS:C0036087 ncithesaurus:Saliva salivary gland secretion FMA:59862 sailva normalis saliva atomaris saliva molecularis The duct of a salivary gland. BTO:0005115 EMAPA:35750 FMA:59908 GAID:939 MA:0001586 MESH:D018987 NCIT:C32486 salivary duct salivary gland duct uberon secretory duct UBERON:0001837 duct of salivary gland The duct of a salivary gland. secretory duct BTO:0005115 A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]. AAO:0011078 BTO:0004685 CALOHA:TS-2080 EMAPA:36580 EV:0100362 FMA:60179 MA:0000238 NCIT:C33227 UMLS:C0458699 VHOG:0001219 XAO:0000193 osseous labyrinth uberon labyrinthus osseus osseus labyrinth UBERON:0001839 Ideally we would place a spatially disjoint from relationship to membranous labyrinth, but there are many parts in common. this should be resolved. bony labyrinth http://upload.wikimedia.org/wikipedia/commons/2/22/Gray920.png FMA MA FMA A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]. UMLS:C0458699 ncithesaurus:Osseous_Labyrinth labyrinthus osseus the spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified]. A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG] Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG] cochlear The association with 'lagena' in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: 'In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)' the cochlea is coiled in most mammals, monotremes being the exceptions. sources vary in connection to bony labyrinth AAO:0000253 BIRNLEX:1190 BTO:0000267 CALOHA:TS-0151 EFO:0000357 EMAPA:17597 EV:0100363 FMA:60201 GAID:724 MA:0000240 MAT:0000144 MESH:D003051 MIAA:0000144 NCIT:C12395 NIFSTD_RETIRED:birnlex_883 OpenCyc:Mx4rvqfJmJwpEbGdrcN5Y29ycA TAO:0000374 UMLS:C0009195 UMLS:C1278895 VHOG:0000691 XAO:0000197 ZFA:0000374 cochlear part of bony labyrinth lagena uberon cochleae cochlear duct cochlear organ lagenas UBERON:0001844 cochlea http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg FMA VHOG XAO ncit the spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified]. ISBN:0-683-40008-8 MP:0000031 A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG] 2012-09-17 VHOG:0000691 VHOG Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG] 2012-09-17 VHOG:0000691 VHOG DOI:10.1016/S0959-4388(98)80033-0 Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998) sources vary in connection to bony labyrinth XAO UMLS:C0009195 BIRNLEX:1190 UMLS:C0009195 ncithesaurus:Cochlea UMLS:C1278895 BIRNLEX:1190 lagena XAO:0000197 cochleae cochlear organ BTO:0000267 lagenas ZFA:0000374 Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation. The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO] The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] AAO:0000238 BIRNLEX:1196 BTO:0000630 CALOHA:TS-0478 EFO:0001363 EHDAA2:0000831 EHDAA:504 EMAPA:16194 EV:0100361 FMA:60909 GAID:871 MA:0000237 MAT:0000145 MESH:D007758 MIAA:0000145 NCIT:C12499 OpenCyc:Mx4rwJ8SsJwpEbGdrcN5Y29ycA TAO:0000217 UMLS:C0022889 UMLS:C1268973 VHOG:0000284 XAO:0000192 ZFA:0000217 galen:InnerEar inner ear uberon auris interna labyrinth otocyst UBERON:0001846 internal ear http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png definitional Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation. ZFIN:curator The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000217 TAO ZFIN:curator The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000284 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366 UMLS:C0022889 BIRNLEX:1196 UMLS:C0022889 ncithesaurus:Internal_Ear UMLS:C1268973 BIRNLEX:1196 auris interna BTO:0000630 cartilage of the pinna and much of the external ear canal. EMAPA:35158 FMA:61013 MA:0001227 cartilage of pinna pinna cartilage uberon UBERON:0001848 auricular cartilage cartilage of the pinna and much of the external ear canal. cartilage of pinna FMA:61013 A collection of channels that connects the conjunctival sac with the nasal cavity, encompassing the lacrimal ducts, the lacrimal sac and the naso-lacrimal duct. TODO - resolve lacrimal canaliculus vs larcimal duct chelonians lack a lacrimal duct, and lacrimal/harderian secretions remain in or spill from the conjunctival sac[PMID:7559104] EMAPA:19245 FMA:61063 MA:0001295 uberon lacrimal duct tear duct UBERON:0001850 lacrimal drainage system FMA FMA A collection of channels that connects the conjunctival sac with the nasal cavity, encompassing the lacrimal ducts, the lacrimal sac and the naso-lacrimal duct. lacrimal duct FMA:61063 MA:0001295 tear duct MA:0001295 Outermost layer of an organ[WP]. cortical this class is used more generically than in FMA, and includes e.g. cortex of hair EFO:0000383 EHDAA:9344 FMA:61109 galen:Cortex cortex cortex of organ uberon UBERON:0001851 cortex Outermost layer of an organ[WP]. this class is used more generically than in FMA, and includes e.g. cortex of hair FMA cortex FMA:61109 Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP]. The composition of sebum varies across species. In humans, the lipid content is as follows: 25% wax monoesters, 41% triglycerides, 16% free fatty acids, 12% squalene; Sapienic acid is a sebum fatty acid that is unique to humans. waterproofs skin BTO:0001981 ENVO:02000037 FMA:61304 GAID:1168 MA:0002538 MESH:D012629 NCIT:C13276 UMLS:C0036511 uberon UBERON:0001866 sebum Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP]. BTO:0001981 UMLS:C0036511 ncithesaurus:Sebum A cartilage that is part of a external ear [Automatically generated definition]. EMAPA:37706 FMA:61339 GAID:103 MA:0001886 MESH:A02.165.207 NCIT:C49225 UMLS:C0013445 external ear cartilage uberon UBERON:0001867 cartilage of external ear A cartilage that is part of a external ear [Automatically generated definition]. OBOL:automatic EMAPA:37706 MA:th UMLS:C0013445 ncithesaurus:External_Ear_Cartilage A zone of skin that is part of a chest [Automatically generated definition]. check FMA:61415 EMAPA:37279 FMA:61416 MA:0000553 anterior thoracic region zone of skin anterolateral part of thorax zone of skin chest skin chest zone of skin front of thorax zone of skin zone of skin of anterior chest zone of skin of anterior part of thorax zone of skin of anterior thoracic region zone of skin of anterolateral part of thorax zone of skin of chest zone of skin of front of thorax uberon zone of skin of pectoral part of chest UBERON:0001868 skin of chest A zone of skin that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37279 MA:th anterior thoracic region zone of skin OBOL:automatic anterolateral part of thorax zone of skin OBOL:automatic chest zone of skin OBOL:automatic front of thorax zone of skin OBOL:automatic zone of skin of anterior chest FMA:61416 zone of skin of anterior part of thorax FMA:61416 zone of skin of anterior thoracic region OBOL:automatic zone of skin of anterolateral part of thorax OBOL:automatic zone of skin of chest OBOL:automatic zone of skin of front of thorax OBOL:automatic zone of skin of pectoral part of chest FMA:61417 One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA] Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO] The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG] AAO:0010480 BAMS:HEM BIRNLEX:1042 BTO:0000231 CALOHA:TS-2007 DMBA:15739 EFO:0002521 EMAPA:16653 FMA:61817 MA:0000133 MBA:403 NCIT:C12351 OpenCyc:Mx4rvigx5ZwpEbGdrcN5Y29ycA UMLS:C0228174 UMLS:C0242202 VHOG:0001639 galen:CerebralHemisphere http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=241 uberon cerebrum hemisphere hemispheric regions hemispherium cerebri medial amygdalar nucleus nucleus amygdaloideus medialis nucleus medialis amygdalae UBERON:0001869 cerebral hemisphere http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png FMA-abduced-lr One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA] FMA:61817 Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO] 2012-06-20 AAO:0010480 AAO AAO:BJB The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG] 2012-09-17 VHOG:0001639 VHOG DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981) UMLS:C0228174 ncithesaurus:Cerebral_Hemisphere UMLS:C0242202 BIRNLEX:1042 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=241 BIRNLEX:1042 cerebrum MA:0000133 VHOG:0001639 hemisphere VHOG:0001639 hemispheric regions BAMS:HEM hemispherium cerebri medial amygdalar nucleus NeuroNames:241 nucleus amygdaloideus medialis NeuroNames:241 nucleus medialis amygdalae NeuroNames:241 Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]. Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally. BTO:0000484 DHBA:10161 DMBA:16002 EMAPA:35357 FMA:242199 GAID:674 MA:0000905 NLXANAT:20090601 cortex of frontal lobe frontal lobe cortex gray matter of frontal lobe grey matter of frontal lobe uberon frontal neocortex UBERON:0001870 frontal cortex http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray729.png Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]. NLXANAT:20090601 Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally. NLXANAT:20090601 cortex of frontal lobe FMA:242199 frontal lobe cortex FMA:242199 gray matter of frontal lobe FMA:242199 frontal neocortex DHBA:10161 Lower lateral part of the cerebral hemisphere. (MSH) BAMS:TL BAMS:Temporal_lobe BIRNLEX:1160 BTO:0001355 CALOHA:TS-1020 DHBA:12139 EFO:0000917 EMAPA:18797 EV:0100169 FMA:61825 GAID:635 HBA:4132 MAT:0000508 MESH:A08.186.211.730.885.213.863 NCIT:C12353 OpenCyc:Mx4rwQLi-ZwpEbGdrcN5Y29ycA UMLS:C0039485 UMLS:C1268978 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=125 lobus temporalis temporal cortex uberon UBERON:0001871 Boundary notes: It is bounded dorsally by the lateral fissure and posteriorly by an arbitrary border shared with the occipital lobe. [Wikipedia:Temporal_lobe] temporal lobe http://upload.wikimedia.org/wikipedia/commons/9/91/Gray730.png FMA Lower lateral part of the cerebral hemisphere. (MSH) BIRNLEX:1160 UMLS:C0039485 BIRNLEX:1160 UMLS:C0039485 ncithesaurus:Temporal_Lobe UMLS:C1268978 BIRNLEX:1160 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=125 BIRNLEX:1160 lobus temporalis Upper central part of the cerebral hemisphere. (MSH) parietal region BAMS:Parietal_lobe BIRNLEX:1148 BTO:0001001 CALOHA:TS-0747 DHBA:12131 EFO:0000914 EV:0100168 FMA:61826 GAID:680 HBA:4084 MAT:0000506 MESH:A08.186.211.730.885.213.670 NCIT:C12354 OpenCyc:Mx4rvg-typwpEbGdrcN5Y29ycA UMLS:C0030560 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=95 regio parietalis uberon lobus parietalis UBERON:0001872 parietal lobe http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray726_parietal_lobe.png FMA Upper central part of the cerebral hemisphere. (MSH) BIRNLEX:1148 UMLS:C0030560 BIRNLEX:1148 UMLS:C0030560 ncithesaurus:Parietal_Lobe_of_the_Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=95 BIRNLEX:1148 regio parietalis FMA:61826 FMA:TA lobus parietalis A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] BAMS:phn BTO:0001063 EHDAA:4677 EMAPA:17813 FMA:6191 GAID:848 MA:0001170 MESH:D010791 NCIT:C52813 OpenCyc:Mx4rvtmdUJwpEbGdrcN5Y29ycA UMLS:C0031774 VHOG:0000728 uberon diaphragmatic nerve nervus phrenicus phrenic UBERON:0001884 phrenic nerve http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. VHOG:0000728 A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] 2012-09-17 VHOG:0000728 VHOG UMLS:C0031774 ncithesaurus:Phrenic_Nerve diaphragmatic nerve BTO:0001063 nervus phrenicus nervus phrenicus BTO:0001063 phrenic BTO:0001063 A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces. TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO] Fringe of the tela choroidea of the brain ventricles[MP] choroidal CP BAMS:CHP BAMS:GHP BAMS:chp BAMS:chpl BTO:0000258 CALOHA:TS-0145 EFO:0001915 EMAPA:32741 FMA:61934 GAID:607 MA:0000823 MBA:108 MESH:D002831 NCIT:C12694 TAO:0001443 UMLS:C0008524 VHOG:0001377 ZFA:0001443 chorioid plexus plexus choroideus uberon choroid plexus of cerebral hemisphere plexus choroideus ventricular choroid plexus UBERON:0001886 choroid plexus http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray708.svg A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces. ISBN:0471888893 A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO] 2012-08-14 TAO:0001443 TAO ZFIN:curator Fringe of the tela choroidea of the brain ventricles[MP] MP:0000820 CP UMLS:C0008524 ncithesaurus:Choroid_Plexus chorioid plexus FMA:61934 plexus choroideus FMA:61934 FMA:TA choroid plexus of cerebral hemisphere FMA:61934 plexus choroideus EHDAA2:0001463 EMAPA:37718 FMA:6198 MA:0001177 phrenic nerve trunk phrenic neural trunk uberon UBERON:0001889 trunk of phrenic nerve EMAPA:37718 MA:th The most anterior region the brain including both the telencephalon and diencephalon. Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] prosencephalic FB AAO:0010147 BAMS:FB BAMS:Forebrain BIRNLEX:1509 BTO:0000478 CALOHA:TS-0380 DHBA:10156 DMBA:15566 EFO:0000909 EHDAA2:0000556 EHDAA:3470 EMAPA:16895 FMA:61992 MA:0000170 MAT:0000105 MESH:D016548 MIAA:0000105 NCIT:C40185 TAO:0000109 UMLS:C0085140 VHOG:0000383 XAO:0000011 ZFA:0000109 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=27 uberon prosencephalon UBERON:0001890 forebrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional The most anterior region the brain including both the telencephalon and diencephalon. ZFIN:ZDB-PUB-961014-576 Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] 2012-06-20 AAO:0010147 AAO AAO:BJB The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000109 TAO ZFIN:curator relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] 2012-08-14 TAO:0000109 TAO In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] 2012-09-17 VHOG:0000383 VHOG PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996) FB BIRNLEX:1509 NIFSTD:NeuroNames_abbrevSource UMLS:C0085140 BIRNLEX:1509 UMLS:C0085140 ncithesaurus:Fore-Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=27 BIRNLEX:1509 The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised Middle part of the brain composed of the optic tectum and penducular region.[AAO] The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] mesencephalic part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships MB AAO:0010149 BAMS:MES BIRNLEX:1667 BM:MB BTO:0000138 CALOHA:TS-0630 DHBA:10648 DMBA:16649 EFO:0000919 EHDAA2:0001162 EHDAA:3694 EMAPA:16974 EV:0100242 FMA:61993 HBA:9001 MA:0000207 MAT:0000106 MBA:313 MESH:D008636 MIAA:0000106 NCIT:C12510 OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001104 TAO:0000128 UMLS:C0025462 VHOG:0000069 XAO:0000014 ZFA:0000128 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 uberon mesencephalon UBERON:0001891 midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG definitional Bgee:AN The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. GO:0030901 Middle part of the brain composed of the optic tectum and penducular region.[AAO] 2012-06-20 AAO:0010149 AAO AAO:BJB The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000128 TAO ZFIN:curator Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000069 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships ABA MB BIRNLEX:1667 NIFSTD:NeuroNames_abbrevSource UMLS:C0025462 BIRNLEX:1667 UMLS:C0025462 ncithesaurus:Mesencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 BIRNLEX:1667 mesencephalon A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] In human embryonic development, the rhombomeres are present by day 29 DHBA divides this into A(1-3),B(4),C(5-7) and D(8) hindbrain segment segment of hindbrain DHBA:12664 EFO:0003617 EMAPA:16148 FMA:295666 MAT:0000272 MIAA:0000272 RETIRED_EHDAA2:0000669 TAO:0001064 VHOG:0000672 XAO:0004079 ZFA:0001064 hindbrain neuromere hindbrain neuromeres rhombomere uberon future rhombencephalon rhombomeres UBERON:0001892 rhombomere A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. ZFIN:curator A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001064 TAO ZFIN:curator Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] 2012-09-17 VHOG:0000672 VHOG DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002) hindbrain segment ZFA:0001064 segment of hindbrain ZFA:0001064 hindbrain neuromeres DHBA:HNM future rhombencephalon MIAA:0000272 rhombomeres VHOG:0000672 Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] cerebral telenencephalic In mammals the cortex covers almost the whole of the cerebral hemispheres. In ray-finned fishes and most pronounced in teleosts the roof plate of the embryonic telencephalon extends laterally with the effect that the paired alar plates forming the hemispheric walls roll out lateroventrally in a process called eversion. This is unlike the development in other vertebrate groups. [ZFA:0000079, ISBN:3764351209] In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. supratentorial region AAO:0010479 BAMS:CB BAMS:CH BAMS:IV BAMS:Tel BIRNLEX:1115 BM:Tel BTO:0000239 CALOHA:TS-1018 DHBA:10158 EFO:0000912 EHDAA2:0001982 EMAPA:16910 EV:0100165 FMA:62000 GAID:621 HBA:4007 MA:0000183 MAT:0000421 MBA:567 MESH:D013687 MIAA:0000421 PBA:128011350 TAO:0000079 UMLS:C0039452 VHOG:0000283 XAO:0000012 ZFA:0000079 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 cerebrum endbrain uberon UBERON:0001893 telencephalon Bgee:AN Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. AAO:0010479 XAO:0000012 Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. FMA:62000 Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] 2012-06-20 AAO:0010479 AAO AAO:BJB The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000079 TAO ZFIN:curator relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] 2012-08-14 TAO:0000079 TAO From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] 2012-09-17 VHOG:0000283 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) In mammals the cortex covers almost the whole of the cerebral hemispheres. In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. supratentorial region UMLS:C0039452 BIRNLEX:1115 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 BIRNLEX:1115 cerebrum BTO:0000239 EMAPA:16910 FMA:62000 endbrain Swanson:2004 The division of the forebrain that develops from the foremost primary cerebral vesicle. The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] diencephalic in ABA, this is part of the brain stem DiE AAO:0010481 BAMS:DI BAMS:Di BAMS:DiE BAMS:IB BAMS:Zh. BIRNLEX:1503 BM:Die BTO:0000342 CALOHA:TS-0199 DHBA:10389 DMBA:16308 EFO:0000911 EHDAA2:0000385 EHDAA:1969 EHDAA:2645 EHDAA:3472 EMAPA:16896 EV:0100194 FMA:62001 GAID:618 HBA:4391 MA:0000171 MAT:0000420 MBA:1129 MESH:A08.186.211.730.385 MIAA:0000420 NCIT:C12456 OpenCyc:Mx4rwC-V0JwpEbGdrcN5Y29ycA PBA:128013010 TAO:0000101 UMLS:C0012144 VHOG:0000318 XAO:0000013 ZFA:0000101 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=288 between brain interbrain mature diencephalon thalamencephalon uberon betweenbrain diencephalon UBERON:0001894 diencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional definitional The division of the forebrain that develops from the foremost primary cerebral vesicle. not well differentiated from the cerebrum. (Ariens, p. 868) The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000101 TAO ZFIN:curator Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] 2012-06-20 AAO:0010481 AAO AAO:BJB Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000318 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) in ABA, this is part of the brain stem ABA DiE BIRNLEX:1503 NIFSTD:NeuroNames_abbrevSource UMLS:C0012144 BIRNLEX:1503 UMLS:C0012144 ncithesaurus:Diencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=288 BIRNLEX:1503 interbrain Swanson:2004 mature diencephalon FMA:62001 thalamencephalon MGI:anna betweenbrain BTO:0000342 diencephalon Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] epencephalon BAMS:Met BIRNLEX:965 BTO:0000673 CALOHA:TS-2029 DHBA:10655 EHDAA2:0001149 EHDAA:5498 EMAPA:17071 FMA:62003 GAID:594 HBA:4833 MA:0000197 MESH:D020540 NCIT:C32741 UMLS:C0376353 UMLS:C1516904 VHOG:0000741 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=543 epencephalon-2 uberon UBERON:0001895 the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA]. metencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. BIRNLEX:965 The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] 2012-09-17 VHOG:0000741 VHOG The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000741 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 epencephalon ncithesaurus:Epencephalon UMLS:C0376353 BIRNLEX:965 UMLS:C1516904 ncithesaurus:Epencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=543 BIRNLEX:965 epencephalon-2 FMA:62003 Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] bulb medulla AAO:0010486 BAMS:MY BAMS:Md BIRNLEX:957 BM:Me BTO:0000041 CALOHA:TS-0607 DMBA:17352 EFO:0000924 EHDAA2:0001088 EHDAA:7588 EMAPA:17550 EV:0100275 FMA:62004 GAID:590 MA:0000206 MAT:0000111 MAT:0000367 MBA:354 MESH:D008526 MIAA:0000111 NCIT:C12442 OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA TAO:0000545 UMLS:C0025148 UMLS:C1269575 VHOG:0000181 XAO:0003100 ZFA:0000545 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 bulbus uberon medulla oblonzata metepencephalon UBERON:0001896 medulla oblongata http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. FMA:62004 GO:0021550 Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] 2012-06-20 AAO:0010486 AAO AAO:BJB The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000181 VHOG Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000181 VHOG DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008) medulla ABA:MY UMLS:C0025148 BIRNLEX:957 UMLS:C0025148 ncithesaurus:Medulla_Oblongata UMLS:C1269575 BIRNLEX:957 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 BIRNLEX:957 bulbus FMA:62004 FMA:TA medulla oblonzata metepencephalon FMA:62004 Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87). One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG] Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO] (...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG] thalamic Th thalamus AAO:0010483 BAMS:TH BAMS:Th BIRNLEX:954 BTO:0001365 CALOHA:TS-1031 DHBA:10390 DMBA:16376 EFO:0000910 EMAPA:17540 EV:0100195 GAID:656 HBA:4392 MA:0000179 MAT:0000109 MBA:549 MESH:A08.186.211.730.385.826 MIAA:0000109 NCIT:C12459 OpenCyc:Mx4rwMPQ65wpEbGdrcN5Y29ycA PBA:128013014 TAO:0001215 UMLS:C0039729 VHOG:0000657 ZFA:0001215 galen:Thalamus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=300 wider thalamus uberon thalamencephalon thalami thalamus opticus UBERON:0001897 dorsal plus ventral thalamus http://upload.wikimedia.org/wikipedia/commons/c/ce/Brain_chrischan_thalamus.jpg FMA-abduced-lr Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87). BIRNLEX:954 One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG] 2012-09-17 VHOG:0000657 VHOG Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO] 2012-06-20 AAO:0010483 AAO AAO:BJB (...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG] 2012-09-17 VHOG:0000657 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.484 Th BIRNLEX:954 NIFSTD:NeuroNames_abbrevSource thalamus FMA:62007 MA:0000179 UMLS:C0039729 BIRNLEX:954 UMLS:C0039729 ncithesaurus:Thalamus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=300 BIRNLEX:954 wider thalamus PMCID:PMC3345571 thalamencephalon NeuroNames:300 thalami VHOG:0000657 thalamus opticus NeuroNames:300 A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]. A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO] Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO] For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG] hypothalamic all vertebrates contain a hypothalamus Hy AAO:0010484 BAMS:HY BAMS:Hy BIRNLEX:734 BM:Die-Hy BTO:0000614 CALOHA:TS-0469 DHBA:10467 EFO:0000107 EHDAA2:0000802 EHDAA:5446 EMAPA:17536 EV:0100225 FMA:62008 GAID:460 HBA:4540 MA:0000173 MAT:0000112 MBA:1097 MESH:A08.186.211.577.482 MIAA:0000112 NCIT:C12458 OpenCyc:Mx4rwEgr9JwpEbGdrcN5Y29ycA TAO:0000032 UMLS:C0020663 VHOG:0000179 XAO:0004070 ZFA:0000032 galen:Hypothalamus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=292 preoptico-hypothalamic area preoptico-hypothalamic region uberon hypothalamus UBERON:0001898 hypothalamus http://upload.wikimedia.org/wikipedia/commons/9/9f/LocationOfHypothalamus.jpg FMA EHDAA2 Wikipedia A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]. ZFIN:curator Lancelets possess a region similar to the hypothalamus (Murakami, 2005) Ariens, p. 1192 A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000032 TAO ZFIN:curator Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO] 2012-06-20 AAO:0010484 AAO AAO:BJB For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000179 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) all vertebrates contain a hypothalamus WP Hy BIRNLEX:734 NIFSTD:NeuroNames_abbrevSource UMLS:C0020663 BIRNLEX:734 UMLS:C0020663 ncithesaurus:Hypothalamus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=292 BIRNLEX:734 hypothalamus Most dorsal part of the thalamus, comprising the pineal gland and habenular nuclei in most vertebrates. In a few vertebrates, it also includes the parietal eye. (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed, 2005, pg. 345-346. Dorsal segment of the diencephalon containing the habenular ganglia, a choroid plexus, and the pineal organ.[AAO] The roof of the diencephalon lying above the thalamus. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-11, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage.[well established][VHOG] epithalamic ETh AAO:0010482 BAMS:EPI BAMS:ETh BAMS:EpT BAMS:Epi BIRNLEX:1710 BM:Die-Epi BTO:0000175 CALOHA:TS-2060 DHBA:10451 EFO:0000918 EHDAA2:0000448 EHDAA:5433 EMAPA:17532 EV:0100220 FMA:62009 GAID:455 HBA:4520 MA:0000172 MAT:0000422 MBA:958 MESH:A08.186.211.577.200 MIAA:0000422 NCIT:C12457 OpenCyc:Mx4rvneLQpwpEbGdrcN5Y29ycA PBA:128013147 TAO:0000509 UMLS:C0152361 VHOG:0000178 ZFA:0000509 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=292 uberon epithalamus UBERON:0001899 epithalamus http://upload.wikimedia.org/wikipedia/commons/c/cb/Epithalamus.png Most dorsal part of the thalamus, comprising the pineal gland and habenular nuclei in most vertebrates. In a few vertebrates, it also includes the parietal eye. (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed, 2005, pg. 345-346. BIRNLEX:1710 Dorsal segment of the diencephalon containing the habenular ganglia, a choroid plexus, and the pineal organ.[AAO] 2012-06-20 AAO:0010482 AAO AAO:BJB The roof of the diencephalon lying above the thalamus. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-11, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000178 VHOG The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage.[well established][VHOG] 2012-09-17 VHOG:0000178 VHOG DOI:10.1046/j.1469-7580.2001.19910063.x Concha ML and Wilson SW, Asymmetry in the epithalamus of vertebrates. J Anat (2001) ETh BIRNLEX:1710 NIFSTD:NeuroNames_abbrevSource UMLS:C0152361 BIRNLEX:1710 UMLS:C0152361 ncithesaurus:Epithalamus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=292 BIRNLEX:1710 epithalamus the epithelial lining of the trachea which contains numerous ciliated cells UBERON:0003227 BTO:0001389 CALOHA:TS-1061 EHDAA2:0002069 EHDAA:5007 EMAPA:16855 EMAPA:18409 FMA:62015 MA:0001862 NCIT:C33797 UMLS:C1179002 VHOG:0001045 epithelial tissue of trachea epithelial tissue of windpipe epithelium of windpipe trachea epithelial tissue trachea epithelium tracheal epithelium windpipe epithelial tissue windpipe epithelium uberon UBERON:0001901 epithelium of trachea the epithelial lining of the trachea which contains numerous ciliated cells ISBN:0-397-51047-0 MGI:cwg MP:0002285 UMLS:C1179002 ncithesaurus:Tracheal_Epithelium epithelial tissue of trachea OBOL:automatic epithelial tissue of windpipe OBOL:automatic epithelium of windpipe OBOL:automatic trachea epithelial tissue OBOL:automatic windpipe epithelial tissue OBOL:automatic windpipe epithelium OBOL:automatic An epithelium that is part of a small intestine [Automatically generated definition]. Intestinal epithelium which lines the lumen of the mid intestine.[TAO] BTO:0001258 CALOHA:TS-2104 EMAPA:35778 FMA:62017 MA:0001553 TAO:0005127 ZFA:0005127 epithelial tissue of small bowel epithelial tissue of small intestine epithelium of small bowel mid intestine epithelium small bowel epithelial tissue small bowel epithelium small intestinal epithelium small intestine epithelial tissue small intestine epithelium uberon UBERON:0001902 epithelium of small intestine An epithelium that is part of a small intestine [Automatically generated definition]. OBOL:automatic Intestinal epithelium which lines the lumen of the mid intestine.[TAO] 2012-08-14 TAO:0005127 TAO ZFIN:curator epithelial tissue of small bowel OBOL:automatic epithelial tissue of small intestine OBOL:automatic epithelium of small bowel OBOL:automatic mid intestine epithelium ZFA:0005127 small bowel epithelial tissue OBOL:automatic small bowel epithelium OBOL:automatic small intestine epithelial tissue OBOL:automatic A midline, cone like structure located in the dorso-caudal roof of the 3rd ventricle, attached by peduncles to the habenular and posterior commissures. The stalk contains nerve fibers, blood vessels, connective tissue and parenchymal cells (Paxinos, The Rat Central Nervous System, 2nd ed, pg 399). A circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon. Kimmel et al, 1995.[TAO] Anatomical structure which is a medial outgrowth of the thalamus on the dorsal surface of the brain. This structure is light sensitive and secretes melatonin when exposed to prolonged darkness.[AAO] relationship loss: part_of pineal complex (TAO:0001359)[TAO] The pineal gland has evolved from a part of the epiphyseal complex of anamniotes, which includes a median light-receptive pineal eye, parietal eye, or both.[well established][VHOG] epiphyseal epiphysial lobulated in humans, homogeneous in mouse. Calcifies with age in humans. Pi AAO:0010549 BAMS:PIN BAMS:Pi BIRNLEX:1184 BM:P BTO:0001067 CALOHA:TS-0789 DHBA:10460 EFO:0000865 EHDAA2:0001466 EHDAA:7523 EMAPA:18778 EV:0100131 EV:0100221 FMA:62033 GAID:453 HBA:4532 MA:0000175 MAT:0000448 MBA:953 MESH:D010870 NCIT:C12398 NLXANAT:1010009 OpenCyc:Mx4rv2FMGpwpEbGdrcN5Y29ycA TAO:0000019 UMLS:C0031939 VHOG:0000051 XAO:0000160 ZFA:0000019 galen:PinealGland http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=297 corpus pineale glandula pinealis pineal gland pineal organ uberon conarium epiphysis epiphysis cerebri frontal organ pineal pineal gland (Galen) stirnorgan UBERON:0001905 pineal body http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg MA ZFA various A midline, cone like structure located in the dorso-caudal roof of the 3rd ventricle, attached by peduncles to the habenular and posterior commissures. The stalk contains nerve fibers, blood vessels, connective tissue and parenchymal cells (Paxinos, The Rat Central Nervous System, 2nd ed, pg 399). BIRNLEX:1184 Hardisty, p. 310 A circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000019 TAO ZFIN:curator Anatomical structure which is a medial outgrowth of the thalamus on the dorsal surface of the brain. This structure is light sensitive and secretes melatonin when exposed to prolonged darkness.[AAO] 2012-06-20 AAO:0010549 AAO AAO:BJB relationship loss: part_of pineal complex (TAO:0001359)[TAO] 2012-08-14 TAO:0000019 TAO The pineal gland has evolved from a part of the epiphyseal complex of anamniotes, which includes a median light-receptive pineal eye, parietal eye, or both.[well established][VHOG] 2012-09-17 VHOG:0000051 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.516 Pi BIRNLEX:1184 NIFSTD:NeuroNames_abbrevSource UMLS:C0031939 BIRNLEX:1184 UMLS:C0031939 ncithesaurus:Pineal_Gland http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=297 BIRNLEX:1184 glandula pinealis FMA:62033 FMA:TA glandula pinealis FMA:TA pineal gland FMA:62033 pineal organ ZFA:0000019 conarium BIRNLEX:1184 epiphysis ZFA:0000019 epiphysis cerebri frontal organ VHOG:0000051 pineal VHOG:0000051 pineal gland (Galen) NeuroNames:297 stirnorgan VHOG:0000051 A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. mammary gland An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0235 mammal milk milk LanguaL curation note: See scope note for *MILK OR MILK COMPONENT*. for lowfat milk use *FAT PARTIALLY REMOVED*; for skim milk, use *FAT FULLY REMOVED* (both found in D3. TREATMENT APPLIED). LanguaL term definition: Milk is a secretion from the mammary glands of female mammals. milk An endothelium that is part of a capillary [Automatically generated definition]. BTO:0004954 CALOHA:TS-0112 EMAPA:36292 FMA:62114 MA:0000711 NCIT:C49215 UMLS:C0006904 blood capillary endothelium capillary endothelium capillary vessel endothelium endothelium of blood capillary endothelium of capillary vessel uberon UBERON:0001915 endothelium of capillary An endothelium that is part of a capillary [Automatically generated definition]. OBOL:automatic UMLS:C0006904 ncithesaurus:Capillary_Endothelium blood capillary endothelium OBOL:automatic capillary vessel endothelium OBOL:automatic endothelium of blood capillary OBOL:automatic endothelium of capillary vessel OBOL:automatic An endothelium that is part of an arteriole [Automatically generated definition]. EMAPA:36286 FMA:62115 MA:0000705 NCIT:C49192 UMLS:C1179024 arteriole endothelium uberon UBERON:0001916 endothelium of arteriole An endothelium that is part of an arteriole [Automatically generated definition]. OBOL:automatic UMLS:C1179024 ncithesaurus:Arteriole_Endothelium An endothelium that is part of an artery [Automatically generated definition]. The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011013 BTO:0004757 EMAPA:35148 FMA:62116 MA:0000707 NCIT:C49194 UMLS:C1179025 VHOG:0001215 XAO:0000357 arterial endothelium artery endothelium uberon UBERON:0001917 endothelium of artery An endothelium that is part of an artery [Automatically generated definition]. OBOL:automatic The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] 2012-06-20 AAO:0011013 AAO XAO:curator Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001215 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 UMLS:C1179025 ncithesaurus:Artery_Endothelium An endothelium that is part of a venule [Automatically generated definition]. EMAPA:36290 FMA:62117 MA:0000716 NCIT:C49319 UMLS:C1179026 venule endothelium uberon UBERON:0001918 endothelium of venule An endothelium that is part of a venule [Automatically generated definition]. OBOL:automatic UMLS:C1179026 ncithesaurus:Venule_Endothelium An endothelium that is part of a vein [Automatically generated definition]. Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011110 BTO:0004756 EMAPA:36288 FMA:62118 MA:0000712 NCIT:C49317 UMLS:C1179027 VHOG:0001216 XAO:0000358 vein endothelium venous endothelium uberon veinous endothelium UBERON:0001919 endothelium of vein An endothelium that is part of a vein [Automatically generated definition]. OBOL:automatic Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001216 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 UMLS:C1179027 ncithesaurus:Vein_Endothelium veinous endothelium VHOG:0001216 Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] MTg tegmentum BAMS:MTg BIRNLEX:1200 BTO:0003388 DHBA:12195 EFO:0000921 EHDAA2:0004475 EMAPA:18215 FMA:62393 HBA:9002 MA:0000212 MAT:0000452 TAO:0000160 UMLS:C0039441 VHOG:0001367 XAO:0004271 ZFA:0000160 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 tegmentum mesencephali tegmentum of midbrain uberon mesencephalic tegmentum tegmentum mesencephalicum UBERON:0001943 'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png ZFA Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. FMA:FMA ISBN:0471888893 Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] 2012-09-17 VHOG:0001367 VHOG DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005) MTg BIRNLEX:1200 NIFSTD:NeuroNames_abbrevSource tegmentum ISBN:0471888893 UMLS:C0039441 BIRNLEX:1200 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 BIRNLEX:1200 tegmentum mesencephali mesencephalic tegmentum VHOG:0001367 tegmentum mesencephalicum NeuroNames:491 A multi-tissue structure that is part of a spinal cord. BIRNLEX:1496 NCIT:C33969 UMLS:C1268166 uberon spinal cord part UBERON:0001948 regional part of spinal cord A multi-tissue structure that is part of a spinal cord. OBOL:automatic UMLS:C1268166 ncithesaurus:Spinal_Cord_Part An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN) The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils BAMS:ISO BAMS:Iso-cortex BAMS:NCX BIRNLEX:2547 BTO:0000920 DHBA:10160 EHDAA2:0004662 EMAPA:32842 EMAPA:35589 FMA:62429 GAID:677 MA:0002754 MBA:315 MESH:A08.186.211.730.885.213.420 PBA:294021746 UMLS:C0175173 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 cerebral neocortex homogenetic cortex homotypical cortex isocortex (sensu lato) neocortex (isocortex) neopallial cortex neopallium isocortex uberon iso-cortex nonolfactory cortex nucleus hypoglossalis UBERON:0001950 neocortex http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN) BIRNLEX:2547 OldNeuroNames:754 The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils UMLS:C0175173 BIRNLEX:2547 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 BIRNLEX:2547 homogenetic cortex ISBN:0471888893 homotypical cortex BIRNLEX:2547 isocortex (sensu lato) FMA:62429 neocortex (isocortex) DHBA:10160 isocortex BRAINSPAN:BRAINSPAN iso-cortex BAMS:iso-cortex nonolfactory cortex BTO:0000920 nucleus hypoglossalis NeuroNames:757 An epithelium that is part of a nasopharynx [Automatically generated definition]. UBERON:0003237 BTO:0004480 CALOHA:TS-0662 EHDAA2:0001241 EHDAA:7090 EMAPA:17672 FMA:62452 MA:0001865 NCIT:C49263 UMLS:C1179157 VHOG:0001038 epithelial tissue of nasal part of pharynx epithelial tissue of nasopharynx epithelial tissue of rhinopharynx epithelium of nasal part of pharynx epithelium of rhinopharynx nasal part of pharynx epithelial tissue nasal part of pharynx epithelium nasopharynx epithelial tissue nasopharynx epithelium rhinopharynx epithelial tissue rhinopharynx epithelium uberon nasopharyngeal epithelium UBERON:0001951 epithelium of nasopharynx An epithelium that is part of a nasopharynx [Automatically generated definition]. OBOL:automatic UMLS:C1179157 ncithesaurus:Nasopharynx_Epithelium epithelial tissue of nasal part of pharynx OBOL:automatic epithelial tissue of nasopharynx OBOL:automatic epithelial tissue of rhinopharynx OBOL:automatic epithelium of nasal part of pharynx OBOL:automatic epithelium of rhinopharynx OBOL:automatic nasal part of pharynx epithelial tissue OBOL:automatic nasal part of pharynx epithelium OBOL:automatic nasopharynx epithelial tissue OBOL:automatic rhinopharynx epithelial tissue OBOL:automatic rhinopharynx epithelium OBOL:automatic nasopharyngeal epithelium BTO:0004480 An epithelium that is part of a oropharynx [Automatically generated definition]. Composition varies with species and time. This is classified as nonkeratinizing stratified squamous in FMA, unilaminar in EHDAA2; the majority of the pharyngeal epithelium is unilaminar in zebrafish EHDAA2:0004083 EMAPA:37705 FMA:62453 MA:0001605 NCIT:C49264 UMLS:C1179158 oropharyngeal epithelium oropharynx epithelial tissue oropharynx epithelium uberon UBERON:0001952 epithelium of oropharynx An epithelium that is part of a oropharynx [Automatically generated definition]. OBOL:automatic Composition varies with species and time. This is classified as nonkeratinizing stratified squamous in FMA, unilaminar in EHDAA2; the majority of the pharyngeal epithelium is unilaminar in zebrafish FMA EMAPA:37705 MA:th UMLS:C1179158 ncithesaurus:Oropharynx_Epithelium oropharynx epithelial tissue OBOL:automatic oropharynx epithelium MA:0001605 The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]. EMAPA:35192 FMA:62649 MA:0001835 NCIT:C49209 UMLS:C0225604 bronchi cartilage bronchial cartilage bronchial cartilage ring bronchial trunk cartilage bronchus cartilage cartilage of bronchi cartilage of bronchial trunk cartilagines bronchiales uberon UBERON:0001956 cartilage of bronchus MP The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]. MP:0010988 UMLS:C0225604 ncithesaurus:Bronchus_Cartilage bronchi cartilage OBOL:automatic bronchial cartilage ring MP:0010988 bronchial trunk cartilage OBOL:automatic cartilage of bronchi OBOL:automatic cartilage of bronchial trunk OBOL:automatic cartilagines bronchiales A submucosa that is part of a bronchus [Automatically generated definition]. BTO:0002108 EMAPA:37449 FMA:62653 MA:0001837 NCIT:C49214 UMLS:C0225601 bronchi submucosa bronchial submucosa bronchial trunk submucosa bronchus submucosa submucosa of bronchi submucosa of bronchial trunk tela submucosa bronchi uberon submucous layer of bronchi UBERON:0001957 submucosa of bronchus A submucosa that is part of a bronchus [Automatically generated definition]. OBOL:automatic EMAPA:37449 MA:th UMLS:C0225601 ncithesaurus:Bronchus_Submucosa bronchi submucosa OBOL:automatic bronchial trunk submucosa OBOL:automatic submucosa of bronchi OBOL:automatic submucosa of bronchial trunk OBOL:automatic tela submucosa bronchi FMA:62653 FMA:TA submucous layer of bronchi BTO:0002108 An epithelium that lines a terminal bronchiole. A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469] EMAPA:36283 FMA:62794 MA:0001774 NCIT:C33755 UMLS:C1179400 bronchiolus terminalis epithelial tissue bronchiolus terminalis epithelium epithelial tissue of bronchiolus terminalis epithelial tissue of terminal bronchiole epithelium of bronchiolus terminalis epithelium of terminal bronchiole terminal bronchiole epithelial tissue terminal bronchiole epithelium uberon UBERON:0001958 terminal bronchiole epithelium An epithelium that lines a terminal bronchiole. UMLS:C1179400 ncithesaurus:Terminal_Bronchiole_Epithelium bronchiolus terminalis epithelial tissue OBOL:automatic bronchiolus terminalis epithelium OBOL:automatic epithelial tissue of bronchiolus terminalis OBOL:automatic epithelial tissue of terminal bronchiole OBOL:automatic epithelium of bronchiolus terminalis OBOL:automatic epithelium of terminal bronchiole FMA:62794 terminal bronchiole epithelial tissue OBOL:automatic diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]. todo - add part relationships to specific layers FMA:62819 MA:0000140 NCIT:C12910 UMLS:C0599921 MALT epithelio-lymphoid tissue mucosa associated lymphatic tissue mucosa associated lymphoid tissue mucosa-associated lymphoid tissue mucosal-associated lymphatic tissue mucosal-associated lymphoid tissue uberon UBERON:0001961 mucosa-associated lymphoid tissue FMA diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]. UMLS:C0599921 ncithesaurus:Mucosa-Associated_Lymphoid_Tissue epithelio-lymphoid tissue FMA:62819 mucosa-associated lymphoid tissue GO:0048537 mucosal-associated lymphatic tissue GO:0048537 mucosal-associated lymphoid tissue GO:0048537 Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]. phylogenetic relationships to be added guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002). FMA:62820 MA:0000136 NCIT:C12936 UMLS:C0596638 gut associated lymphoid tissue uberon GALT UBERON:0001962 gut-associated lymphoid tissue Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]. UMLS:C0596638 ncithesaurus:Gut_Associated_Lymphoid_Tissue A diffuse collection of lymphpoid cells that participate in airway immune responses FMA:62821 MA:0000135 NCIT:C32234 UMLS:C1179418 bronchus associated lymphoid tissue uberon BALT UBERON:0001963 Lymphoid tissue associated with airways in mice has functional similarities to human BALT[ISBN:0123813611] Notes: FMA classifies this as organized, not diffuse bronchial-associated lymphoid tissue ISBN:0123813611 A diffuse collection of lymphpoid cells that participate in airway immune responses ISBN:0123813611 UMLS:C1179418 ncithesaurus:Bronchus-Associated_Lymphoid_Tissue Organism substance that is composed of sperm cells suspended in seminal fluid. seminal Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530). BTO:0001230 CALOHA:TS-0917 EMAPA:31488 FMA:62966 GAID:1169 MA:0002522 MESH:D012661 NCIT:C13277 NCIT:C13713 OpenCyc:Mx4rvgC-zpwpEbGdrcN5Y29ycA UMLS:C1518159 UMLS:C2756969 uberon ejaculate sperm UBERON:0001968 semen http://upload.wikimedia.org/wikipedia/commons/4/40/Human_semen_in_petri_dish2.jpg Organism substance that is composed of sperm cells suspended in seminal fluid. UMLS:C1518159 ncithesaurus:Male_Genital_System_Fluid_or_Secretion UMLS:C2756969 ncithesaurus:Semen sperm BTO:0001230 The liquid component of blood, in which erythrocytes are suspended. plasma portion of plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 NCIT:C13356 OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw UMLS:C0032105 blood plasm portion of blood plasma uberon UBERON:0001969 blood plasma The liquid component of blood, in which erythrocytes are suspended. plasma MA:0002501 portion of plasma FMA:62970 UMLS:C0032105 ncithesaurus:Plasma vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum. aids the process of digestion of lipids in the small intestine bile salts function to emulsify dietary fats and facilitate their intestinal absorption elimination of cholesterol major excretory route for potentially harmful exogenous lipophilic substances many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine BTO:0000121 CALOHA:TS-1172 ENVO:02000023 FMA:62971 GAID:1157 MA:0002513 MESH:D001646 NCIT:C13192 UMLS:C0005388 ZFA:0005857 galen:Bile uberon fel gall UBERON:0001970 bile vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. UMLS:C0005388 ncithesaurus:Bile fel BTO:0000121 gall BTO:0000121 . BTO:0000501 FMA:62972 GAID:1160 MA:0002519 MESH:D005750 NCIT:C32661 UMLS:C0017133 galen:GastricJuice stomach secretion uberon succus gastricus UBERON:0001971 gastric juice . UMLS:C0017133 ncithesaurus:Gastric_Secretion succus gastricus BTO:0000501 A submucosa that is part of a esophagus [Automatically generated definition]. BTO:0002109 EMAPA:35325 FMA:62997 MA:0002724 esophageal submucosa esophagus submucosa gullet submucosa oesophagus submucosa submucosa of esophagus submucosa of gullet submucosa of oesophagus tela submucosa (oesophagus) tela submucosa esophagi tela submucosa oesophageae tela submucosa of esophagus uberon submucous layer of esophagus tela submucosa oesophagi UBERON:0001972 submucosa of esophagus A submucosa that is part of a esophagus [Automatically generated definition]. OBOL:automatic gullet submucosa OBOL:automatic oesophagus submucosa OBOL:automatic submucosa of gullet OBOL:automatic submucosa of oesophagus OBOL:automatic tela submucosa (oesophagus) FMA:62997 FMA:TA tela submucosa esophagi BTO:0002109 tela submucosa oesophageae FMA:62997 FMA:TA submucous layer of esophagus BTO:0002109 tela submucosa oesophagi BTO:0002109 A lamina propria that is part of a esophagus [Automatically generated definition]. EMAPA:26987 FMA:63050 MA:0001568 NCIT:C49223 UMLS:C1707949 esophagus lamina propria esophagus lamina propria mucosa esophagus lamina propria mucosae gullet lamina propria gullet lamina propria mucosa gullet lamina propria mucosae lamina propria mucosa of esophagus lamina propria mucosa of gullet lamina propria mucosa of oesophagus lamina propria mucosae of esophagus lamina propria mucosae of gullet lamina propria mucosae of oesophagus lamina propria of gullet lamina propria of oesophagus oesophagus lamina propria mucosa oesophagus lamina propria mucosae uberon esophageal lamina propria oesophagus lamina propria UBERON:0001974 lamina propria of esophagus FMA A lamina propria that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C1707949 ncithesaurus:Esophageal_Lamina_Propria esophagus lamina propria mucosa OBOL:automatic esophagus lamina propria mucosae OBOL:automatic gullet lamina propria OBOL:automatic gullet lamina propria mucosa OBOL:automatic gullet lamina propria mucosae OBOL:automatic lamina propria mucosa of esophagus OBOL:automatic lamina propria mucosa of gullet OBOL:automatic lamina propria mucosa of oesophagus OBOL:automatic lamina propria mucosae of gullet OBOL:automatic lamina propria mucosae of oesophagus OBOL:automatic lamina propria of gullet OBOL:automatic lamina propria of oesophagus OBOL:automatic oesophagus lamina propria mucosa OBOL:automatic oesophagus lamina propria mucosae OBOL:automatic esophageal lamina propria EMAPA:26987 A serous membrane that is part of a esophagus [Automatically generated definition]. EMAPA:35322 FMA:63057 MA:0001571 esophagus serosa esophagus serous membrane gullet serosa gullet serous membrane oesophagus serous membrane serosa of abdominal part of esophagus serosa of gullet serosa of oesophagus serous coat of oesophagus serous membrane of esophagus serous membrane of gullet serous membrane of oesophagus tunica serosa oesophageae uberon oesophagus serosa UBERON:0001975 serosa of esophagus A serous membrane that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus serous membrane OBOL:automatic gullet serosa OBOL:automatic gullet serous membrane OBOL:automatic oesophagus serous membrane OBOL:automatic serosa of gullet OBOL:automatic serous membrane of esophagus OBOL:automatic serous membrane of gullet OBOL:automatic serous membrane of oesophagus OBOL:automatic tunica serosa oesophageae FMA:63057 FMA:TA the epithelial layer that lines the luminal space of the esophagus TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO] BTO:0001578 CALOHA:TS-0698 EFO:0003041 EHDAA2:0001287 EMAPA:16835 FMA:63063 MA:0001565 NCIT:C49221 TAO:0001499 UMLS:C1179544 ZFA:0001499 epithelial tissue of esophagus epithelial tissue of gullet epithelial tissue of oesophagus epithelium of gullet epithelium of oesophagus esophageal epithelium esophagus epithelial tissue esophagus epithelium gullet epithelial tissue gullet epithelium oesophagus epithelial tissue uberon oesophagus epithelium UBERON:0001976 epithelium of esophagus FMA the epithelial layer that lines the luminal space of the esophagus ISBN:0-683-40008-8 MP:0000468 Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO] 2012-08-14 TAO:0001499 TAO ZFIN:curator UMLS:C1179544 ncithesaurus:Esophageal_Epithelium epithelial tissue of esophagus OBOL:automatic epithelial tissue of gullet OBOL:automatic epithelial tissue of oesophagus OBOL:automatic epithelium of gullet OBOL:automatic epithelium of oesophagus OBOL:automatic esophagus epithelial tissue OBOL:automatic gullet epithelial tissue OBOL:automatic gullet epithelium OBOL:automatic oesophagus epithelial tissue OBOL:automatic The portion of blood plasma that excludes clotting factors. BTO:0000133 BTO:0001239 CALOHA:TS-0923 EHDAA2:0004728 EMAPA:35770 FMA:63083 MA:0002502 NCIT:C13325 UMLS:C0229671 serum uberon UBERON:0001977 blood serum The portion of blood plasma that excludes clotting factors. UMLS:C0229671 ncithesaurus:Serum EMAPA:32925 FMA:63120 MA:0000724 VHOG:0001430 pancreas parenchyma pancreatic parenchyma uberon UBERON:0001978 parenchyma of pancreas One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] BTO:0002626 EMAPA:35917 FMA:63130 MA:0000071 MESH:A07.231.432.952 NCIT:C12818 TAO:0005315 UMLS:C0042520 VHOG:0001765 ZFA:0005315 uberon venula UBERON:0001979 venule Illu:capillary.jpg One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins MESH:A07.231.432.952 MP:0004125 Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] 2012-08-14 TAO:0005315 TAO ZFIN:curator UMLS:C0042520 ncithesaurus:Venule venula The smallest division of the artery located between the muscular arteries and the capillaries[GO]. Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] Small, terminal branch of an artery which generally connects to capillaries.[AAO] AAO:0010253 BTO:0001997 EMAPA:35146 FMA:63182 MA:0000063 MESH:D001160 NCIT:C12672 TAO:0002138 UMLS:C0003847 VHOG:0001763 ZFA:0005255 uberon arteriola UBERON:0001980 arteriole Illu:capillary.jpg MA The smallest division of the artery located between the muscular arteries and the capillaries[GO]. GO:0014830 Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] 2012-08-14 TAO:0002138 TAO ZFIN:curator Small, terminal branch of an artery which generally connects to capillaries.[AAO] 2012-06-20 AAO:0010253 AAO AAO:BJB UMLS:C0003847 ncithesaurus:Arteriole arteriola A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] annelids have blood vessels, but this class is not applicable to annelids. FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 BTO:0001102 CALOHA:TS-0080 EFO:0000817 EHDAA2:0003252 EHDAA:240 EMAPA:32743 EMAPA:35993 FMA:50722 FMA:63183 GAID:169 MA:0000060 MAT:0000393 MESH:D001808 NCIT:C12679 NLXANAT:090901 OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA TAO:0002137 UMLS:C0005847 VHOG:0001250 XAO:0001011 ZFA:0005314 region of vascular tree organ vascular tree organ region uberon vas sanguineum UBERON:0001981 blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg EHDAA2 GO:0072360 A vessel through which blood circulates in the body. BTO:0001102 Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] 2012-09-17 VHOG:0001250 VHOG Any of the vessels through which blood circulates in the body.[AAO] 2012-06-20 AAO:0011004 AAO AAO:EJS The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001250 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX FMA vascular element EMAPA:35993 UMLS:C0005847 ncithesaurus:Blood_Vessel region of vascular tree organ FMA:50722 vascular tree organ region FMA:50722 vas sanguineum Any of the smallest blood vessels connecting arterioles with venules. not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs AAO:0010252 BTO:0002045 CALOHA:TS-2006 EFO:0001906 EMAPA:35198 EV:0100035 FMA:63194 MA:0000065 MESH:A07.231.432.410 NCIT:C12685 NLXANAT:090902 OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA TAO:0005250 UMLS:C0935624 VHOG:0001253 XAO:0000116 ZFA:0005250 blood capillary capillary vessel uberon UBERON:0001982 capillary http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg FMA MA XAO ZFA Any of the smallest blood vessels connecting arterioles with venules. ISBN:0073040584 Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] 2012-06-20 AAO:0010252 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001253 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) UMLS:C0935624 ncithesaurus:Capillary A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. CALOHA:TS-0172 EMAPA:35935 FMA:63882 GAID:891 MA:0001242 MESH:D004728 NCIT:C12707 TAO:0002186 UMLS:C0014259 ZFA:0001687 cornea endothelium endothelium of cornea uberon epithelium posterius corneae UBERON:0001985 corneal endothelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. UMLS:C0014259 ncithesaurus:Corneal_Endothelium cornea endothelium OBOL:automatic endothelium of cornea OBOL:automatic epithelium posterius corneae A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 FMA:63916 GAID:520 MESH:D004727 NCIT:C12481 UMLS:C0014257 galen:Endothelium uberon UBERON:0001986 The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980) endothelium FMA-text-def A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] FMA:63916 MESH:A10.272.491 UMLS:C0014257 ncithesaurus:Endothelium organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG] placental Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: DOI:10.1002/jmor.11011 BTO:0001078 CALOHA:TS-0799 EFO:0001407 EMAPA:35689 EV:0100119 FMA:63934 GAID:379 MA:0000386 MAT:0000279 MESH:A16.759 MIAA:0000279 NCIT:C13272 OpenCyc:Mx4rvv4zZ5wpEbGdrcN5Y29ycA UMLS:C0032043 VHOG:0001266 allantoic placenta eutherian placenta uberon UBERON:0001987 Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities. placenta http://upload.wikimedia.org/wikipedia/commons/6/66/Placenta.jpg http://upload.wikimedia.org/wikipedia/commons/f/f1/Placenta.svg ISBN:0073040584 Wikipedia ISBN:0073040584 organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG] 2012-09-17 VHOG:0001266 VHOG DOI:10.1038/35054550 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001) UMLS:C0032043 ncithesaurus:Placenta allantoic placenta ISBN:0073040584 Portion of semisolid bodily waste discharged through the anus[MW,modified] Excretion in semisolid state processed by the intestine.[FMA] fecal excreta BTO:0000440 CALOHA:TS-2345 ENVO:00002003 FMA:64183 GAID:1199 MA:0002509 MAT:0000053 MESH:D005243 MIAA:0000053 NCIT:C13234 OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA UMLS:C0015733 galen:Feces faeces fecal material fecal matter matières fécales@fr merde@fr partie de la merde@fr piece of shit porción de mierda@es portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool teil der fäkalien@de cow dung cow pat dung fewmet frass guano portion of dung portion of guano portion of scat scat spraint uberon droppings excrement ordure spoor UBERON:0001988 feces Portion of semisolid bodily waste discharged through the anus[MW,modified] Excretion in semisolid state processed by the intestine.[FMA] FMA:64183 UMLS:C0015733 ncithesaurus:Feces piece of shit portionem cacas cow dung cow pat fewmet frass guano spraint excrement BTO:0000440 Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance. Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]. Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO] EMAPA:35414 FMA:64783 MA:0000109 NCIT:C32746 UMLS:C0225362 VSAO:0000094 XAO:0004029 hyaline cartilage uberon chondroid cartilage UBERON:0001994 hyaline cartilage tissue http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg FMA Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance. GO_REF:0000034 PSPUB:0000170 VSAO:0000094 Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]. FMA:64783 Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO] 2012-08-14 VSAO:0000094 VSAO PSPUB:0000170 UMLS:C0225362 ncithesaurus:Hyaline_Cartilage hyaline cartilage MA:0000109 chondroid cartilage Cartilage tissue that is flexible and contains abundant elastic fibers. Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which consists of elastic fibers[FMA:64785]. Cartilage tissue that is flexible and contains abundant elastic fibers.[VSAO] MA has a distinct class for yellow FMA:64785 MA:0000107 MA:0000485 NCIT:C32494 UMLS:C0682559 VSAO:0000091 XAO:0004197 elastic cartilage elastic cartilage tissue yellow elastic cartilage yellow elastic cartilage tissue uberon reticular cartilage yellow cartilage UBERON:0001996 elastic cartilage tissue http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray904.png VSAO VSAO Cartilage tissue that is flexible and contains abundant elastic fibers. GO_REF:0000034 PSPUB:0000170 VSAO:0000091 Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which consists of elastic fibers[FMA:64785]. FMA:64785 Cartilage tissue that is flexible and contains abundant elastic fibers.[VSAO] 2012-08-14 VSAO:0000091 VSAO PSPUB:0000170 MA has a distinct class for yellow MA UMLS:C0682559 ncithesaurus:Elastic_Cartilage elastic cartilage MA:0000107 elastic cartilage tissue VSAO:0000091 yellow elastic cartilage reticular cartilage yellow cartilage Any joint that connects a rib to another structure (or another rib). Examples: costochondral, costovertebral, interchondral, sternocostal joints. FMA_RETIRED:64994 MA:0001508 NCIT:C49575 UMLS:C1261194 rib joint uberon UBERON:0002001 joint of rib cjm Any joint that connects a rib to another structure (or another rib). Examples: costochondral, costovertebral, interchondral, sternocostal joints. UMLS:C1261194 ncithesaurus:Joint_of_the_Rib Peripheral portion of the lymph node, underneath the capsule[WP]. EMAPA:35525 FMA:66253 MA:0000740 NCIT:C33029 UMLS:C0933402 lymph node cortex uberon cortex nodi lymphoidei UBERON:0002006 cortex of lymph node http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png Peripheral portion of the lymph node, underneath the capsule[WP]. UMLS:C0933402 ncithesaurus:Lymph_Node_Cortex cortex nodi lymphoidei The mdeullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells. EMAPA:35529 FMA:66254 MA:0000745 lymph node medulla uberon medulla nodi lymphoidei UBERON:0002007 medulla of lymph node The mdeullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells. medulla nodi lymphoidei An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Major artery which supplies blood to the lungs.[AAO] One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP] AAO:0010221 BTO:0000778 CALOHA:TS-0839 EFO:0001399 EHDAA2:0001575 EHDAA:4351 EMAPA:17008 FMA:66326 GAID:505 MA:0002031 MESH:D011651 NCIT:C12774 OpenCyc:Mx4rvVjbIpwpEbGdrcN5Y29ycA UMLS:C0034052 VHOG:0000982 XAO:0004162 galen:PulmonaryArtery pulmonary arterial tree pulmonary arterial tree organ part uberon arteria pulmonalis pulmonary arterial subtree truncus pulmonalis UBERON:0002012 pulmonary artery Alveoli:diagram.png Wikipedia EHDAA2 XAO EHDAA2 An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Major artery which supplies blood to the lungs.[AAO] 2012-06-20 AAO:0010221 AAO AAO:BJB One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] 2012-09-17 VHOG:0000982 VHOG On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0000982 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0034052 ncithesaurus:Pulmonary_Artery pulmonary arterial tree FMA:66326 pulmonary arterial tree organ part FMA:66326 arteria pulmonalis pulmonary arterial subtree FMA:66326 truncus pulmonalis the tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage provides some protection from trauma and damage. The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule] EMAPA:18679 FMA:66610 MA:0000370 NCIT:C12885 UMLS:C0227637 galen:CapsuleOfKidney capsula fibrosa renis capsule of kidney fibrous capsule of kidney renal capsule uberon UBERON:0002015 kidney capsule Illu:kidney.jpg the tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage MGI:anna MP:0011383 UMLS:C0227637 ncithesaurus:Renal_Capsule capsula fibrosa renis FMA:66610 FMA:TA fibrous capsule of kidney FMA:66610 renal capsule GO:0072127 Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] the veins that return oxygenated blood from the lungs to the left atrium of the heart On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] AAO:0010521 BTO:0001799 CALOHA:TS-0840 EHDAA2:0001579 EHDAA:2629 EMAPA:18645 FMA:66643 GAID:543 MA:0002206 MESH:D011667 NCIT:C12776 UMLS:C0034090 VHOG:0001133 XAO:0000394 galen:PulmonaryVein pulmonary venous tree organ part uberon venae pulmonales UBERON:0002016 pulmonary vein Alveoli:diagram.png Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. GO:0060577 Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] 2012-06-20 AAO:0010521 AAO AAO:BJB One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] 2012-09-17 VHOG:0001133 VHOG the veins that return oxygenated blood from the lungs to the left atrium of the heart MP:0002726,MGI:cwg On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0001133 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0034090 ncithesaurus:Pulmonary_Vein venae pulmonales A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]. BTO:0001792 CALOHA:TS-0814 EHDAA2:0001485 EHDAA:6510 EMAPA:17349 FMA:66645 GAID:540 MA:0002198 MESH:D011169 NCIT:C33343 OpenCyc:Mx4rv_bem5wpEbGdrcN5Y29ycA UMLS:C0032718 VHOG:0000656 XAO:0000392 galen:PortalVein portal venous tree organ part uberon UBERON:0002017 portal vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png FMA A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]. BTO:0001792 UMLS:C0032718 ncithesaurus:Portal_Vein portal venous tree organ part FMA:66645 Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints). Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG] synovial layer synovial membrane synovium AEO:0000181 BTO:0001823 EFO:0001393 EHDAA2_RETIRED:0003181 EMAPA:37476 EV:0100143 FMA:9865 GAID:264 MA:0000114 MESH:D013583 NCIT:C12473 UMLS:C0039099 VHOG:0001282 galen:SynovialMembrane membrana synovialis (capsula articularis) membrana synovialis capsulae articularis stratum synoviale stratum synoviale (capsula articularis) uberon synovial layer of articular capsule of synovial joint synovial membrane of articular capsule of synovial joint synovium of articular capsule of synovial joint UBERON:0002018 synovial membrane of synovial joint http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png http://upload.wikimedia.org/wikipedia/commons/5/5d/Synovium.png FMA EHDAA2 GAID Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints). Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001282 VHOG PMID:11068553 O'Connel JX, Pathology of the synovium. American Journal of Clinical Pathology (2000) synovial layer FMA:66762 synovial membrane AEO:0000181 synovium BTO:0001823 VHOG:0001282 EMAPA:37476 MA:th UMLS:C0039099 ncithesaurus:Synovial_Membrane membrana synovialis (capsula articularis) FMA:9865 FMA:TA membrana synovialis capsulae articularis stratum synoviale FMA:66762 FMA:TA stratum synoviale (capsula articularis) FMA:9865 FMA:TA synovial layer of articular capsule of synovial joint FMA:9865 synovial membrane of articular capsule of synovial joint FMA:9865 synovium of articular capsule of synovial joint FMA:9865 A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] AAO:0010476 BAMS:11n BAMS:XIn BIRNLEX:812 EHDAA2:0000106 EHDAA:2855 EMAPA:17265 FMA:6720 FMA:80284 GAID:825 HBA:9340 MA:0001088 MBA:717 MESH:D000055 NCIT:C32041 OpenCyc:Mx4rwTEwI5wpEbGdrcN5Y29ycA UMLS:C0000905 UMLS:C1305777 VHOG:0000699 XAO:0004214 Willis' nerve accessory XI accessory XI nerve accessory nerve accessory nerve [XI] cervical accessory nerve cranial nerve XI eleventh cranial nerve nervus accessorius [XI] pars spinalis nervus accessorius radix spinalis nervus accessorius spinal accessory nerve spinal accessory nerve tree spinal part of accessory nerve uberon CN-XI accessory spinal nerve UBERON:0002019 accessory XI nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. BIRNLEX:812 http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7 VHOG Wikipedia A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. ISBN:080184780X XAO:0004214 Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000699 VHOG Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] 2012-06-20 AAO:0010476 AAO AAO:EJS Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] 2012-09-17 VHOG:0000699 VHOG In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve GO FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] FMA UMLS:C0000905 BIRNLEX:812 UMLS:C0000905 ncithesaurus:Accessory_Nerve UMLS:C1305777 BIRNLEX:812 accessory XI EHDAA2:0000106 cranial nerve XI BIRNLEX:812 eleventh cranial nerve BIRNLEX:812 nervus accessorius [XI] FMA:6720 FMA:TA pars spinalis nervus accessorius FMA:6720 FMA:TA radix spinalis nervus accessorius FMA:6720 FMA:TA spinal accessory nerve FMA:6720 CN-XI VHOG:0000699 accessory spinal nerve BAMS:XIn A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] AEO:0001012 EHDAA2:0003136 EHDAA2_RETIRED:0004658 EMAPA:37596 FMA:67242 HBA:4006 MA:0001112 NCIT:C32695 OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA TAO:0002197 UMLS:C0018220 VHOG:0001768 ZFA:0001681 gray matter gray matter of neuraxis grey matter grey matter of neuraxis grey substance neuronal grey matter substantia grisea uberon gray mater grisea UBERON:0002020 gray matter Spinal:nerve.svg A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] 2012-08-14 TAO:0002197 TAO ZFIN:curator EMAPA:37596 MA:th UMLS:C0018220 ncithesaurus:Gray_Matter gray matter of neuraxis FMA:67242 neuronal grey matter AEO:0001012 substantia grisea FMA:67242 FMA:TA gray mater ZFA:0001681 grisea The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] rhombencephalic in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps AAO:0010150 BAMS:HB BIRNLEX:942 BTO:0000672 CALOHA:TS-0457 DHBA:10653 DMBA:16808 EFO:0000923 EHDAA2:0000746 EHDAA:3514 EHDAA:6487 EMAPA:16916 FMA:67687 MA:0000195 MAT:0000107 MBA:1065 MESH:D012249 MIAA:0000107 NCIT:C40336 TAO:0000029 UMLS:C0035507 UMLS:C1522180 VHOG:0000070 XAO:0000015 ZFA:0000029 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 uberon rhombencephalon UBERON:0002028 hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg modified-source-relation ABA Bgee:AN The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. ZFA:0000029 ZFIN:curator Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] 2012-06-20 AAO:0010150 AAO AAO:BJB The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000029 TAO ZFIN:curator relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] 2012-08-14 TAO:0000029 TAO Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000070 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps MA UMLS:C0035507 BIRNLEX:942 UMLS:C0035507 ncithesaurus:Hind-Brain UMLS:C1522180 BIRNLEX:942 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 BIRNLEX:942 The simple columnar epithelial lining of the gall bladder. BTO:0001449 CALOHA:TS-1304 EMAPA:35370 FMA:67711 MA:0001632 NCIT:C49227 UMLS:C1180206 epithelial tissue of gall bladder epithelial tissue of gallbladder epithelium of gallbladder gall bladder epithelial tissue gall bladder epithelium gallbladder epithelial tissue gallbladder epithelium uberon biliary epithelium UBERON:0002029 epithelium of gall bladder The simple columnar epithelial lining of the gall bladder. MP:0009492 UMLS:C1180206 ncithesaurus:Gallbladder_Epithelium epithelial tissue of gall bladder OBOL:automatic epithelial tissue of gallbladder OBOL:automatic epithelium of gallbladder OBOL:automatic gall bladder epithelial tissue OBOL:automatic gallbladder epithelial tissue OBOL:automatic gallbladder epithelium OBOL:automatic An epithelium that is part of a bronchus [Automatically generated definition]. BTO:0001845 CALOHA:TS-1240 EFO:0000307 EMAPA:32691 FMA:67782 MA:0001839 NCIT:C32231 UMLS:C0599333 bronchi epithelial tissue bronchi epithelium bronchial epithelium bronchial trunk epithelial tissue bronchial trunk epithelium bronchus epithelial tissue bronchus epithelium epithelial tissue of bronchi epithelial tissue of bronchial trunk epithelial tissue of bronchus epithelium of bronchi epithelium of bronchial trunk uberon UBERON:0002031 epithelium of bronchus An epithelium that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C0599333 ncithesaurus:Bronchial_Epithelium bronchi epithelial tissue OBOL:automatic bronchi epithelium OBOL:automatic bronchial trunk epithelial tissue OBOL:automatic bronchial trunk epithelium OBOL:automatic bronchus epithelial tissue OBOL:automatic epithelial tissue of bronchi OBOL:automatic epithelial tissue of bronchial trunk OBOL:automatic epithelial tissue of bronchus OBOL:automatic epithelium of bronchi OBOL:automatic epithelium of bronchial trunk OBOL:automatic A tiny smooth muscle that connects the hair follicle with the dermis. When contracted the arrector pili causes the raising of the hair BTO:0005132 EMAPA:26775 FMA:67821 MA:0000778 arrector pili arrector pili muscle arrector pili smooth muscle arrector pilli arrector pilli muscle arrector pilorum arrector pilorum muscle of hair uberon arectores pilorum erector pili erectores pilorum pilomotor muscle UBERON:0002033 arrector muscle of hair FMA FMA A tiny smooth muscle that connects the hair follicle with the dermis. arrector pili FMA:67821 MA:0000778 arrector pili muscle EMAPA:26779 MP:0010679 arrector pili smooth muscle MA:0000778 arrector pilli MP:0010679 arrector pilli muscle MP:0010679 arrector pilorum ISBN:0123813611 arrector pilorum muscle of hair ISBN:0123813611 arectores pilorum BTO:0005132 erector pili BTO:0005132 erectores pilorum BTO:0005132 pilomotor muscle BTO:0005132 Muscle tissue that contains fibers that are divided by transverse bands into striations. Voluntary muscle tissue arranged in bundles of fibers.[AAO] AAO:0010762 AEO:0000140 CALOHA:TS-2047 EHDAA2:0003140 EMAPA:36390 FMA:67905 MA:0002438 NCIT:C12436 OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA UMLS:C1331262 WBbt:0005779 galen:StriatedMuscle striated muscle uberon UBERON:0002036 striated muscle tissue Muscle tissue that contains fibers that are divided by transverse bands into striations. CL:0000737 GOC:dph GOC:mtg_muscle Voluntary muscle tissue arranged in bundles of fibers.[AAO] 2012-06-20 AAO:0010762 AAO AAO:CAM UMLS:C1331262 ncithesaurus:Striated_Muscle_Tissue cerebellum Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO] Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO] However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG] cerebellar The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full] almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem infratentorial region AAO:0010485 BAMS:CB BAMS:Cb BIRNLEX:1489 BM:CB BTO:0000232 CALOHA:TS-0125 DHBA:10656 EFO:0000327 EHDAA2:0000232 EMAPA:17787 EV:0100293 FMA:67944 GAID:595 HBA:4696 MA:0000198 MAT:0000110 MBA:512 MESH:D002531 MIAA:0000110 NCIT:C12445 OpenCyc:Mx4rvl1eipwpEbGdrcN5Y29ycA TAO:0000100 UMLS:C0007765 UMLS:C1268981 VHOG:0000024 XAO:0003098 ZFA:0000100 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=643 epencephalon-1 uberon corpus cerebelli parencephalon UBERON:0002037 cerebellum Cerebellum:NIH.png FMA MA definitional Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. BTO:0000232 ISBN:3764351209 MESH:A08.186.211.132.810.428.200 ZFA:0000100 ISBN:0471888893 Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO] 2012-06-20 AAO:0010485 AAO AAO:BJB Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000100 TAO ZFIN:curator However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG] 2012-09-17 VHOG:0000024 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem ABA infratentorial region UMLS:C0007765 BIRNLEX:1489 UMLS:C0007765 ncithesaurus:Cerebellum UMLS:C1268981 BIRNLEX:1489 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=643 BIRNLEX:1489 epencephalon-1 FMA:67944 corpus cerebelli NeuroNames:643 parencephalon NeuroNames:643 A systemic artery that supplies the lung with with oxygenated blood. EMAPA:18608 FMA:68109 GAID:477 MA:0001923 MESH:D001981 NCIT:C32230 OpenCyc:Mx4r4sy0UiNbEd2AAAACs6hRXg UMLS:C0006257 bronchial arterial tree uberon arteriae bronchiales rami bronchiales partis thoracicae aortae UBERON:0002040 Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. bronchial artery http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png A systemic artery that supplies the lung with with oxygenated blood. UBERON:cjm UMLS:C0006257 ncithesaurus:Bronchial_Artery arteriae bronchiales rami bronchiales partis thoracicae aortae An endothelium that is part of a lymphatic vessel [Automatically generated definition]. The vascular endothelium that lines the lymph vessels.[TAO] BTO:0004303 CALOHA:TS-2156 EMAPA:35533 FMA:68444 MA:0000750 MESH:D004729 NCIT:C49258 TAO:0005258 UMLS:C1180786 ZFA:0005258 endothelium of lymph vessel endothelium of lymphatic vessel lymph vessel endothelium lymphatic endothelium lymphatic vessel endothelium uberon UBERON:0002042 lymphatic vessel endothelium An endothelium that is part of a lymphatic vessel [Automatically generated definition]. OBOL:automatic The vascular endothelium that lines the lymph vessels.[TAO] 2012-08-14 TAO:0005258 TAO ZFIN:curator UMLS:C1180786 ncithesaurus:Lymphatic_Vessel_Endothelium endothelium of lymph vessel OBOL:automatic endothelium of lymphatic vessel FMA:68444 lymph vessel endothelium OBOL:automatic lymphatic endothelium BTO:0004303 thyroid gland A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG] In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine) In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species AAO:0010544 BTO:0001379 CALOHA:TS-1047 EFO:0000861 EHDAA2:0002028 EHDAA:2148 EHDAA:2975 EMAPA:17068 EV:0100133 FMA:9603 GAID:465 MA:0000129 MAT:0000081 MESH:D013961 MIAA:0000081 NCIT:C12400 OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA UMLS:C0040132 VHOG:0000418 XAO:0000162 galen:ThyroidGland thyroid uberon glandula thyroidea UBERON:0002046 thyroid gland http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. BTO:0001379 Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO] 2012-06-20 AAO:0010544 AAO AAO:BJB (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG] 2012-09-17 VHOG:0000418 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes NCBITaxon:32443 Romer In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine) NCBITaxon:7746 Romer In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species NCBITaxon:32523 Romer UMLS:C0040132 ncithesaurus:Thyroid_Gland glandula thyroidea The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. BAMS:PnR BAMS:RA-PONS BAMS:RPn BIRNLEX:1110 DHBA:12471 DHBA:12475 FMA:68875 HBA:9159 MA:0001022 MBA:238 UMLS:C0175423 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=589 raphe of pons raphe pontis uberon nucleus raphe pontis nucleus raphes pontis raphe (mediana pontina) raphe pontis nucleus UBERON:0002047 pontine raphe nucleus Wikipedia The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. UMLS:C0175423 BIRNLEX:1110 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=589 BIRNLEX:1110 raphe pontis FMA:68875 FMA:TA nucleus raphe pontis NeuroNames:589 nucleus raphes pontis raphe (mediana pontina) NeuroNames:589 lung Respiration organ that develops as an oupocketing of the esophagus. Respiration organ that develops as an outpocketing of the esophagus. lung http://langual.org Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0024109 VHOG:0000310 XAO:0000119 galen:Lung http://www.langual.org/langual_thesaurus.asp?termid=C0187 pulmo uberon UBERON:0002048 Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung https://github.com/obophenotype/uberon/issues/701 some species only have a single lung Respiration organ that develops as an oupocketing of the esophagus. Respiration organ that develops as an outpocketing of the esophagus. Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] 2012-06-20 AAO:0010567 AAO AAO:SBH Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000310 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011) UMLS:C0024109 ncithesaurus:Lung pulmo An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? vascular BTO:0003718 FMA:69050 TAO:0005249 ZFA:0005249 vascular network uberon UBERON:0002049 vasculature http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg FMA An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. ZFA:0005249 vascular network FMA:69050 Anatomical structure that is part of an embryo. Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 NCIT:C13229 RETIRED_EHDAA2:0003169 TAO:0001105 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure embryonic anatomical structure uberon developing structure embryonale Struktur embryonic structures UBERON:0002050 embryonic structure Anatomical structure that is part of an embryo. BTO:0000174 ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] 2012-06-20 AAO:0000138 AAO AAO:BJB Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] 2012-08-14 TAO:0001105 TAO ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] 2012-08-14 VSAO:0000178 VSAO ZFIN:curator in FMA embryo is_a embryonic structure FMA UMLS:C0013948 ncithesaurus:Embryonic_Structure developing embryonic structure FBbt:00004208 embryonic anatomical structure RETIRED_EHDAA2:0003169 embryonale Struktur BTO:0000174 embryonic structures ZFA:0001105 An epithelium that is part of a bronchiole [Automatically generated definition]. in FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however there are two distinct terms for the corresponding epithelium. BTO:0001866 CALOHA:TS-0570 EMAPA:32693 FMA:62497 FMA:69077 MA:0001772 NCIT:C48942 UMLS:C1181296 bronchiolar epithelium bronchiole epithelial tissue bronchiole epithelium epithelial tissue of bronchiole epithelial tissue of lobular bronchiole epithelium of lobular bronchiole lobular bronchiole epithelial tissue lobular bronchiole epithelium uberon UBERON:0002051 epithelium of bronchiole An epithelium that is part of a bronchiole [Automatically generated definition]. OBOL:automatic in FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however there are two distinct terms for the corresponding epithelium. FMA UMLS:C1181296 ncithesaurus:Bronchiole_Epithelium bronchiolar epithelium BTO:0001866 bronchiole epithelial tissue OBOL:automatic epithelial tissue of bronchiole OBOL:automatic epithelial tissue of lobular bronchiole OBOL:automatic epithelium of lobular bronchiole OBOL:automatic lobular bronchiole epithelial tissue OBOL:automatic lobular bronchiole epithelium OBOL:automatic the thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. FMA:69087 MA:0000117 NCIT:C32050 UMLS:C1181304 capsule of adrenal gland uberon adrenal capsule UBERON:0002052 adrenal gland capsule the thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. MP:0013565 UMLS:C1181304 ncithesaurus:Adrenal_Gland_Capsule capsule of adrenal gland FMA:69087 Each renal artery gives off some small inferior suprarenal branches to the suprarenal gland, the ureter, and the surrounding cellular tissue and muscles. [WP,unvetted]. EMAPA:37088 FMA:69264 MA:0002056 NCIT:C52737 UMLS:C0226334 uberon arteria suprarenalis inferior UBERON:0002056 inferior suprarenal artery http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png Each renal artery gives off some small inferior suprarenal branches to the suprarenal gland, the ureter, and the surrounding cellular tissue and muscles. [WP,unvetted]. EMAPA:37088 MA:th UMLS:C0226334 ncithesaurus:Inferior_Suprarenal_Artery arteria suprarenalis inferior An artery that supplies the diaphragm In humans this includes the superior and inferior phrenic arteries EMAPA:37108 FMA:69330 MA:0002019 NCIT:C33320 UMLS:C1181536 uberon UBERON:0002057 phrenic artery An artery that supplies the diaphragm EMAPA:37108 MA:th UMLS:C1181536 ncithesaurus:Phrenic_Artery the ganglion associated with the lingual nerve that provides postsynaptic fibers to the submandibular and sublingual glands BTO:0001318 EHDAA2:0001942 EHDAA:6710 EMAPA:36276 FMA:6966 MA:0002470 NCIT:C52558 UMLS:C0229063 mandibular ganglion uberon Blandin`s ganglion ganglion submandibulare lingual ganglion maxillary ganglion submaxillary ganglion UBERON:0002059 submandibular ganglion http://upload.wikimedia.org/wikipedia/commons/8/83/Gray778.png http://upload.wikimedia.org/wikipedia/en/thumb/8/83/Gray778.png/200px-Gray778.png the ganglion associated with the lingual nerve that provides postsynaptic fibers to the submandibular and sublingual glands ISBN:0-683-40008-8 MP:0001035 UMLS:C0229063 ncithesaurus:Submandibular_Ganglion mandibular ganglion UBERON:cjm Blandin`s ganglion BTO:0001318 ganglion submandibulare ganglion submandibulare BTO:0001318 lingual ganglion MA:0002470 maxillary ganglion MA:0002470 submaxillary ganglion MA:0002470 The femoral artery is a large artery in the muscles of the thigh. It is a continuation of external iliac artery where it enters the femoral triangle at the mid inguinal point behind the inguinal ligament. It leaves femoral triangle through apex beneath the sartorius muscle. It enters the popliteal fossa by passing through the 5th osseo-aponeurotic(adductor hiatus) opening of adductor magnus where it becomes the Popliteal Artery. [WP,unvetted]. Artery which supplies blood via branches to the hindlimbs.[AAO] AAO:0010222 BTO:0001624 CALOHA:TS-0321 EMAPA:35342 FMA:70248 GAID:494 MA:0001951 MESH:D005263 NCIT:C12715 OpenCyc:Mx4rwHMI05wpEbGdrcN5Y29ycA UMLS:C0015801 galen:FemoralArtery uberon arteria femoralis UBERON:0002060 femoral artery http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray546.png FMA WP The femoral artery is a large artery in the muscles of the thigh. It is a continuation of external iliac artery where it enters the femoral triangle at the mid inguinal point behind the inguinal ligament. It leaves femoral triangle through apex beneath the sartorius muscle. It enters the popliteal fossa by passing through the 5th osseo-aponeurotic(adductor hiatus) opening of adductor magnus where it becomes the Popliteal Artery. [WP,unvetted]. Artery which supplies blood via branches to the hindlimbs.[AAO] 2012-06-20 AAO:0010222 AAO AAO:BJB UMLS:C0015801 ncithesaurus:Femoral_Artery arteria femoralis The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. assume spelling error for ncit EHDAA2:0004143 EMAPA:35887 FMA:70301 GAID:554 MA:0000103 MESH:D014338 NCIT:C34317 OpenCyc:Mx4rquH9YKgNEdudWQACs5b6Bw UMLS:C1519589 uberon UBERON:0002061 truncus arteriosus EHDAA2 FMA MA EHDAA2 EHDAA2 The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. assume spelling error for ncit ncit UMLS:C1519589 ncithesaurus:Trancus_Arteriosus The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] EHDAA2:0000434 EHDAA2:0004028 EHDAA:2586 EMAPA:16696 FMA:70302 MA:0000078 TAO:0001317 VHOG:0000932 XAO:0004189 ZFA:0001317 AV cushion atrioventricular cushion cardiac cushion endocardial cushion tissue uberon atrioventricular canal cushion endocardial cushions UBERON:0002062 GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form endocardial cushion http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png ZFA The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. GO:0003197 ZFIN:curator Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] 2012-08-14 TAO:0001317 TAO ZFIN:curator relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] 2012-08-14 TAO:0001317 TAO (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] 2012-09-17 VHOG:0000932 VHOG DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3 atrioventricular cushion cardiac cushion endocardial cushion tissue EHDAA2:0000434 atrioventricular canal cushion FMA:70302 endocardial cushions The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616] In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract inflow tract AAO:0010505 EHDAA2:0001839 EHDAA:480 EMAPA:16237 FMA:70303 NCIT:C34299 NCIT:C34300 TAO:0000154 UMLS:C0225857 UMLS:C0231084 VHOG:0000177 ZFA:0000154 uberon sinus venarum sinus venosus cordis venarum venarum sinus venosus UBERON:0002063 sinus venosus http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png VHOG Bgee:AN The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000154 TAO ZFIN:curator Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] 2012-06-20 AAO:0010505 AAO AAO:BJB In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] 2012-09-17 VHOG:0000177 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract ZFA:0000154 inflow tract ZFA:0000154 UMLS:C0225857 ncithesaurus:Sinus_Venarum UMLS:C0231084 ncithesaurus:Sinus_Venosus sinus venarum sinus venosus cordis venarum venarum sinus venosus dermis The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Consider adding a layer-of-skin grouping class for all skin layers A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] dermal AAO:0000128 BTO:0000294 CALOHA:TS-2076 EFO:0000953 EMAPA:17527 EV:0100154 FMA:70323 GAID:1321 MA:0000152 MAT:0000153 MESH:D020405 MIAA:0000153 NCIT:C12701 TAO:0001119 UMLS:C0011646 VHOG:0000108 XAO:0000217 ZFA:0001119 vertebrate dermis uberon corium cutis UBERON:0002067 dermis http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg FMA definitional The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. ZFIN:curator A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001119 TAO ZFIN:curator When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] 2012-09-17 VHOG:0000108 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1 UMLS:C0011646 ncithesaurus:Dermis corium corium BTO:0000294 cutis BTO:0000294 Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. hypodermal subcutaneous subcutaneus BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO:0001314 CALOHA:TS-2366 EMAPA:37505 FMA:70544 NCIT:C33645 TAO:0001136 UMLS:C0278403 ZFA:0001136 hypoderm vertebrate hypodermis uberon sub-tegumental tissue subcutaneous tissue subcutis subtegumental tissue superficial fascia tela subcutanea UBERON:0002072 hypodermis http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg ZFA FMA-modified Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001136 TAO ZFIN:curator A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. FMA:70544 BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO EMAPA:37505 MA:th UMLS:C0278403 ncithesaurus:Subcutis sub-tegumental tissue BTO:0004525 subcutaneous tissue subtegumental tissue BTO:0004525 superficial fascia tela subcutanea A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]. The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG] BTO:0000554 CALOHA:TS-0432 EFO:0002464 EMAPA:18771 EMAPA:29741 EV:0100156 FMA:70660 GAID:934 MA:0000154 MESH:D018859 NCIT:C13317 OpenCyc:Mx4rvVjOI5wpEbGdrcN5Y29ycA UMLS:C0221971 VHOG:0001268 uberon folliculus pili UBERON:0002073 Development notes:Formation largely takes place during fetal and perinatal skin development. However, after skin wounding de novo hair follicle formation may also occur in adult mouse and rabbit skin[DOI:10.1016/j.cub.2008.12.005]. hair follicle Hair:follicle-en.svg FMA A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]. The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG] 2012-09-17 VHOG:0001268 VHOG ISBN:978-4431998051 Morioka K, Hair follicle: differentiation under the electron microscope, An atlas (2005) p.3 UMLS:C0221971 ncithesaurus:Hair_Follicle folliculus pili The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla. TODO - add distinct subclasses for coat hair vs vibrissa hair TODO - check definition of trichocyte in CL BTO:0004672 EMAPA:36498 FMA:70728 MA:0000159 NCIT:C33543 UMLS:C0221961 shaft of hair uberon scapus pili UBERON:0002074 hair shaft The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla. UMLS:C0221961 ncithesaurus:Shaft_of_the_Hair scapus pili BTO:0004672 An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 EMAPA:16245 FMA:7085 MA:0000019 MESH:D014781 NCIT:C28287 RETIRED_EHDAA2:0002201 UMLS:C0042779 XAO:0003034 visceral organ visceral organ system uberon Organsystem@de splanchnic tissue viscera visceral tissue UBERON:0002075 viscus An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. BTO:0001491 An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] 2012-06-20 AAO:0010386 AAO BTO:0001491 general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. FMA UMLS:C0042779 ncithesaurus:Viscera visceral organ RETIRED_EHDAA2:0002201 visceral organ system MA:0000019 Organsystem@de BTO:0001491 splanchnic tissue BTO:0001491 visceral tissue BTO:0001491 A cortex that is part of a hair [Automatically generated definition]. EMAPA:35387 FMA:70934 MA:0000156 coat hair cortex coat/hair cortex cortex of coat hair cortex of coat/hair hair cortex uberon UBERON:0002077 cortex of hair A cortex that is part of a hair [Automatically generated definition]. OBOL:automatic coat hair cortex OBOL:automatic coat/hair cortex OBOL:automatic cortex of coat hair OBOL:automatic cortex of coat/hair OBOL:automatic A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010248 BTO:0001703 EHDAA2:0000290 EMAPA:17321 FMA:7096 MA:0000075 NCIT:C12868 OpenCyc:Mx4runNcs6fqEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw UMLS:C0225844 VHOG:0000328 XAO:0003192 galen:RightAtrium cardiac right atrium heart right atrium right atrium right atrium of heart right cardiac atrium uberon atrium dextrum UBERON:0002078 right cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] FMA:7096 The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000328 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0225844 ncithesaurus:Right_Atrium heart right atrium MA:0000075 right atrium VHOG:0000328 atrium dextrum A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] The chamber of the heart that receives blood from the lungs[XAO:EJS]. The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010247 BTO:0001702 EHDAA2:0000275 EMAPA:17315 FMA:7097 MA:0000074 NCIT:C12869 OpenCyc:Mx4rkJN1AagEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw UMLS:C0225860 VHOG:0000369 XAO:0003191 galen:LeftAtrium atrium sinistrum cardiac left atrium heart left atrium left atrium left atrium of heart left cardiac atrium uberon UBERON:0002079 left cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] FMA:7097 The chamber of the heart that receives blood from the lungs[XAO:EJS]. XAO:EJS The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000369 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0225860 ncithesaurus:Left_Atrium atrium sinistrum heart left atrium MA:0000074 left atrium VHOG:0000369 A cardiac ventricle that is in the right side of the heart. The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with the pulmonary arteries BTO:0001630 CALOHA:TS-0443 EHDAA2:0000196 EMAPA:17340 FMA:7098 MA:0000093 NCIT:C12870 OpenCyc:Mx4rRMlc0KgNEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA UMLS:C0225883 VHOG:0000717 galen:RightVentricle cardiac right ventricle right ventricle right ventricle of heart uberon right cardiac ventricle ventriculus dexter UBERON:0002080 heart right ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg cjm A cardiac ventricle that is in the right side of the heart. The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] 2012-09-17 VHOG:0000717 VHOG UMLS:C0225883 ncithesaurus:Right_Ventricle right ventricle FMA:7098 right cardiac ventricle EMAPA:17340 ventriculus dexter Cardiac chamber in which blood enters the heart. One of four heart chambers.[TAO] One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] AAO:0010246 BTO:0000903 CALOHA:TS-0437 EFO:0000277 EHDAA2:0000154 EHDAA:1265 EMAPA:16688 EV:0100019 FMA:7099 GAID:555 MA:0000073 MAT:0000496 MESH:D006325 NCIT:C12728 TAO:0000471 UMLS:C0018792 VHOG:0000175 ZFA:0000471 galen:Atrium atria atrium atrium of heart cardiac atria heart atrium uberon atrial tissue UBERON:0002081 cardiac atrium Cardiac chamber in which blood enters the heart. One of four heart chambers.[TAO] 2012-08-14 TAO:0000471 TAO ZFIN:curator One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] 2012-06-20 AAO:0010246 AAO AAO:BJB In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] 2012-09-17 VHOG:0000175 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 UMLS:C0018792 ncithesaurus:Cardiac_Atrium atria atrium ZFA:0000471 cardiac atria atrial tissue BTO:0000903 Cardiac chamber through which blood leaves the heart. A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] One of four heart chambers.[TAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] ventricle AAO:0010249 BTO:0000862 CALOHA:TS-0444 EFO:0000317 EHDAA2:0004164 EHDAA:1912 EMAPA:17331 EV:0100020 FMA:7100 GAID:568 MA:0000091 MAT:0000497 MESH:D006352 NCIT:C12730 OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA TAO:0000009 UMLS:C0018827 VHOG:0000435 XAO:0003193 ZFA:0000009 galen:Ventricle heart ventricle lower chamber of heart ventricle of heart uberon UBERON:0002082 cardiac ventricle Bgee:AN Cardiac chamber through which blood leaves the heart. A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] 2012-06-20 AAO:0010249 AAO AAO:BJB One of four heart chambers.[TAO] 2012-08-14 TAO:0000009 TAO ZFIN:curator In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] 2012-09-17 VHOG:0000435 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 UMLS:C0018827 ncithesaurus:Cardiac_Ventricle A cardiac ventricle that is in the left side of the heart. Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with aorta BTO:0001629 CALOHA:TS-0439 EHDAA2:0002178 EMAPA:17337 FMA:7101 MA:0000092 NCIT:C12871 OpenCyc:Mx4rtW8v46gEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA UMLS:C0225897 VHOG:0000718 galen:LeftVentricle cardiac left ventricle left cardiac ventricle left ventricle left ventricle of heart uberon ventriculus sinister cordis UBERON:0002084 heart left ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg GO A cardiac ventricle that is in the left side of the heart. Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000718 VHOG The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] 2012-09-17 VHOG:0000718 VHOG DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010) UMLS:C0225897 ncithesaurus:Left_Ventricle left ventricle FMA:7101 ventriculus sinister cordis A cardiac septum that divides the left and right atria of the heart. The partition separating the right and left atria of the heart. [TFD][VHOG] The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] EHDAA2:0000838 EHDAA:1896 EMAPA:17011 FMA:7108 MA:0000084 NCIT:C32818 OpenCyc:Mx4rpd49nLYEEduAAAACs2IKfQ OpenCyc:Mx4rwGvku5wpEbGdrcN5Y29ycA UMLS:C0225836 VHOG:0000385 galen:InteratrialSeptum atrial septum atrium septum interatrial septal wall uberon UBERON:0002085 interatrial septum http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png A cardiac septum that divides the left and right atria of the heart. The partition separating the right and left atria of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000385 VHOG The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000385 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0225836 ncithesaurus:Interatrial_Septum The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 MIAA:0000148 TAO:0000317 VHOG:0000317 VSAO:0000093 XAO:0003073 ZFA:0000317 post-cranial axial skeleton uberon UBERON:0002090 previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. postcranial axial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. ZFA:0000317 Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000093 VSAO PSPUB:0000170 The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] 2012-06-20 AAO:0000034 AAO AAO:LAP The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] 2012-08-14 TAO:0000317 TAO ZFIN:curator The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0000317 VHOG DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) axial skeleton FMA:71221 EMAPA:37721 MA:th Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. AAO:0000747 EFO:0000951 EMAPA:32729 FMA:71222 MA:0000290 MAT:0000278 MIAA:0000278 NCIT:C49477 UMLS:C0222646 VHOG:0001666 VSAO:0000076 XAO:0003166 appendicular skeleton entire appendicular skeleton paired fin skeleton uberon skeleton appendiculare UBERON:0002091 appendicular skeleton https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. UBERONREF:0000003 Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] 2012-08-14 VSAO:0000076 VSAO PSPUB:0000170 Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] 2012-08-14 TAO:0000027 TAO TAO:wd The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] 2012-06-20 AAO:0000747 AAO AAO:LAP ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. FMA UMLS:C0222646 ncithesaurus:Appendicular_Skeleton entire appendicular skeleton paired fin skeleton skeleton appendiculare The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer. The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:32668 EV:0100313 FMA:71236 MA:0000815 NCIT:C49332 UMLS:C0459393 VHOG:0000270 cranial dura mater dura mater cranialis dura mater encephali dura mater of brain uberon UBERON:0002092 brain dura mater The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer. MP:0009025 The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000270 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000270 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C0459393 ncithesaurus:Cerebral_Dura_Mater cranial dura mater FMA:71236 dura mater cranialis FMA:71236 FMA:TA A dura mater that is part of a spinal cord [Automatically generated definition]. The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17806 FMA:71237 MA:0001132 NCIT:C49799 UMLS:C0228124 VHOG:0000411 dura mater of neuraxis of spinal cord dura mater of spinal cord spinal cord dura mater spinal cord dura mater of neuraxis uberon UBERON:0002093 spinal dura mater A dura mater that is part of a spinal cord [Automatically generated definition]. OBOL:automatic The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] 2012-09-17 VHOG:0000411 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000411 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C0228124 ncithesaurus:Spinal_Cord_Dura_Mater dura mater of neuraxis of spinal cord OBOL:automatic spinal cord dura mater of neuraxis OBOL:automatic Cardiac septum which separates the right ventricle from the left ventricle.[FMA] The partition separating the right and left ventricles of the heart. [TFD][VHOG] The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) BTO:0002483 EFO:0001956 EHDAA:2603 EMAPA:17333 FMA:7133 MA:0000085 NCIT:C32874 OpenCyc:Mx4rwA7lp5wpEbGdrcN5Y29ycA UMLS:C0225870 VHOG:0000386 galen:InterventricularSeptum heart interventricular septum heart ventricular septum uberon interventricular septum of heart interventriculare cordis intraventricular septum s. interventriculare cordis septum inferius septum membranaceum ventricle septum ventricular septum UBERON:0002094 interventricular septum http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png Cardiac septum which separates the right ventricle from the left ventricle.[FMA] FMA:7133 The partition separating the right and left ventricles of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000386 VHOG The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] 2012-09-17 VHOG:0000386 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430 involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) ISBN:0124020607 UMLS:C0225870 ncithesaurus:Interventricular_Septum heart interventricular septum MA:0000085 heart ventricular septum MA:0000085 interventricular septum of heart BTO:0002483 interventriculare cordis BTO:0002483 intraventricular septum s. interventriculare cordis septum inferius septum membranaceum ventricular septum ventricular septum MA:0000085 Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon. mesenteric in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery. AAO:0011061 BTO:0001380 EV:0100083 FMA:7144 GAID:21 MESH:A01.047.025.600.451 NCIT:C33103 UMLS:C0025474 galen:Mesentery generic mesentery mesentery (generic) uberon UBERON:0002095 mesentery http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon. FMA:7144 in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery. FMA UMLS:C0025474 ncithesaurus:Mesentery generic mesentery mesentery (generic) The organ covering the body that consists of the dermis and epidermis. consider 'integumentary system' for invertebrates MA uses the term skin to refer to what is called here: zone of skin BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MESH:D012867 MFMO:0000099 NCIT:C12470 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA UMLS:C1123023 XAO:0000023 galen:Skin entire skin skin organ uberon entire integument integument integumental organ pelt skin UBERON:0002097 skin of body http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg Wikipathways:WP2062 The organ covering the body that consists of the dermis and epidermis. UBERON:cjm MA uses the term skin to refer to what is called here: zone of skin FMA UMLS:C1123023 ncithesaurus:Skin The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. 'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations' in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this EMAPA:35400 FMA:7180 GAID:562 MA:0000083 MESH:D006346 NCIT:C49485 UMLS:C0018819 XAO:0004141 cardiac septa heart septa heart septum septum of heart uberon spiral septa UBERON:0002099 cardiac septum The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. MESH:A07.541.459 in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this GO UMLS:C0018819 ncithesaurus:Heart_Septum cardiac septa heart septa spiral septa XAO:0004141 Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 CALOHA:TS-1071 EFO:0000966 EMAPA:31857 FMA:7181 MA:0000004 MAT:0000296 MIAA:0000296 NCIT:C33816 OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA TAO:0001115 UMLS:C0460005 XAO:0000054 XAO:0003025 ZFA:0001115 galen:Trunk thoracolumbar region torso trunk region uberon Rumpf UBERON:0002100 trunk Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. TAO:0001115 UBERONREF:0000006 Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] 2012-06-20 AAO:0010339 AAO AAO:BJB Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] 2012-08-14 TAO:0001115 TAO ZFIN:curator UMLS:C0460005 ncithesaurus:Trunk trunk region XAO:0000054 Rumpf BTO:0001493 A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts. Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] AAO:0010336 AEO:0000172 CALOHA:TS-0552 EFO:0000876 EHDAA2:0003172 EHDAA:1697 EHDAA:8273 EMAPA:16405 FMA:24875 GAID:36 MA:0000007 MAT:0000090 MIAA:0000090 NCIT:C12429 OpenCyc:Mx4rvn1uSZwpEbGdrcN5Y29ycA UMLS:C0015385 VHOG:0000336 VSAO:0000121 XAO:0003027 galen:Extremity free limb limb sensu Vertebrata pentadactyl limb tetrapod limb flipper uberon extremities extremity UBERON:0002101 limb Sarcopterygians A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts. UBERONREF:0000003 Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO] 2012-06-20 AAO:0010336 AAO AAO:BJB Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000336 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 UMLS:C0015385 ncithesaurus:Limb free limb FMA:24875 limb sensu Vertebrata MAT:0000090 flipper extremities A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts. Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm Upper limb, which connects the manus with the pectoral girdle.[AAO] note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb AAO:0000205 BTO:0001729 CALOHA:TS-2214 EFO:0000882 EHDAA2:0002133 EHDAA:6208 EMAPA:17412 EV:0100014 FMA:24878 GAID:1215 GAID:51 MA:0000025 MAT:0000394 MESH:D005552 MIAA:0000394 NCIT:C12671 UMLS:C1140618 VHOG:0000338 VSAO:0000148 XAO:0003030 galen:UpperExtremity anteriormost limb fore limb forelimb free part of upper limb free upper limb membrum superius pectoral limb superior member upper extremity upper limb pectoral flipper uberon foreleg UBERON:0002102 forelimb A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts. UBERONREF:0000003 Upper limb, which connects the manus with the pectoral girdle.[AAO] 2012-06-20 AAO:0000205 AAO AAO:LAP note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb FMA UMLS:C1140618 ncithesaurus:Upper_Extremity free part of upper limb FMA:24878 free upper limb FMA:24878 UBERONREF:0000003 membrum superius FMA:7183 FMA:TA pectoral flipper A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts. Lower limb, which connects the pes with the pelvic girdle.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] crural note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton AAO:0000219 BTO:0002345 CALOHA:TS-2215 EFO:0000883 EHDAA2:0001033 EHDAA:6094 EMAPA:17458 EV:0100015 FMA:24879 GAID:1221 GAID:38 MA:0000026 MAT:0000395 MESH:D006614 MIAA:0000395 NCIT:C12742 NCIT:C77625 UMLS:C0023216 UMLS:C1522391 VHOG:0000337 VSAO:0000150 XAO:0003031 galen:LowerExtremity free lower limb hind limb hind-limb hindlimb inferior member lower limb membrum inferius uberon free part of lower limb lower extremity membrum inferius pelvic appendage UBERON:0002103 hindlimb http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts. UBERONREF:0000003 Lower limb, which connects the pes with the pelvic girdle.[AAO] 2012-06-20 AAO:0000219 AAO AAO:LAP Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000337 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton FMA UMLS:C0023216 ncithesaurus:Lower_Extremity UMLS:C1522391 ncithesaurus:Hind_Limb free lower limb FMA:24879 UBERONREF:0000003 hind-limb VSAO:0000150 membrum inferius FMA:7184 FMA:TA free part of lower limb FMA:24879 membrum inferius The sensory system subserving the sense of vision. The sensory system used for sight.[AAO] UBERON:0007036 AAO:0000632 BILA:0000140 EMAPA:36003 FMA:7191 MA:0002444 NCIT:C12888 OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA TAO:0001127 UMLS:C0587900 XAO:0003198 ZFA:0001127 photosensory system visual organ system uberon UBERON:0002104 visual system The sensory system subserving the sense of vision. NIFSTD:FMAID_7191 The sensory system used for sight.[AAO] 2012-06-20 AAO:0000632 AAO AAO:EJS UMLS:C0587900 ncithesaurus:Visual_System photosensory system BILA:0000140 Sensory system responsible for the perception of spatial orientation and auditory stimuli. The sensory system used for balance and hearing.[AAO] AAO:0000631 EMAPA:36002 EMAPA:37985 FMA:78500 TAO:0001138 XAO:0003195 ZFA:0001138 auditory organ system vestibuloauditory system uberon auditory system auditory/vestibular system vestibuloauditory system UBERON:0002105 vestibulo-auditory system http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg Sensory system responsible for the perception of spatial orientation and auditory stimuli. ZFA:0001138 The sensory system used for balance and hearing.[AAO] 2012-06-20 AAO:0000631 AAO AAO:EJS EMAPA:37985 MA:th spleen the organ that functions to filter blood and to store red corpuscles and platelets spleen http://langual.org An organ involved in red blood cell filtration and immune response.[AAO] With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG] lienal splenic In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells AAO:0010395 BTO:0001281 CALOHA:TS-0956 EFO:0000869 EMAPA:18767 EV:0100055 FMA:7196 GAID:1289 MA:0000141 MAT:0000085 MESH:A15.382.520.604.713 MIAA:0000085 NCIT:C12432 OpenCyc:Mx4rvVjgw5wpEbGdrcN5Y29ycA TAO:0000436 UMLS:C0037993 VHOG:0000120 XAO:0000328 ZFA:0000436 galen:Spleen http://www.langual.org/langual_thesaurus.asp?termid=C0191 uberon lien UBERON:0002106 spleen Illu:spleen.jpg the organ that functions to filter blood and to store red corpuscles and platelets ISBN:0-683-40008-8 MP:0000689 An organ involved in red blood cell filtration and immune response.[AAO] 2012-06-20 AAO:0010395 AAO AAO:BMZ With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG] 2012-09-17 VHOG:0000120 VHOG ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94 Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96) UMLS:C0037993 ncithesaurus:Spleen lien liver An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. http://langual.org Organ which secretes bile and participates in formation of certain blood proteins.[AAO] relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] hepatic An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003). The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates. secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. AAO:0010111 BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 NCIT:C12392 OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA TAO:0000123 UMLS:C0023884 VHOG:0000257 XAO:0000133 ZFA:0000123 galen:Liver http://www.langual.org/langual_thesaurus.asp?termid=C0176 uberon iecur jecur UBERON:0002107 liver Leber:Schaf.jpg BTO EHDAA2 GO-def ZFA ZFA-weakened EHDAA2 An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. BTO:0000759 Organ which secretes bile and participates in formation of certain blood proteins.[AAO] 2012-06-20 AAO:0010111 AAO AAO:BJB relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] 2012-06-20 AAO:0010111 AAO All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000257 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. ZFA UMLS:C0023884 ncithesaurus:Liver iecur jecur Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010397 BTO:0000651 CALOHA:TS-0942 EFO:0000841 EMAPA:32834 EV:0100072 FMA:7200 GAID:313 MA:0000337 MAT:0000047 MESH:A03.492.411.620 MIAA:0000047 NCIT:C12386 OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA TAO:0001323 UMLS:C0021852 VHOG:0000055 XAO:0000130 ZFA:0001323 galen:SmallIntestine small bowel small intestine uberon anterior intestine intestinum tenue mid intestine UBERON:0002108 small intestine http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg 2 cjm Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. ISBN:0073040584 The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0001323 TAO ZFIN:curator Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000055 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 UMLS:C0021852 ncithesaurus:Small_Intestine intestinum tenue intestinum tenue BTO:0000651 2 2 Pair of nostrils. this is a 'set of anatomical planes' in FMA FMA:72005 OpenCyc:Mx4rvViCLpwpEbGdrcN5Y29ycA nares set nostrils pair of nostrils uberon nares set of nares UBERON:0002109 pair of nares Pair of nostrils. this is a 'set of anatomical planes' in FMA FMA set of nares FMA:72005 An organ that aids digestion and stores bile produced by the liver[WP]. Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO] relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG] AAO:0010114 BTO:0000493 CALOHA:TS-0394 EFO:0000853 EHDAA2:0000699 EHDAA:8062 EMAPA:17202 EV:0100090 FMA:7202 MA:0000356 MAT:0000072 MESH:D005704 MIAA:0000072 NCIT:C12377 OpenCyc:Mx4rvVkGr5wpEbGdrcN5Y29ycA TAO:0000208 UMLS:C0016976 VHOG:0000221 XAO:0000135 ZFA:0000208 galen:Gallbladder gall bladder gallbladder uberon vesica biliaris vesica fellea UBERON:0002110 Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988) gall bladder Abdomal:organs.svg https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg BTO MA ZFA cjm definitional An organ that aids digestion and stores bile produced by the liver[WP]. Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000221 VHOG Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO] 2012-06-20 AAO:0010114 AAO AAO:BJB relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] 2012-06-20 AAO:0010114 AAO The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG] 2012-09-17 VHOG:0000221 VHOG DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997) UMLS:C0016976 ncithesaurus:Gallbladder gallbladder FMA:7202 vesica biliaris vesica fellea A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. BTO:0000087 CALOHA:TS-1198 EMAPA:36285 FMA:72024 MA:0000708 NCIT:C49195 UMLS:C1706851 arterial smooth muscle artery smooth muscle artery smooth muscle tissue smooth muscle of artery uberon arterial smooth muscle cell UBERON:0002111 artery smooth muscle tissue A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. OBOL:automatic UMLS:C1706851 ncithesaurus:Artery_Smooth_Muscle_Tissue arterial smooth muscle BTO:0000087 smooth muscle of artery FMA:72024 arterial smooth muscle cell BTO:0000087 A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]. EMAPA:35323 FMA:72025 MA:0001573 esophageal smooth muscle esophagus involuntary muscle esophagus non-striated muscle esophagus smooth muscle esophagus smooth muscle tissue gullet involuntary muscle gullet non-striated muscle gullet smooth muscle gullet smooth muscle tissue involuntary muscle of esophagus involuntary muscle of gullet involuntary muscle of oesophagus non-striated muscle of esophagus non-striated muscle of gullet non-striated muscle of oesophagus oesophagus involuntary muscle oesophagus non-striated muscle oesophagus smooth muscle tissue smooth muscle of gullet smooth muscle of oesophagus smooth muscle tissue of esophagus smooth muscle tissue of gullet smooth muscle tissue of oesophagus uberon oesophagus smooth muscle UBERON:0002112 smooth muscle of esophagus A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus involuntary muscle OBOL:automatic esophagus non-striated muscle OBOL:automatic esophagus smooth muscle tissue OBOL:automatic gullet involuntary muscle OBOL:automatic gullet non-striated muscle OBOL:automatic gullet smooth muscle OBOL:automatic gullet smooth muscle tissue OBOL:automatic involuntary muscle of esophagus OBOL:automatic involuntary muscle of gullet OBOL:automatic involuntary muscle of oesophagus OBOL:automatic non-striated muscle of esophagus OBOL:automatic non-striated muscle of gullet OBOL:automatic non-striated muscle of oesophagus OBOL:automatic oesophagus involuntary muscle OBOL:automatic oesophagus non-striated muscle OBOL:automatic oesophagus smooth muscle tissue OBOL:automatic smooth muscle of gullet OBOL:automatic smooth muscle of oesophagus OBOL:automatic smooth muscle tissue of esophagus OBOL:automatic smooth muscle tissue of gullet OBOL:automatic smooth muscle tissue of oesophagus OBOL:automatic A paired organ of the urinary tract which has the production of urine as its primary function. kidney http://langual.org One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] renal AAO:0000250 BTO:0000671 CALOHA:TS-0510 EFO:0000929 EMAPA:17373 EV:0100096 FMA:7203 GAID:423 MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 NCIT:C12415 OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA UMLS:C0022646 XAO:0003267 galen:Kidney http://www.langual.org/langual_thesaurus.asp?termid=C0196 reniculate kidney uberon UBERON:0002113 kidney FMA definitional A paired organ of the urinary tract which has the production of urine as its primary function. One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] 2012-06-20 AAO:0000250 AAO AAO:BJB UMLS:C0022646 ncithesaurus:Kidney reniculate kidney The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] duodenal In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. AAO:0010402 BTO:0000365 CALOHA:TS-0214 EFO:0000851 EMAPA:18852 EV:0100073 FMA:7206 GAID:284 MA:0000338 MAT:0000044 MESH:A03.492.411.620.270 MIAA:0000044 NCIT:C12263 OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA UMLS:C0013303 VHOG:0000052 XAO:0000236 galen:Duodenum uberon proximal intestine upper intestine UBERON:0002114 duodenum http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg 3 cjm The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). ISBN:0815318960 The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000052 VHOG In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. NCBITaxon:32443 In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. NCBITaxon:9606 UMLS:C0013303 ncithesaurus:Duodenum proximal intestine BTO:0000365 upper intestine BTO:0000365 the portion of the small intestine that extends from the jejunum to the colon TODO consider ZFA:0000706 posterior intestine, see also colon Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] ileal The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.[Wikipedia:Ileum] AAO:0010403 BTO:0000620 CALOHA:TS-0472 EFO:0001334 EMAPA:32764 EV:0100075 FMA:7208 GAID:315 MA:0000339 MAT:0000282 MESH:A03.492.411.620.484 MIAA:0000282 NCIT:C12387 OpenCyc:Mx4rvdcLHZwpEbGdrcN5Y29ycA UMLS:C0020885 VHOG:0000647 XAO:0000237 galen:Ileum uberon distal intestine intestinum ileum lower intestine posterior intestine UBERON:0002116 ileum http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg 3 cjm the portion of the small intestine that extends from the jejunum to the colon ISBN:0-683-40008-8 MGI:csmith MP:0002581 Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000647 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0020885 ncithesaurus:Ileum distal intestine BTO:0000620 intestinum ileum BTO:0000620 lower intestine BTO:0000620 posterior intestine An ovary that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37367 FMA:7213 MA:0001705 NCIT:C33487 UMLS:C0227873 uberon UBERON:0002118 right ovary An ovary that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37367 MA:th UMLS:C0227873 ncithesaurus:Right_Ovary An ovary that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo EMAPA:37366 FMA:7214 MA:0001704 NCIT:C32969 UMLS:C0227874 uberon UBERON:0002119 left ovary An ovary that is part of a left side of organism [Automatically generated definition]. OBOL:automatic In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo EMAPA:37366 MA:th UMLS:C0227874 ncithesaurus:Left_Ovary In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] pronephric UBERON:0005794 AAO:0011089 BTO:0001541 EFO:0000927 EHDAA2:0001570 EHDAA:1017 EMAPA:16579 FMA:72170 MAT:0000117 MIAA:0000117 NCIT:C34280 TAO:0000151 UMLS:C0231048 VHOG:0000037 XAO:0002000 ZFA:0000151 pronephric kidney uberon archinephron embryonic kidney pronephron UBERON:0002120 Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros GO OG ZFA In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. GO:0048793 A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] 2012-09-17 VHOG:0000037 VHOG Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] 2012-06-20 AAO:0011089 AAO XAO:curator The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000151 TAO ZFIN:curator In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] 2012-09-17 VHOG:0000037 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637 UMLS:C0231048 ncithesaurus:Pronephros pronephric kidney XAO:0002000 archinephron BTO:0001541 embryonic kidney BTO:0001541 pronephron BTO:0001541 The fibrous connective tissue surrounding the thymus. EMAPA:19306 FMA:72204 MA:0000766 NCIT:C33770 UMLS:C0229945 thymic capsule thymus capsule uberon UBERON:0002122 capsule of thymus The fibrous connective tissue surrounding the thymus. MP:0002368 UMLS:C0229945 ncithesaurus:Thymic_Capsule the outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes Histologically, the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. The cortex and medulla play different roles in the development of T cells. Cells in the thymus can be divided into thymic stromal cells and cells of hematopoietic origin[WP] BTO:0002934 EMAPA:35863 FMA:72205 MA:0000767 NCIT:C33774 UMLS:C0229948 thymic cortex thymus cortex uberon UBERON:0002123 cortex of thymus the outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes ISBN:0-683-40008-8 MP:0002371 UMLS:C0229948 ncithesaurus:Thymus_Cortex thymic cortex BTO:0002934 thymus cortex MA:0000767 Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size. BTO:0004560 EFO:0001969 EMAPA:19305 FMA:72206 MA:0000771 NCIT:C33775 UMLS:C0229949 medulla of thymus gland thymus gland medulla thymus medulla uberon UBERON:0002124 medulla of thymus Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size. UMLS:C0229949 ncithesaurus:Thymus_Medulla medulla of thymus gland OBOL:automatic thymus gland medulla OBOL:automatic A lobule that is part of a thymus. Divided into an outer cortex and inner medulla and separated from each other by connective tissue septa, but with the medullary tissue continuous from lobule to lobule.[ncit,modified]. in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP] Lymphocytes, reticular cells and macrophages are found in the lobules FMA:72215 MA:0000770 NCIT:C33772 UMLS:C1522462 lobule of thymus thymic lobule thymus lobule uberon UBERON:0002125 thymus lobule A lobule that is part of a thymus. Divided into an outer cortex and inner medulla and separated from each other by connective tissue septa, but with the medullary tissue continuous from lobule to lobule.[ncit,modified]. ncithesaurus:Thymic_Lobule UMLS:C1522462 ncithesaurus:Thymic_Lobule lobule of thymus FMA:72215 thymus lobule MA:0000770 A a collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718] The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates. BAMS:SOC BIRNLEX:1307 DHBA:12462 EMAPA:35840 EV:0100263 FMA:72247 HBA:9177 MA:0001026 MBA:398 UMLS:C0175427 VHOG:0001381 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=569 nucleus olivaris superior superior olivary nuclei uberon regio olivaris superioris superior olivary nucleus superior olivary nucleus (Barr & Kiernan) superior olive UBERON:0002128 superior olivary complex http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png NIFSTD A a collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. ISBN:0-19-502694-2 UMLS:C0175427 BIRNLEX:1307 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=569 BIRNLEX:1307 nucleus olivaris superior FMA:72247 FMA:TA superior olivary nuclei FMA:72247 regio olivaris superioris NeuroNames:569 superior olivary nucleus FMA:72247 superior olivary nucleus (Barr & Kiernan) NeuroNames:569 superior olive FMA:72247 ISBN:0-19-502694-2 The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695]. BAMS:CB BAMS:CBX BAMS:CbCx BIRNLEX:1566 BM:CB-Cbx BTO:0000043 CALOHA:TS-2000 DHBA:10657 DMBA:16939 EMAPA:35211 EV:0100294 FMA:72248 GAID:596 HBA:4697 MA:0000199 MBA:528 MESH:D002525 NCIT:C49216 UMLS:C0007759 UMLS:C1284087 VHOG:0001597 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=647 cortex of cerebellar hemisphere uberon cortex cerebellaris cortex cerebelli UBERON:0002129 The circuits in the cerebellar cortex look similar across all classes of vertebrates, including fish, reptiles, birds, and mammals (e.g., Fig. 2). This has been taken as evidence that the cerebellum performs functions important to all vertebrate species. (Wikipedia) cerebellar cortex Cerebellum:NIH.png The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer. BIRNLEX:1566 The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695]. GO:0021695 UMLS:C0007759 BIRNLEX:1566 UMLS:C0007759 ncithesaurus:Cerebellar_Cortex UMLS:C1284087 BIRNLEX:1566 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=647 BIRNLEX:1566 cortex of cerebellar hemisphere DMBA:CbHCx cortex cerebellaris BTO:0000043 cortex cerebelli NeuroNames:647 The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. TODO - check ZFA/pons. also GO says part of dorsorostral pons BAMS:CAE BAMS:LC BIRNLEX:905 BM:Pons-LC BTO:0001408 DHBA:12819 DMBA:16972 EFO:0001963 EMAPA:35502 FMA:72478 GAID:577 HBA:9148 MA:0001017 MBA:147 MESH:D008125 NCIT:C97333 TAO:0000539 UMLS:C0023951 ZFA:0000539 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=583 blue nucleus caerulean nucleus locus caeruleus locus coeruleu locus coeruleus nucleus caeruleus nucleus of locus caeruleus nucleus pigmentosus pontis substantia ferruginea uberon loci coeruleus locus cinereus locus coeruleus (Vicq d'Azyr) nucleus loci caerulei UBERON:0002148 locus ceruleus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png check ZFA NIFSTD The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. GAID:577 GO:0021703 UMLS:C0023951 BIRNLEX:905 UMLS:C0023951 ncithesaurus:Locus_Coeruleus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=583 BIRNLEX:905 blue nucleus BIRNLEX:905 locus caeruleus BIRNLEX:905 nucleus caeruleus FMA:72478 FMA:TA nucleus pigmentosus pontis BIRNLEX:905 substantia ferruginea BIRNLEX:905 loci coeruleus ZFA:0000539 locus cinereus BTO:0001408 locus coeruleus (Vicq d'Azyr) NeuroNames:583 nucleus loci caerulei NeuroNames:583 Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). BAMS:SSN BAMS:SuS BIRNLEX:1131 DHBA:12435 EHDAA2:0004646 EMAPA:37756 FMA:72482 HBA:9194 MA:0001027 MBA:462 UMLS:C0175447 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=590 superior salivary nucleus uberon nucleus salivarius superior nucleus salivatorius cranialis nucleus salivatorius rostralis nucleus salivatorius superior UBERON:0002149 superior salivatory nucleus http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png definitional Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). BIRNLEX:1131 EMAPA:37756 MA:th UMLS:C0175447 BIRNLEX:1131 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=590 BIRNLEX:1131 superior salivary nucleus GO:0021753 nucleus salivarius superior NeuroNames:590 nucleus salivatorius cranialis NeuroNames:590 nucleus salivatorius rostralis NeuroNames:590 nucleus salivatorius superior NeuroNames:590 The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. Layer that lines the lumen of the heart.[TAO] Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. UBERON:0006225 AAO:0010408 BTO:0000387 CALOHA:TS-2075 EFO:0000821 EHDAA2:0004153 EMAPA:17868 EMAPA:32686 EV:0100021 FMA:7280 GAID:550 MA:0000076 MAT:0000455 MESH:D004699 NCIT:C13004 OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw TAO:0001320 UMLS:C0014124 VHOG:0000084 XAO:0000066 ZFA:0001320 galen:Endocardium endocardial lining endocardial tissue heart endocardium uberon heart endocardial tissue UBERON:0002165 fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 endocardium http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png Bgee:AN The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. GO:0003157 Layer that lines the lumen of the heart.[TAO] 2012-08-14 TAO:0001320 TAO ZFIN:curator Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] 2012-06-20 AAO:0010408 AAO AAO:BJB Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. FMA:7280 UMLS:C0014124 ncithesaurus:Endocardium endocardial lining EMAPA:32686 endocardial tissue EMAPA:17868 heart endocardial tissue VHOG:0000084 Endocardium that is part of the atrium. EMAPA:32745 FMA:7284 MA:0000077 TAO:0002169 VHOG:0000606 ZFA:0001614 Cardiac atria endocardium atrial endocardium atrium endocardium atrium of heart endocardium cardiac atrium endocardium endocardium of Cardiac atria endocardium of atrium of heart endocardium of cardiac atrium endocardium of heart atrium heart atrium endocardium uberon atrium endocardial tissue UBERON:0002166 endocardium of atrium Endocardium that is part of the atrium. ZFIN:curator Cardiac atria endocardium OBOL:automatic atrium of heart endocardium OBOL:automatic cardiac atrium endocardium OBOL:automatic endocardium of Cardiac atria OBOL:automatic endocardium of atrium of heart OBOL:automatic endocardium of cardiac atrium OBOL:automatic endocardium of heart atrium OBOL:automatic heart atrium endocardium OBOL:automatic atrium endocardial tissue VHOG:0000606 Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001730 EHDAA:4969 EMAPA:17661 FMA:7309 MA:0000426 NCIT:C33483 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0225706 VHOG:0000301 uberon UBERON:0002167 right lung http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] FMA:FMA Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000301 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 UMLS:C0225706 ncithesaurus:Right_Lung Lung which consists of the left upper lobe and left lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000943 EHDAA:4947 EMAPA:17653 FMA:7310 MA:0000425 NCIT:C32967 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0225730 VHOG:0000618 uberon UBERON:0002168 left lung http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png Lung which consists of the left upper lobe and left lower lobe.[FMA] FMA:FMA Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000618 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 UMLS:C0225730 ncithesaurus:Left_Lung the upper conducting airways of the lung; these airways arise from the terminus of the trachea Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] bronchial In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue BTO:0001340 CALOHA:TS-1229 EFO:0000932 EMAPA:32689 EV:0100041 FMA:7409 GAID:346 MA:0000436 MAT:0000133 MESH:D001980 MIAA:0000133 NCIT:C12683 UMLS:C0006255 VHOG:0000262 XAO:0000121 bronchi bronchial trunk uberon bronchial tissue UBERON:0002185 bronchus http://upload.wikimedia.org/wikipedia/commons/1/18/Respiratory_system_complete_numbered.svg the upper conducting airways of the lung; these airways arise from the terminus of the trachea ISBN:0-397-51047-0 MESH:A04.411.125 MGI:cwg MP:0002264 Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000262 VHOG UMLS:C0006255 ncithesaurus:Bronchus bronchi bronchial trunk FMA:7409 bronchial tissue BTO:0001340 the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching bronchiolar lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer BTO:0002375 CALOHA:TS-2003 EHDAA:8171 EHDAA:8183 EHDAA:8199 EHDAA:8221 EMAPA:32697 FMA:7410 MA:0000422 NCIT:C12684 OpenCyc:Mx4rvl9iDpwpEbGdrcN5Y29ycA UMLS:C0006270 VHOG:0000675 lobular bronchiole uberon bronchioli bronchiolus UBERON:0002186 bronchiole Alveoli:diagram.png ncit the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching ISBN:0-397-51047-0 MGI:cwg MP:0002267 lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer ISBN:0123813611 UMLS:C0006270 ncithesaurus:Bronchiole lobular bronchiole FMA:7410 bronchioli bronchiolus BTO:0002375 the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls BTO:0003223 EMAPA:36282 FMA:7411 MA:0000424 NCIT:C33754 OpenCyc:Mx4rwS7IU5wpEbGdrcN5Y29ycA UMLS:C0225666 bronchiolus terminalis uberon bronchioli terminalis terminal bronchiole tube UBERON:0002187 terminal bronchiole Alveoli:diagram.png the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls ISBN:0-397-51047-0 MGI:cwg MP:0002268 UMLS:C0225666 ncithesaurus:Terminal_Bronchiole bronchiolus terminalis bronchioli terminalis A portion of adipose tissue that is part of the hypodermis, beneath the dermis. the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] UBERON:0008875 panniculus adiposus BTO:0004042 EMAPA:35829 FMA:74315 MA:0000473 fatty layer of subcutaneous tissue hypodermis fat layer panniculus adiposus (tela subcutanea) panniculus adiposus telae subcutaneae subcutaneous fat layer uberon fatty layer of superficial fascia subcutaneous fat UBERON:0002190 subcutaneous adipose tissue A portion of adipose tissue that is part of the hypodermis, beneath the dermis. the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] MP:0011156 panniculus adiposus MP:0011156 fatty layer of subcutaneous tissue FMA:74315 hypodermis fat layer MP:0011156 panniculus adiposus (tela subcutanea) FMA:74315 FMA:TA panniculus adiposus telae subcutaneae FMA:74315 FMA:TA subcutaneous fat layer MP:0011156 fatty layer of superficial fascia FMA:74315 subcutaneous fat BTO:0004042 Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. CALOHA:TS-2018 EHDAA2:0004615 EMAPA:18765 FMA:74562 MA:0000013 hematolymphoid system lymphomyeloid complex uberon haemolymphoid system UBERON:0002193 hemolymphoid system MA Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers. from its internal surface are given off a number of membranous processes or trabeculae, consisting, in man, of connective tissue, with a small admixture of plain muscle fibers; but in many of the lower animals composed almost entirely of involuntary muscle[WP] EMAPA:35524 FMA:74604 MA:0000739 NCIT:C33028 UMLS:C0229699 capsula nodi lymphoidei lymph node capsule uberon UBERON:0002194 capsule of lymph node Lymphknoten:(Schwein).jpg Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers. UMLS:C0229699 ncithesaurus:Lymph_Node_Capsule capsula nodi lymphoidei FMA:74604 FMA:TA Membranous process coming from capsule of lymph node[WP]. FMA:74605 MA:0000746 NCIT:C33035 UMLS:C1184179 lymph node trabecula lymph node trabeculum uberon UBERON:0002195 trabecula of lymph node http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray598.png Membranous process coming from capsule of lymph node[WP]. UMLS:C1184179 ncithesaurus:Lymph_Node_Trabecula The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA]. Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO] The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head[NCBIBook:NBK53175]. AHP AAO:0010540 BAMS:AHY BAMS:AL BAMS:APit BIRNLEX:1581 BM:AHy BTO:0000040 CALOHA:TS-0794 EFO:0000230 EHDAA2:0000109 EMAPA:17514 FMA:74627 MA:0000177 MESH:A06.407.747.608 NCIT:C12772 TAO:0001282 UMLS:C0032008 UMLS:C1280369 VHOG:0000141 ZFA:0001282 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=407 anterior hypophysis anterior lobe (hypophysis) anterior lobe of hypophysis anterior lobe of pituitary anterior lobe of pituitary gland anterior pituitary lobus anterior (glandula pituitaria) lobus anterior hypophysis pituitary gland, anterior lobe uberon anterior lobe of the pituitary anterior pituitary gland cranial lobe lobus anterior pituitary anterior lobe pituitary glandanterior lobe rostral lobe UBERON:0002196 adenohypophysis http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray1181.png NCBIBook:NBK53175 ZFA lexical The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA]. ZFIN:curator Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO] 2012-06-20 AAO:0010540 AAO AAO:BJB The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO] 2012-08-14 TAO:0001282 TAO ZFIN:curator It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000141 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5 In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish ZFA AHP BIRNLEX:1581 NIFSTD:NeuroNames_abbrevSource UMLS:C0032008 BIRNLEX:1581 UMLS:C0032008 ncithesaurus:Anterior_Lobe_of_the_Pituitary_Gland UMLS:C1280369 BIRNLEX:1581 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=407 BIRNLEX:1581 anterior hypophysis ZFA:0001282 lobus anterior (glandula pituitaria) FMA:74627 FMA:TA lobus anterior hypophysis FMA:74627 FMA:TA anterior lobe of the pituitary BAMS:APit anterior pituitary gland BTO:0000040 cranial lobe BTO:0000496 lobus anterior NeuroNames:407 pituitary anterior lobe EMAPA:17514 pituitary glandanterior lobe BAMS:AL rostral lobe BTO:0000496 The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon. request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon' The infundibular part of the pituitary gland consisting of two regions.[AAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19) NHP AAO:0010537 BAMS:NHP BAMS:NHY BAMS:NL BAMS:PPit BIRNLEX:1586 BM:NY BTO:0000937 CALOHA:TS-0815 DMBA:15691 EHDAA2:0001271 EHDAA:7536 EMAPA:17519 FMA:74628 MA:0000178 MESH:A06.407.747.734 NCIT:C12773 TAO:0001271 UMLS:C0032009 UMLS:C1280368 VHOG:0000142 ZFA:0001271 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=401 infundibular process lobus nervosus neurohypophysis lobus posterior (glandula pituitaria) lobus posterior hypophysis neural lobe neural lobe of pituitary neural lobe of pituitary gland neuro hypophysis neurohypophysis pituitary gland, posterior lobe posterior lobe of pituitary posterior lobe of pituitary gland posterior pituitary uberon lobus nervosus lobus posterior pituitary gland neural lobe pituitary gland, neural lobe posterior lobe of hypophysis posterior pituitary gland UBERON:0002198 neurohypophysis http://upload.wikimedia.org/wikipedia/commons/b/b9/Pituitary_gland_representation.PNG MA ZFA lexical The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon. MP:0004164 request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon' Ariens, p. 1192 The infundibular part of the pituitary gland consisting of two regions.[AAO] 2012-06-20 AAO:0010537 AAO AAO:BJB It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000142 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5 todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19) EMAPA NHP BIRNLEX:1586 NIFSTD:NeuroNames_abbrevSource UMLS:C0032009 BIRNLEX:1586 UMLS:C0032009 ncithesaurus:Posterior_Lobe_of_the_Pituitary_Gland UMLS:C1280368 BIRNLEX:1586 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=401 BIRNLEX:1586 infundibular process FMA:74628 lobus nervosus neurohypophysis FMA:74628 FMA:TA lobus posterior (glandula pituitaria) FMA:74628 FMA:TA lobus posterior hypophysis FMA:74628 FMA:TA neural lobe FMA:74628 neural lobe of pituitary BIRNLEX:1586 neural lobe of pituitary gland FMA:74628 posterior lobe of pituitary gland FMA:74628 lobus nervosus NeuroNames:401 lobus posterior NeuroNames:401 pituitary gland neural lobe BAMS:NL pituitary gland, neural lobe NeuroNames:401 posterior lobe of hypophysis NeuroNames:401 posterior pituitary gland BTO:0000937 The dermis, epidermis and hypodermis. in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition. Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] Surface structure that is the outer protective covering of the body.[VSAO] The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] integumental integumentary AAO:0000239 BTO:0000634 EMAPA:37504 FMA:74657 TAO:0000368 VSAO:0000029 ZFA:0000368 galen:Integument dermis plus epidermis plus hypodermis integumentum commune skin and subcutaneous tissue skin plus hypodermis the integument uberon Hautsystem@de dermal system dermoid system skin tegument vertebrate integument UBERON:0002199 integument FMA FMA The dermis, epidermis and hypodermis. Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] 2012-06-20 AAO:0000239 AAO AAO:EJS Surface structure that is the outer protective covering of the body.[VSAO] 2012-08-14 VSAO:0000029 VSAO PSPUB:0000170 The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000368 TAO ZFIN:curator EMAPA:37504 MA:th integumentum commune FMA:74657 FMA:TA the integument FMA:74657 Hautsystem@de BTO:0000634 dermal system BTO:0000634 dermoid system BTO:0000634 tegument BTO:0000634 Vasculature that is part of a head [Automatically generated definition]. EFO:0003656 FMA:74710 TAO:0001267 XAO:0004152 ZFA:0001267 adult head vascular network adult head vasculature cranial vasculature head vascular network vascular network of adult head vascular network of head vasculature of adult head uberon head vasculature UBERON:0002200 vasculature of head Vasculature that is part of a head [Automatically generated definition]. OBOL:automatic adult head vascular network OBOL:automatic adult head vasculature OBOL:automatic head vascular network OBOL:automatic vascular network of adult head OBOL:automatic vascular network of head OBOL:automatic vasculature of adult head OBOL:automatic A vasculature that is part of a trunk [Automatically generated definition]. FMA:74712 TAO:0005024 ZFA:0005024 torso vascular network torso vasculature trunk vascular network trunk vasculature vascular network of torso vascular network of trunk vasculature of torso uberon UBERON:0002201 vasculature of trunk A vasculature that is part of a trunk [Automatically generated definition]. OBOL:automatic torso vascular network OBOL:automatic torso vasculature OBOL:automatic trunk vascular network OBOL:automatic vascular network of torso OBOL:automatic vascular network of trunk OBOL:automatic vasculature of torso OBOL:automatic A submucosa that is part of a trachea. BTO:0002115 EMAPA:35879 FMA:7472 MA:0001860 NCIT:C49307 UMLS:C0225586 submucosa of windpipe trachea submucosa tracheal submucosa windpipe submucosa uberon submucous layer of trachea UBERON:0002202 submucosa of trachea A submucosa that is part of a trachea. OBOL:automatic UMLS:C0225586 ncithesaurus:Trachea_Submucosa submucosa of windpipe OBOL:automatic windpipe submucosa OBOL:automatic submucous layer of trachea BTO:0002115 Vasculature that is part of the eye region. not part of the eye in ZFA. Note this changed to a blood vessel in ZFA FMA:74743 TAO:0007057 ZFA:0007057 eye vascular network ocular blood vessel ocular vasculature vascular network of eye uberon eye vasculature optic vasculature UBERON:0002203 vasculature of eye ISBN:0781772214 Vasculature that is part of the eye region. OBOL:automatic not part of the eye in ZFA. Note this changed to a blood vessel in ZFA ZFA eye vascular network OBOL:automatic ocular blood vessel ZFA:0007057 vascular network of eye OBOL:automatic Anatomical system that consists of the muscular and skeletal systems. Anatomical system that provides locomotion and physical support to the organism.[AAO] There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 EV:0100139 FMA:7482 GAID:98 MA:0002418 MESH:D009141 NCIT:C12754 OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g UMLS:C0026860 VHOG:0001275 VSAO:0000031 XAO:0000168 musculo-skeletal system uberon UBERON:0002204 musculoskeletal system check ctenophore Anatomical system that consists of the muscular and skeletal systems. VSAO:0000031 VSAO:curator Anatomical system that provides locomotion and physical support to the organism.[AAO] 2012-06-20 AAO:0010546 AAO AAO:EJS There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] 2012-09-17 VHOG:0001275 VHOG DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) UMLS:C0026860 ncithesaurus:Musculoskeletal_System Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA] A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO] AEO:0000178 EHDAA2:0003178 EMAPA:35344 FMA:7492 MA:0000321 TAO:0005156 ZFA:0005156 articulatio fibrosa uberon junctura fibrosa UBERON:0002209 fibrous joint FMA Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA] FMA:FMA A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO] 2012-08-14 TAO:0005156 TAO ZFIN:curator junctura fibrosa Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA] EMAPA:36581 FMA:7496 MA:0000320 TAO:0005155 ZFA:0005155 articulatio cartilaginea uberon junctura cartilaginea UBERON:0002213 cartilaginous joint FMA Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA] FMA:FMA junctura cartilaginea Cartilaginous joint in which the articulating bones or cartilages are connected by hyaline cartilage. Examples: spheno-occipital synchondrosis, first sternocostal joint.[FMA] WP considers epiphyseal plates as subtypes of this consider adding link to hyaline cartilage EMAPA:35846 FMA:7497 MA:0001501 cartilago epiphysialis primary cartilaginous joint uberon epiphysial cartilage UBERON:0002215 synchondrosis http://upload.wikimedia.org/wikipedia/commons/7/76/Gray297.png Cartilaginous joint in which the articulating bones or cartilages are connected by hyaline cartilage. Examples: spheno-occipital synchondrosis, first sternocostal joint.[FMA] FMA:FMA cartilago epiphysialis FMA:7497 FMA:TA primary cartilaginous joint FMA:7497 epiphysial cartilage FMA:7497 Cartilaginous joint in which the articulating bones or cartilages are connected by fibrocartilage. Examples: pubic symphysis, intervertebral symphysis, manubriosternal joint.[FMA] consider adding fibrocartilage class EMAPA:37758 FMA:7498 MA:0001504 secondary cartilaginous joint uberon UBERON:0002216 symphysis http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray298.png MA FMA Cartilaginous joint in which the articulating bones or cartilages are connected by fibrocartilage. Examples: pubic symphysis, intervertebral symphysis, manubriosternal joint.[FMA] FMA:FMA EMAPA:37758 MA:th secondary cartilaginous joint FMA:7498 Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] AEO:0000183 CALOHA:TS-2138 EHDAA2:0003183 FMA:7501 MA:0000322 NCIT:C32461 OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA TAO:0005153 ZFA:0005153 galen:SynovialJoint articulatio synoviale diarthroses diarthrosis diarthrosis joint uberon diarthrodial joints UBERON:0002217 synovial joint Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] FMA:7501 Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] 2012-08-14 TAO:0005153 TAO ZFIN:Curator diarthroses ZFA:0005153 diarthrodial joints ZFA:0005153 Anatomical structure that is a membranous gap between bones of the skull[TAO]. In humans: Fontanelles are soft spots on a baby's head which, during birth, enable the bony plates of the skull to flex, allowing the child's head to pass through the birth canal. The ossification of the bones of the skull cause the fontanelles to close over by a child's second birthday. The closures eventually form the sutures of the neurocranium. Although there are the two anterior and posterior fontanelles, there are two more fontanelles of interest, the mastoid fontanelle, and the sphenoidal fontanelle[WP]. TODO - check Anatomical structure that is a membranous gap between bones of the skull.[TAO] FMA:75438 MA:0001465 NCIT:C32621 TAO:0001738 UMLS:C0224548 ZFA:0005536 fontanel fontanelles fontanels uberon fonticuli cranii UBERON:0002221 fontanelle http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray197.png FMA MA ZFA Anatomical structure that is a membranous gap between bones of the skull[TAO]. In humans: Fontanelles are soft spots on a baby's head which, during birth, enable the bony plates of the skull to flex, allowing the child's head to pass through the birth canal. The ossification of the bones of the skull cause the fontanelles to close over by a child's second birthday. The closures eventually form the sutures of the neurocranium. Although there are the two anterior and posterior fontanelles, there are two more fontanelles of interest, the mastoid fontanelle, and the sphenoidal fontanelle[WP]. Anatomical structure that is a membranous gap between bones of the skull.[TAO] 2012-08-14 TAO:0001738 TAO TAO:wd UMLS:C0224548 ncithesaurus:Fontanelle fontanelles TAO:0001738 fontanels TAO:0001738 fonticuli cranii The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 MA:0000032 MESH:A01.911.800 NCIT:C12905 OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA UMLS:C0230139 cavitas thoracis cavity of chest cavity of thorax chest cavity pectoral cavity space of thoracic compartment thoracic lumen uberon UBERON:0002224 thoracic cavity http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. UBERON:cjm UMLS:C0230139 ncithesaurus:Thoracic_Cavity cavitas thoracis space of thoracic compartment FMA:7565 An intersegmental rod-shaped bone that forms in the peritoneal membrane and attach to the vertebral parapophyses. Endochondral bone that is intersegmental and rod-shaped, forming in the peritoneal membrane and attached to the vertebral parapophyses. Ribs protect and support internal organs.[TAO] Endochondral, rodlike element that articulates with the transverse process and parapophysis (double-headed rib), or with the transverse process only (single-headed rib); it extends into the body wall and provides a site for muscle attachment.[AAO] costal In most vertebrates, ribs surround the chest. In some species, especially snakes, ribs may provide support and protection for the entire body They protect and support internal organs and enable lungs to expand by expanding the chest. AAO:0000545 CALOHA:TS-2209 EFO:0003066 EMAPA:18010 FMA:7574 GAID:245 MA:0000315 MESH:D012272 NCIT:C12782 OpenCyc:Mx4rvVjNoZwpEbGdrcN5Y29ycA TAO:0000538 UMLS:C0035561 VHOG:0001154 ZFA:0000538 galen:Rib uberon dorsal rib pleural rib ribs UBERON:0002228 rib definitional An intersegmental rod-shaped bone that forms in the peritoneal membrane and attach to the vertebral parapophyses. ZFIN:curator Endochondral bone that is intersegmental and rod-shaped, forming in the peritoneal membrane and attached to the vertebral parapophyses. Ribs protect and support internal organs.[TAO] 2012-08-14 TAO:0000538 TAO ZFIN:curator Endochondral, rodlike element that articulates with the transverse process and parapophysis (double-headed rib), or with the transverse process only (single-headed rib); it extends into the body wall and provides a site for muscle attachment.[AAO] 2012-06-20 AAO:0000545 AAO AAO:Pugener_2002 UMLS:C0035561 ncithesaurus:Rib ribs TAO:0000538 A proximal phalanx that is part of a finger [Automatically generated definition]. EMAPA:37307 FMA:75816 MA:0001395 NCIT:C52786 UMLS:C0730117 hand proximal phalanx phalanx proximalis manus proximal manual phalanx proximal phalanx of finger proximal phalanx of fore digit proximal phalanx of hand proximal phalanx of manual digit uberon UBERON:0002234 proximal phalanx of manus A proximal phalanx that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37307 MA:th UMLS:C0730117 ncithesaurus:Proximal_Phalanx_of_Hand hand proximal phalanx MA:0001395 phalanx proximalis manus FMA:75816 FMA:TA proximal phalanx of finger FMA:75816 Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) TODO - add superclass to unify with VNC? Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010151 BAMS:SP BAMS:Spinal BIRNLEX:1709 BM:SpC BTO:0001279 CALOHA:TS-0953 DHBA:12890 DMBA:17651 EFO:0000110 EHDAA2:0001255 EHDAA:2863 EMAPA:17577 EV:0100316 FMA:7647 GAID:695 MA:0000216 MAT:0000183 MESH:D013116 MIAA:0000183 NCIT:C12464 OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA TAO:0000075 UMLS:C0037925 VHOG:0000601 XAO:0000020 ZFA:0000075 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 uberon SpC cerebro-cerebellar fissure cerebrocerebellar fissure fissura cerebro-cerebellaris fissura cerebrocerebellaris medulla spinalis spinal cord structure spinal medulla UBERON:0002240 spinal cord http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg definitional definitional Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) BIRNLEX:1709 Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] 2012-06-20 AAO:0010151 AAO AAO:BJB (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000601 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 UMLS:C0037925 BIRNLEX:1709 UMLS:C0037925 ncithesaurus:Spinal_Cord http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 BIRNLEX:1709 SpC cerebro-cerebellar fissure NeuroNames:22 cerebrocerebellar fissure NeuroNames:22 fissura cerebro-cerebellaris NeuroNames:22 fissura cerebrocerebellaris NeuroNames:22 medulla spinalis medulla spinalis BTO:0001279 spinal cord structure ZFA:0000075 spinal medulla BTO:0001279 Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal) Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] chondrocranial covers the brain dorsally in chondrichthyans AAO:0010169 EHDAA2:0000243 EMAPA:17681 TAO:0001424 VHOG:0000288 ZFA:0001424 uberon calvarium neurocranium UBERON:0002241 chondrocranium Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] 2012-06-20 AAO:0010169 AAO AAO:BJB Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] 2012-08-14 TAO:0001424 TAO ZFIN:curator calvarium MA:0000317 neurocranium MA:0000317 the jelly-like substance in the middle of the spinal disc which is a remnant of the notochord The nucleus pulposus consists of chondrocytes, collagen fibrils, and proteoglycan aggrecans that have hyaluronic long chains which attract water. Attached to each hyaluronic chain are side chains of chondroitin sulfate and keratan sulfate[Wikipedia:Nucleus_pulposus] we group two FMA classes together BTO:0003626 EMAPA:18008 FMA:13550 FMA:76703 MA:0000112 nucleus pulposus (diskus intervertebralis) pulpy nucleus uberon nucleus propulsus nucleus propulsus of intervertebral disk nucleus pulposus of intervertebral disk UBERON:0002242 Function noyes: It functions to distribute hydraulic pressure in all directions within each disc under compressive loads. nucleus pulposus http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png mah ISBN:0073040584 Wikipedia the jelly-like substance in the middle of the spinal disc which is a remnant of the notochord MGI:llw2 MP:0006392 we group two FMA classes together FMA nucleus pulposus (diskus intervertebralis) FMA:13550 nucleus propulsus nucleus propulsus of intervertebral disk nucleus pulposus of intervertebral disk FMA:13550 An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint AAO:0010180 BTO:0001772 FBbt:00005158 FMA:77659 VHOG:0000287 XAO:0000273 olfactory organ olfactory sense organ olfactory sensory organ main olfactory organ primary olfactory organ uberon olfactory neuroepithelium organ olfactus organum olfactorium UBERON:0002268 olfactory organ An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. UBERON:cjm olfactory organ BTO:0001772 olfactory sensory organ FBbt:00005158 olfactory neuroepithelium BTO:0001772 organ olfactus BTO:0001772 organum olfactorium BTO:0001772 A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation. It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain. FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure BAMS:RET EMAPA:35188 FMA:77719 MA:0003185 MESH:D012154 NLX:143558 brain stem reticular formation brainstem reticular formation reticular formation (classical) reticular formation of the brainstem uberon UBERON:0002275 reticular formation http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). NeuroNames:1223 FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure FMA brain stem reticular formation NeuroNames:1223 brainstem reticular formation MA:0003185 brainstem reticular formation NeuroNames:1223 reticular formation (classical) NeuroNames:1223 reticular formation of the brainstem NeuroNames:1223 A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP]. The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO]. The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] BAMS:LV BAMS:Tel-V BIRNLEX:1263 BM:Tel-LV BTO:0000879 CALOHA:TS-1230 DHBA:10596 DMBA:126651562 EFO:0001961 EHDAA2:0001984 EHDAA:3502 EHDAA:6576 EMAPA:16914 EV:0100307 FMA:78448 GAID:611 HBA:9419 MA:0000192 MBA:81 MESH:D020547 NCIT:C12834 OpenCyc:Mx4rvYsFdZwpEbGdrcN5Y29ycA TAO:0000696 UMLS:C0152279 VHOG:0000643 ZFA:0000696 lateral ventricle lateral ventricles telencephalic ventricle telencephalon lateral ventricle uberon forebrain ventricle lateral ventricle of brain tectal ventricle telencephalic ventricles telencephalic vesicle UBERON:0002285 modeled as space in EHDAA2 telencephalic ventricle http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png material to immaterial EHDAA2 A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP]. The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO]. GO:0021670 The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000643 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 UMLS:C0152279 BIRNLEX:1263 UMLS:C0152279 ncithesaurus:Lateral_Ventricle lateral ventricle MA:0000192 lateral ventricles telencephalic ventricle VHOG:0000643 ZFA:0000696 telencephalon lateral ventricle EHDAA2:0001984 lateral ventricle of brain BTO:0000879 telencephalic ventricles BAMS:Tel-V telencephalic vesicle ZFA:0000696 Choroid plexus of the fourth ventricle BAMS:chp4 BAMS:cp4v DHBA:12808 EMAPA:32742 FMA:78492 HBA:9710 MA:0000983 NCIT:C32308 NLX:27388 TAO:0001446 UMLS:C0152293 VHOG:0001375 ZFA:0001446 chorioid plexus of cerebral hemisphere of fourth ventricle chorioid plexus of fourth ventricle choroid plexus fourth ventricle fourth ventricle chorioid plexus of cerebral hemisphere fourth ventricle choroid plexus uberon 4th ventricle choroid plexus UBERON:0002290 choroid plexus of fourth ventricle Choroid plexus of the fourth ventricle NLX:27388 UMLS:C0152293 ncithesaurus:Choroid_Plexus_of_the_Fourth_Ventricle chorioid plexus of cerebral hemisphere of fourth ventricle OBOL:automatic choroid plexus fourth ventricle ZFA:0001446 fourth ventricle chorioid plexus of cerebral hemisphere OBOL:automatic Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). FMA:79646 GAID:279 MA:0001273 MESH:D001659 NCIT:C12678 biliary apparatus uberon biliary tract UBERON:0002294 biliary system http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). biliary apparatus FMA:79646 biliary tract FMA:79646 MA:0001273 The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA]. The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO] EHDAA2:0004560 EHDAA:3019 EHDAA:3033 EHDAA:3921 EHDAA:3934 EHDAA:3957 EHDAA:3971 FMA:79795 TAO:0005130 ZFA:0005130 uberon dorsal mesogastrium mesenterium dorsale commune UBERON:0002296 dorsal mesentery http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png EHDAA2 The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA]. ZFIN:curator The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO] 2012-08-14 TAO:0005130 TAO ZFIN:curator dorsal mesogastrium mesenterium dorsale commune Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] BAMS:BS BIRNLEX:1565 BTO:0000146 CALOHA:TS-0093 EFO:0001962 EMAPA:32678 EV:0100241 FMA:79876 MA:0000169 MBA:343 MESH:D001933 NCIT:C12441 TAO:0002156 UMLS:C0006121 VHOG:0001457 ZFA:0001707 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 brain stem truncus encephali uberon accessory medullary lamina of pallidum lamella pallidi incompleta lamina medullaris accessoria lamina medullaris incompleta pallidi lamina pallidi incompleta truncus encephalicus UBERON:0002298 'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions). brainstem http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. ISBN:0471888893 MP:0005277 ZFA:0001707 Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] 2012-08-14 TAO:0002156 TAO ISBN:3764351209 Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. ZFA:0001707 the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] MP:0005277 UMLS:C0006121 BIRNLEX:1565 UMLS:C0006121 ncithesaurus:Brain_Stem http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 BIRNLEX:1565 brain stem ABA:BS truncus encephali accessory medullary lamina of pallidum NeuroNames:236 lamella pallidi incompleta NeuroNames:236 lamina medullaris accessoria NeuroNames:236 lamina medullaris incompleta pallidi NeuroNames:236 lamina pallidi incompleta NeuroNames:236 truncus encephalicus BTO:0000146 One of the layers of the neocortex. cortical layer ABA:CTX1-6b EMAPA:35588 FMA:83138 MA:0000186 layer of neocortex neocortex layer uberon cerebral cortex layer lamina of neocortex UBERON:0002301 layer of neocortex One of the layers of the neocortex. layer of neocortex FMA:83138 neocortex layer MA:0000186 cerebral cortex layer MA:0000186 lamina of neocortex FMA:83138 the atrial part of middle layer of the heart, comprised of involuntary muscle As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] EFO:0003087 EMAPA:32746 FMA:83509 MA:0000081 TAO:0001374 VHOG:0000602 ZFA:0001374 atrial myocardium atrium myocardium uberon atrium cardiac muscle UBERON:0002302 myocardium of atrium the atrial part of middle layer of the heart, comprised of involuntary muscle ISBN:0-683-40008-8 MP:0010493 As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] 2012-09-17 VHOG:0000602 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 atrial myocardium ZFA:0001374 atrium cardiac muscle VHOG:0000602 Part of choroid plexus contained in the lateral ventricle BAMS:cplv DHBA:10601 EHDAA2:0004449 EMAPA:17769 FMA:83711 HBA:9708 MA:0000961 NCIT:C32309 NLX:32548 TAO:0001447 UMLS:C0152289 VHOG:0001376 ZFA:0001447 chorioid plexus of cerebral hemisphere of lateral ventricle chorioid plexus of lateral ventricle choroid plexus telencephalic ventricle lateral ventricle chorioid plexus of cerebral hemisphere lateral ventricle choroid plexus uberon UBERON:0002307 choroid plexus of lateral ventricle Part of choroid plexus contained in the lateral ventricle NLX:32548 UMLS:C0152289 ncithesaurus:Choroid_Plexus_of_the_Lateral_Ventricle chorioid plexus of cerebral hemisphere of lateral ventricle OBOL:automatic choroid plexus telencephalic ventricle ZFA:0001447 lateral ventricle chorioid plexus of cerebral hemisphere OBOL:automatic A neural nucleus that is part of the brain. EMAPA:35185 FMA:83840 MA:0000811 NCIT:C49346 UMLS:C1706993 ZFA:0005575 brain nucleus uberon brain nuclei UBERON:0002308 nucleus of brain A neural nucleus that is part of the brain. UMLS:C1706993 ncithesaurus:Brain_Nucleus brain nuclei ZFA:0005575 The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. BAMS:Scgrey DHBA:146035048 EMAPA:35792 FMA:256580 MA:0000002 NCIT:C32696 NLXANAT:100204 UMLS:C0475853 gray matter of spinal cord gray substance of spinal cord grey matter of spinal cord grey substance of spinal cord spinal cord gray matter spinal cord grey matter spinal cord grey substance substantia grisea medullae spinalis uberon UBERON:0002315 gray matter of spinal cord The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. MP:0008503 UMLS:C0475853 ncithesaurus:Gray_Matter_of_the_Spinal_Cord gray matter of spinal cord OBOL:automatic gray substance of spinal cord FMA:256580 spinal cord gray matter OBOL:automatic spinal cord grey substance OBOL:automatic substantia grisea medullae spinalis FMA:256580 FMA:TA The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. check the FMA placement here; ncit placement of body cavity here probably not correct Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 TAO:0001438 UMLS:C0333343 ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen main body cavity space of body compartment ventral body cavity uberon celom coelom coelome hemocoel UBERON:0002323 coelemic cavity lumen definitional The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. 2012-09-12 ZFA:0001438 ZFA ZFIN:curator The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. 2012-09-12 BTO:0001707 BTO BTO body cavity BTO:0001707 UMLS:C0333343 ncithesaurus:Cavity coelomic cavity EHDAA2:0000267 coelomic cavity lumen EHDAA2:0000267 space of body compartment FMA:85006 ventral body cavity NCBITaxon:7742 celom BTO:0001707 coelome BTO:0001707 hemocoel FBbt:00005060 Any muscle organ that is part of a back [Automatically generated definition]. EMAPA:35161 FMA:85216 MA:0000496 back muscle back muscle organ muscle organ of back uberon UBERON:0002324 muscle of back prolog Any muscle organ that is part of a back [Automatically generated definition]. OBOL:automatic back muscle organ OBOL:automatic muscle organ of back OBOL:automatic The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. EMAPA:31518 FMA:85275 MA:0001686 NCIT:C49309 UMLS:C1710584 epithelial tissue of urethra urethra epithelial tissue urethra epithelium uberon urethral epithelium urethral plate urethral seam UBERON:0002325 epithelium of urethra GO The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.. GO:0061071 UMLS:C1710584 ncithesaurus:Urethra_Epithelium epithelial tissue of urethra OBOL:automatic urethra epithelial tissue OBOL:automatic urethral plate EMAPA:31518 urethral seam EMAPA:31518 A lamina propria that is part of a urethra [Automatically generated definition]. EMAPA:37785 FMA:85276 MA:0001689 lamina propria mucosa of urethra lamina propria mucosae of urethra urethra lamina propria urethra lamina propria mucosa urethra lamina propria mucosae uberon urethral lamina propria UBERON:0002326 lamina propria of urethra A lamina propria that is part of a urethra [Automatically generated definition]. OBOL:automatic EMAPA:37785 MA:th lamina propria mucosa of urethra OBOL:automatic lamina propria mucosae of urethra OBOL:automatic urethra lamina propria mucosa OBOL:automatic urethra lamina propria mucosae OBOL:automatic EMAPA:18227 EMAPA:37720 FMA:85315 MA:0001176 intercostal nerve trunk intercostal neural trunk uberon UBERON:0002327 trunk of intercostal nerve EMAPA:37720 MA:th A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] notochordal In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 EHDAA2:0001277 EHDAA:1241 EHDAA:6021 EMAPA:16191 EV:0100002 FMA:85521 GAID:1311 MAT:0000281 MESH:A16.254.610 NCIT:C12463 TAO:0000135 UMLS:C0028439 VHOG:0000199 VSAO:0000032 XAO:0000055 ZFA:0000135 embryonic notocord notocord uberon notochorda UBERON:0002328 The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB] notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png VSAO ZFA EHDAA2 A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. ISBN:0815318960 Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] 2012-08-14 VSAO:0000032 VSAO PSPUB:0000170 Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000135 TAO ZFIN:curator Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] 2012-06-20 AAO:0000327 AAO AAO:LAP relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] 2012-06-20 AAO:0000327 AAO (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000199 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 UMLS:C0028439 ncithesaurus:Notochord notocord ZFA:0000135 notochorda Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] somitic mesodermal cluster AAO:0010569 AEO:0001015 BTO:0001558 EHDAA2:0003436 EHDAA:366 EHDAA:699 EMAPA:31169 FMA:85522 GAID:1306 MAT:0000068 MESH:A16.254.425.660.750 MIAA:0000068 NCIT:C34302 TAO:0000155 UMLS:C0376449 VHOG:0000191 XAO:0000058 ZFA:0000155 uberon epimere epimere mesoderm epithelial somite somites somitic mesoderm somitus UBERON:0002329 When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248] somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 ZFA Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] 2012-06-20 AAO:0010569 AAO AAO:EJS Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000155 TAO ZFIN:curator relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] 2012-06-20 AAO:0010569 AAO (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000191 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) mesodermal cluster GO:0001756 UMLS:C0376449 ncithesaurus:Somite epimere ISBN:0073040584 epithelial somite somites somitus Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. CALOHA:TS-2057 EHDAA2:0002225 EMAPA:35329 FMA:85539 MA:0002411 NCIT:C12957 UMLS:C1516995 WikipediaCategory:Exocrine_system exocrine glandular system uberon UBERON:0002330 exocrine system Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. UMLS:C1516995 ncithesaurus:Exocrine_System exocrine glandular system EHDAA2:0002225 The connecting cord from the developing embryo to the placenta. The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP]. umbilical BTO:0001415 CALOHA:TS-1078 EFO:0001415 EHDAA2:0000312 EHDAA:158 EMAPA:26115 EV:0100127 FMA:85541 GAID:517 MAT:0000280 MESH:A16.254.789 MIAA:0000280 NCIT:C34320 OpenCyc:Mx4rvyewDJwpEbGdrcN5Y29ycA UMLS:C0041633 chorda umbilicalis funiculus umbilicalis uberon birth cord connecting stalk funiculus umbilicalis yolk stalk UBERON:0002331 See notes for connecting stalk umbilical cord http://upload.wikimedia.org/wikipedia/commons/f/f3/Umbilicalcord.jpg The connecting cord from the developing embryo to the placenta. ISBN:0-683-40008-8 MP:0001725 The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP]. UMLS:C0041633 ncithesaurus:Umbilical_Cord chorda umbilicalis MP:0012134 funiculus umbilicalis MP:0012134 birth cord funiculus umbilicalis yolk stalk BTO:0001415 An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] EHDAA2:0001576 EHDAA:9831 EMAPA:17015 FMA:8612 MA:0002033 NCIT:C116918 OpenCyc:Mx4rv-6d0ZwpEbGdrcN5Y29ycA VHOG:0001134 galen:PulmonaryTrunk pulmonary artery (trunk) trunk of pulmonary arterial tree uberon main pulmonary artery UBERON:0002333 pulmonary trunk Alveoli:diagram.png MA An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] 2012-09-17 VHOG:0001134 VHOG As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] 2012-09-17 VHOG:0001134 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 main pulmonary artery the duct of the submadibular gland that opens at the sublingual papilla near the frenulum of the tongue FMA also has 'main submandibular duct' (FMA:59899) BTO:0004556 EMAPA:35833 FMA:86266 MA:0002698 NCIT:C33649 UMLS:C0227472 uberon Wharton's duct ductus submandibularis ductus submaxillaris submandibular salivary duct submaxillar gland duct submaxillary duct UBERON:0002334 submandibular duct http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray1024.png the duct of the submadibular gland that opens at the sublingual papilla near the frenulum of the tongue ISBN:0-683-40008-8 MP:0009525 FMA also has 'main submandibular duct' (FMA:59899) FMA UMLS:C0227472 ncithesaurus:Submandibular_Duct Wharton's duct FMA:59899 ductus submandibularis BTO:0004556 ductus submaxillaris submaxillar gland duct BTO:0004556 The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle. CALOHA:TS-1266 EMAPA:35310 FMA:86487 MA:0002734 NCIT:C32516 UMLS:C0227849 endometrium stroma stroma of endometrium uberon UBERON:0002337 endometrial stroma The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle. ncithesaurus:Endometrial_Stroma UMLS:C0227849 ncithesaurus:Endometrial_Stroma A lamina propria that is part of a bronchus [Automatically generated definition]. EMAPA:35194 FMA:86619 MA:0001836 NCIT:C49212 UMLS:C1707054 bronchi lamina propria bronchi lamina propria mucosa bronchi lamina propria mucosae bronchial trunk lamina propria bronchial trunk lamina propria mucosa bronchial trunk lamina propria mucosae bronchus lamina propria bronchus lamina propria mucosa bronchus lamina propria mucosae lamina propria mucosa of bronchi lamina propria mucosa of bronchial trunk lamina propria mucosa of bronchus lamina propria mucosae of bronchi lamina propria mucosae of bronchial trunk lamina propria mucosae of bronchus lamina propria of bronchi lamina propria of bronchial trunk uberon bronchial lamina propria UBERON:0002338 lamina propria of bronchus true A lamina propria that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707054 ncithesaurus:Bronchus_Lamina_Propria bronchi lamina propria OBOL:automatic bronchi lamina propria mucosa OBOL:automatic bronchi lamina propria mucosae OBOL:automatic bronchial trunk lamina propria OBOL:automatic bronchial trunk lamina propria mucosa OBOL:automatic bronchial trunk lamina propria mucosae OBOL:automatic bronchus lamina propria mucosa OBOL:automatic bronchus lamina propria mucosae OBOL:automatic lamina propria mucosa of bronchi OBOL:automatic lamina propria mucosa of bronchial trunk OBOL:automatic lamina propria mucosa of bronchus OBOL:automatic lamina propria mucosae of bronchi OBOL:automatic lamina propria mucosae of bronchial trunk OBOL:automatic lamina propria mucosae of bronchus OBOL:automatic lamina propria of bronchi OBOL:automatic lamina propria of bronchial trunk OBOL:automatic bronchial lamina propria EMAPA:35194 A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 EHDAA2:0004419 EMAPA:32737 FMA:86666 GAID:1310 MAT:0000066 MESH:A16.254.600 MIAA:0000066 NCIT:C34222 TAO:0000045 UMLS:C0027789 VHOG:0000057 XAO:0000048 ZFA:0000045 NC uberon crista neuralis neural crest material UBERON:0002342 Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells. neural crest Neural:Crest.png http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png XAO BTO A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 ISBN:0073040584 A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000045 TAO ZFIN:curator Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] 2012-06-20 AAO:0010578 AAO AAO:EJS A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] 2012-09-17 VHOG:0000057 VHOG DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) UMLS:C0027789 ncithesaurus:Neural_Crest NC XAO:0000048 crista neuralis neural crest material VHOG:0000057 Set of all muscles in abdomen. distinction between abdomen muscle and abdomen musculature FMA:71294 FMA:86917 TAO:0001327 ZFA:0001327 abdominal musculature muscle group of abdomen muscles of abdomen musculature of abdomen musculature of abdominal wall set of muscles of abdomen uberon UBERON:0002343 abdomen musculature Set of all muscles in abdomen. OBOL:automatic muscle group of abdomen FMA:71294 muscles of abdomen FMA:71294 musculature of abdominal wall FMA:86917 set of muscles of abdomen FMA:71294 Embryonic ectoderm that gives rise to nervous tissue. (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] neurectodermal we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 EHDAA2:0001248 EHDAA:1498 EHDAA:255 EMAPA:16073 EV:0100004 FBbt:00001061 FMA:87657 MAT:0000176 MIAA:0000176 NCIT:C34228 TAO:0001120 UMLS:C1518271 VHOG:0000150 XAO:0000042 ZFA:0001120 neural ectoderm neuroectoderm uberon epithelium tubi neuralis; neuroectoderma neuaral ectoderm presumptive central nervous system ventral neurogenic region UBERON:0002346 neurectoderm Embryonic ectoderm that gives rise to nervous tissue. (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] 2012-09-17 VHOG:0000150 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) UMLS:C1518271 ncithesaurus:Neuroectoderm epithelium tubi neuralis; neuroectoderma ventral neurogenic region VHOG:0000150 A thoracic vertebra endochondral element that is composed primarily of a bone tissue. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs EMAPA:18011 FMA:9139 GAID:244 MA:0000314 MESH:D013904 NCIT:C12798 OpenCyc:Mx4rvdZIBpwpEbGdrcN5Y29ycA UMLS:C0039987 dorsal vertebra thorax vertebra vertebra of thorax vertebra thoracica uberon UBERON:0002347 thoracic vertebra http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png A thoracic vertebra endochondral element that is composed primarily of a bone tissue. OBOL:automatic UMLS:C0039987 ncithesaurus:Thoracic_Vertebra thorax vertebra OBOL:automatic vertebra of thorax OBOL:automatic a region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer. External layer of the heart.[TAO] The inner layer of the pericardium that is in contact with the surface of the heart.[AAO] The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium] AAO:0010409 EHDAA2:0002202 FMA:9461 NCIT:C13164 TAO:0005057 UMLS:C0225968 VHOG:0000119 XAO:0000316 ZFA:0005057 galen:Epicardium heart epicardium visceral serous pericardium of heart visceral serous pericardium proper uberon pericardium visceral mesothelium UBERON:0002348 epicardium multiple FMA-inferred FMA a region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. External layer of the heart.[TAO] 2012-08-14 TAO:0005057 TAO ZFIN:curator The inner layer of the pericardium that is in contact with the surface of the heart.[AAO] 2012-06-20 AAO:0010409 AAO AAO:BJB UMLS:C0225968 ncithesaurus:Epicardium visceral serous pericardium of heart FMA:9461 visceral serous pericardium proper FMA:9461 pericardium visceral mesothelium EMAPA:16589 the middle layer of the heart, comprised mainly of striated cardiac muscle fibers TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The middle layer of the heart, consisting of cardiac muscle.[AAO] myocardial AAO:0010410 BSA:0000089 BTO:0000901 CALOHA:TS-0440 EFO:0000819 EHDAA2:0004150 EMAPA:32688 EV:0100022 FMA:9462 GAID:173 MA:0000164 MAT:0000453 MESH:D009206 NCIT:C12371 OpenCyc:Mx4ro36AFrCvEduAAAAOpmP6tw RETIRED_EHDAA2:0001220 TAO:0001319 UMLS:C0027061 VHOG:0000083 XAO:0000065 ZFA:0001319 galen:Myocardium heart myocardium muscle of heart uberon cardiac muscle heart muscle UBERON:0002349 myocardium http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg the middle layer of the heart, comprised mainly of striated cardiac muscle fibers ISBN:0-683-40008-8 MP:0005329 Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000083 VHOG The middle layer of the heart, consisting of cardiac muscle.[AAO] 2012-06-20 AAO:0010410 AAO AAO:BJB UMLS:C0027061 ncithesaurus:Myocardium muscle of heart FMA:9462 cardiac muscle ZFA:0001319 heart muscle FMA:9462 heart muscle ZFA:0001319 The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO] EHDAA2 divides the system from the tissue The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] EFO:0003909 EHDAA2:0004185 EMAPA:35428 EV:0100025 FMA:9476 MA:0000094 MESH:D006329 TAO:0005063 VHOG:0001271 ZFA:0005063 cardiac conducting system cardiac conduction system cardiac impulse conducting system cardionector complexus stimulans cordis heart conduction system impulse conducting system systema conducente cordis uberon central conduction system UBERON:0002350 conducting system of heart FMA The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO] GO:0003161 The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] 2012-09-17 VHOG:0001271 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) cardiac conducting system VHOG:0001271 cardiac impulse conducting system GO:0003161 complexus stimulans cordis FMA:9476 FMA:TA heart conduction system GO:0003161 impulse conducting system MA:0000094 systema conducente cordis FMA:9476 FMA:TA The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. pelvic MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs BTO:0001006 CALOHA:TS-2227 EFO:0002805 EMAPA:35931 EV:0100012 FMA:9578 GAID:87 MA:0000030 MESH:A01.673 NCIT:C12767 OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA UMLS:C0030797 galen:Pelvis lesser pelvis pelvic region pelvis pelvis region true pelvis uberon UBERON:0002355 pelvic region of trunk The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs MA UMLS:C0030797 ncithesaurus:Pelvis lesser pelvis FMA:9578 pelvis FMA:9578 MA:0000030 true pelvis FMA:9578 Serous membrane which is divided into parietal and visceral serous pericardium. EMAPA:19030 FMA:9582 MA:0002739 serous portion of pericardium uberon pericardium serosum UBERON:0002357 serous pericardium FMA FMA Serous membrane which is divided into parietal and visceral serous pericardium. serous portion of pericardium FMA:9582 pericardium serosum peritoneum A serous membrane that lines the peritoneal cavity[VHOG,modified]. TODO - in ZFA is_a epithelium An epithelium that lines the peritoneal cavity.[TAO] Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] peritoneal todo: check MA/EMAPA. AAO:0010814 BTO:0001472 CALOHA:TS-2072 EV:0100087 FMA:9584 GAID:18 MA:0000449 MESH:A01.047.025.600 NCIT:C12770 OpenCyc:Mx4rvjJ72ZwpEbGdrcN5Y29ycA TAO:0005120 UMLS:C0031153 VHOG:0001257 XAO:0000139 ZFA:0005120 galen:Peritoneum uberon peritonaeum UBERON:0002358 peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png MP A serous membrane that lines the peritoneal cavity[VHOG,modified]. VHOG:0001257 An epithelium that lines the peritoneal cavity.[TAO] 2012-08-14 TAO:0005120 TAO ZFIN:curator Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] 2012-06-20 AAO:0010814 AAO AAO:JMG todo: check MA/EMAPA. MA UMLS:C0031153 ncithesaurus:Peritoneum peritonaeum VHOG:0001257 Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA] most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium] EMAPA:19029 FMA:9586 MA:0002738 fibrous portion of pericardium uberon pericardium fibrosum UBERON:0002359 fibrous pericardium FMA FMA WP Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA] FMA:9586 pericardium fibrosum Membrane organ that surrounds the brain and the spinal cord. Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] meningeal Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx). Not consider part of the CNS/neuraxis in FMA BTO:0000144 CALOHA:TS-1177 EFO:0000867 EMAPA:32660 EV:0100312 FMA:9589 GAID:687 MA:0001113 MAT:0000113 MESH:D008578 NCIT:C12348 NLXANAT:090204 OpenCyc:Mx4rwDOl8JwpEbGdrcN5Y29ycA TAO:0001355 UMLS:C0025285 VHOG:0001295 ZFA:0001355 layer of meninges meningeal layer meninx primitiva uberon UBERON:0002360 meninx Illu:meninges.jpg FMA Bgee:AN Membrane organ that surrounds the brain and the spinal cord. FMA:9589 Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG] 2012-09-17 VHOG:0001295 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0001295 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 Not consider part of the CNS/neuraxis in FMA FMA https://github.com/obophenotype/uberon/issues/1261 UMLS:C0025285 ncithesaurus:Meninges meninx primitiva VHOG:0001295 The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals. consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater]. BTO:0001635 EHDAA2:0004318 EHDAA:1367 EHDAA:1961 EHDAA:2001 EHDAA:2099 EHDAA:2685 EHDAA:2833 EHDAA:2867 EHDAA:3692 EHDAA:3710 EHDAA:6566 EHDAA:6583 EMAPA:32663 EV:0100315 FMA:9590 GAID:693 MA:0001116 MESH:D010841 NCIT:C33321 NLXANAT:090209 OpenCyc:Mx4rvtesBZwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001464 UMLS:C0031869 pia mater of neuraxis pial membrane uberon pia UBERON:0002361 pia mater http://upload.wikimedia.org/wikipedia/commons/3/31/Gray770-en.svg http://upload.wikimedia.org/wikipedia/commons/6/65/Gray770.png The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals. NLXANAT:090209 delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater]. UMLS:C0031869 ncithesaurus:Pia_Mater pial membrane NLXANAT:090209 pia NLXANAT:090209 A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space. BTO:0001636 CALOHA:TS-0052 EMAPA:32659 EV:0100314 FMA:9591 GAID:688 MA:0001114 MESH:D001099 NCIT:C32136 NLXANAT:090208 OpenCyc:Mx4rve5HlJwpEbGdrcN5Y29ycA UMLS:C1510935 arachnoid arachnoid mater of neuraxis arachnoid membrane uberon arachnoidea mater UBERON:0002362 arachnoid mater http://upload.wikimedia.org/wikipedia/commons/a/a0/Gray767.png A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space. ISBN:0471888893 UMLS:C1510935 ncithesaurus:Arachnoid_Membrane arachnoid membrane NLXANAT:090208 arachnoidea mater BTO:0001636 Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections. the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater]. capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288 some ontologies consider dura mater part of the CNS, others dispute this and claim it surrounds it (e.g. DOI:10.1111/joa.12381)[https://github.com/obophenotype/uberon/issues/1261] BTO:0001637 CALOHA:TS-2008 EMAPA:32664 EV:0100313 FMA:9592 GAID:691 MA:0001115 MESH:D004388 NCIT:C32488 NLXANAT:090206 OpenCyc:Mx4rvvmzqZwpEbGdrcN5Y29ycA UMLS:C0013313 dura mater of neuraxis pachymeninges uberon dura UBERON:0002363 dura mater http://upload.wikimedia.org/wikipedia/commons/8/8e/Meninges-en.svg definitional Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections. NLXANAT:090206 the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater]. UMLS:C0013313 ncithesaurus:Dura_Mater pachymeninges NLXANAT:090206 dura BTO:0001637 A thin membrane that separates the external ear from the middle ear, consisting of two epithelia (one part of the the external accoustic meatus epithelium, the other part of the tympanic cavity epithelium) with a fibrous layer between them. Its function is to transmit sound from the air to the ossicles inside the middle ear. The malleus bone bridges the gap between the eardrum and the other ossicles. Rupture or perforation of the eardrum can lead to conductive hearing loss. [WP,unvetted]. The thin membrane which closes externally the cavity of the middle ear and is deeply sited at the bottom of the external auditory meatus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals.[well established][VHOG] The tympanic membrane (TM) has three layers, two epithelia provided by the external acoustic meatus (EAM) and the MEC, derived respectively from the first pharyngeal cleft and pouch, and a mesenchymally derived fibrous stratum most AOs consider this part of the middle ear, so we go with this and place it in the middle ear as a border to the external, although it could be considered to overlap the external ear in that it has an EAM layer as part - for this reason we do not consider middle and external ear to be spatially disjoint. EMAPA:19062 EV:0100358 FMA:9595 GAID:870 MA:0000257 MESH:A09.246.397.873 NCIT:C12502 UMLS:C0041445 VHOG:0001146 XAO:0000212 Rivinus' membrane ear drum eardrum lateral wall of tympanic cavity membranous wall of tympanic cavity myrinx paries membranaceus cavi tympani uberon tympanum UBERON:0002364 tympanic membrane FMA MA Wikipedia cjm A thin membrane that separates the external ear from the middle ear, consisting of two epithelia (one part of the the external accoustic meatus epithelium, the other part of the tympanic cavity epithelium) with a fibrous layer between them. Its function is to transmit sound from the air to the ossicles inside the middle ear. The malleus bone bridges the gap between the eardrum and the other ossicles. Rupture or perforation of the eardrum can lead to conductive hearing loss. [WP,unvetted]. The thin membrane which closes externally the cavity of the middle ear and is deeply sited at the bottom of the external auditory meatus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0001146 VHOG In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals.[well established][VHOG] 2012-09-17 VHOG:0001146 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418 most AOs consider this part of the middle ear, so we go with this and place it in the middle ear as a border to the external, although it could be considered to overlap the external ear in that it has an EAM layer as part - for this reason we do not consider middle and external ear to be spatially disjoint. UMLS:C0041445 ncithesaurus:Tympanic_Membrane paries membranaceus cavi tympani FMA:9595 FMA:TA tympanum A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses AEO:0000097 BTO:0000765 CALOHA:TS-2012 EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 NCIT:C12712 UMLS:C0015282 ducted gland glandula exocrina uberon UBERON:0002365 exocrine gland A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas UMLS:C0015282 ncithesaurus:Exocrine_Gland ducted gland AEO:0000097 glandula exocrina prostate gland The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. TODO - FMA treats the gland as part of the prostate - see also FMA:74119. prostatic BTO:0001129 CALOHA:TS-0828 EFO:0000858 EMAPA:19287 EV:0100104 FMA:9600 GAID:392 MA:0000404 MAT:0000078 MESH:D011467 MIAA:0000078 NCIT:C12410 OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA UMLS:C0033572 VHOG:0001261 galen:ProstateGland male prostate prostate uberon prostata UBERON:0002367 prostate gland http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. GO:0030850 UMLS:C0033572 ncithesaurus:Prostate_Gland male prostate prostata Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. AEO:0000098 BTO:0001488 CALOHA:TS-1300 EHDAA2:0003098 EMAPA:35999 FMA:9602 GAID:335 MA:0002563 MESH:D004702 NCIT:C12704 OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA UMLS:C0014133 ductless gland glandula endocrina uberon ductless gland glandulae endocrinae UBERON:0002368 endocrine gland http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. UMLS:C0014133 ncithesaurus:Endocrine_Gland ductless gland AEO:0000098 ductless gland glandulae endocrinae adrenal gland Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. AAO:0010551 BTO:0000047 CALOHA:TS-0016 EFO:0000238 EMAPA:18426 EV:0100135 FMA:9604 GAID:446 MA:0000116 MAT:0000071 MESH:D000311 MIAA:0000071 NCIT:C12666 OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA UMLS:C0001625 VHOG:0001141 XAO:0000164 galen:AdrenalGland glandula adrenalis glandula suprarenalis uberon adrenal adrenal capsule adrenal medulla cell atrabiliary capsule epinephric gland epinephros glandula suprarenalis interrenal gland suprarenal capsule suprarenal gland UBERON:0002369 adrenal gland http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg FMA-abduced-lr Wikipedia Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. BTO:0000047 Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] 2012-06-20 AAO:0010551 AAO AAO:BJB All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001141 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 UMLS:C0001625 ncithesaurus:Adrenal_Gland glandula adrenalis glandula suprarenalis adrenal BTO:0000047 adrenal capsule BTO:0000047 atrabiliary capsule BTO:0000047 epinephric gland epinephros BTO:0000047 glandula suprarenalis BTO:0000047 interrenal gland GO:0030325 suprarenal capsule BTO:0000047 suprarenal gland Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland. thymus http://langual.org Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO] A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG] thymic AAO:0010548 BTO:0001374 CALOHA:TS-1043 EFO:0000860 EHDAA2:0002017 EHDAA:9119 EMAPA:18768 EV:0100138 FMA:9607 GAID:464 MA:0000142 MAT:0000080 MESH:A06.407.850 MIAA:0000080 NCIT:C12433 OpenCyc:Mx4rvpIympwpEbGdrcN5Y29ycA TAO:0001078 UMLS:C0040113 VHOG:0000253 XAO:0000163 ZFA:0001078 http://www.langual.org/langual_thesaurus.asp?termid=C0273 thymus gland thymus organ uberon UBERON:0002370 thymus Illu:thymus.jpg EHDAA2 ZFA Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop. NLM:thymus Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO] 2012-06-20 AAO:0010548 AAO AAO:BJB A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG] 2012-09-17 VHOG:0000253 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.558 UMLS:C0040113 ncithesaurus:Thymus_Gland bone marrow the soft tissue that fills the cavities of bones TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs consider placement of NCIT:C53466 medullary bone bone marrow http://langual.org The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] AAO:0011007 BTO:0000141 BTO:0000829 CALOHA:TS-0087 EFO:0000868 EMAPA:32760 EV:0100046 FMA:9608 GAID:1287 MA:0000134 MAT:0000084 MESH:D001853 MIAA:0000084 NCIT:C12431 OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA UMLS:C0005953 VHOG:0001218 XAO:0000123 galen:BoneMarrow http://www.langual.org/langual_thesaurus.asp?termid=C0149 medulla ossea medulla ossium uberon medulla of bone medullary bone UBERON:0002371 bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg FMA MA the soft tissue that fills the cavities of bones MGI:cwg MP:0002397 The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] 2012-09-17 VHOG:0001218 VHOG DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006) UMLS:C0005953 ncithesaurus:Bone_Marrow medulla ossea BTO:0000141 FMA:9608 medulla ossium BTO:0000141 medulla of bone BTO:0000141 either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region BTO:0001387 CALOHA:TS-1053 EFO:0001401 EMAPA:35871 EV:0100052 FMA:9609 GAID:341 MA:0000143 MESH:A03.867.603.925 NCIT:C12802 OpenCyc:Mx4rvVivrZwpEbGdrcN5Y29ycA UMLS:C0836921 UMLS:C1519547 UMLS:C1519548 VHOG:0001139 uberon Mandel UBERON:0002372 tonsil cjm either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx MGI:cwg MP:0002380 UMLS:C0836921 ncithesaurus:Tonsil UMLS:C1519547 ncithesaurus:Tonsilar_Tissue UMLS:C1519548 ncithesaurus:Tonsillar_Lymphoid_Tissue Mandel BTO:0001387 tonsils on the left and right sides at the back of the throat. one of the mucosa-associated lymphoid tissues (MALT), located at the entrance to the upper respiratory and gastrointestinal tracts to protect the body from the entry of exogenous material through mucosal sites[WP]. tonsillar fossa develops from dorsal portion of pouch 2. Note that pharyngeal and lingual tonsils do not develop from pharyngeal pouches tonsil BTO:0004714 EFO:0001977 EMAPA:35644 EV:0100393 FMA:9610 MA:0000775 MAT:0000291 MIAA:0000291 NCIT:C33250 UMLS:C0040421 VHOG:0001140 faucial tonsil uberon Gaumenmandel@de tonsilla palatina UBERON:0002373 palatine tonsil Illu:mouth.jpg the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract ISBN:1607950324 MP:anna Wikipedia tonsils on the left and right sides at the back of the throat. one of the mucosa-associated lymphoid tissues (MALT), located at the entrance to the upper respiratory and gastrointestinal tracts to protect the body from the entry of exogenous material through mucosal sites[WP]. tonsillar fossa develops from dorsal portion of pouch 2. Note that pharyngeal and lingual tonsils do not develop from pharyngeal pouches ISBN:1607950324 UMLS:C0040421 ncithesaurus:Palatine_Tonsil Gaumenmandel@de BTO:0004714 tonsilla palatina A bone that is part of the metacarpal skeleton. EFO:0003886 EMAPA:36158 FMA:9612 MA:0000302 NCIT:C12751 OpenCyc:Mx4rv1Bk45wpEbGdrcN5Y29ycA UMLS:C0025526 galen:Metacarpal metacarpal uberon UBERON:0002374 metacarpal bone Metacarpals:numbered-en.svg true A bone that is part of the metacarpal skeleton. UMLS:C0025526 ncithesaurus:Metacarpal_Bone Any skeletal muscle that is part of the head region. UBERON:0003899 AAO:0000107 BTO:0000021 EFO:0003524 EHDAA2:0000322 EMAPA:18172 FMA:9616 MA:0000578 ZFA:0001652 cephalic muscle cephalic musculature head muscle head muscle organ muscle of head muscle organ of adult head muscle organ of head musculus caput adult head muscle organ uberon cranial muscle head muscles UBERON:0002376 defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) cranial muscle EHDAA2-abduced Any skeletal muscle that is part of the head region. cephalic muscle ZFA:0001652 head muscle MA:0000578 head muscle organ OBOL:automatic muscle of head FMA:9616 muscle organ of adult head OBOL:automatic muscle organ of head OBOL:automatic adult head muscle organ OBOL:automatic cranial muscle ZFA:0001652 Any muscle that is part of the cervical (neck) region. EMAPA:36050 FMA:9617 GAID:149 MA:0000587 MESH:D009334 NCIT:C33163 UMLS:C0027532 muscle organ of neck muscle organ of neck (volume) neck (volume) muscle organ neck muscle neck muscle organ uberon UBERON:0002377 muscle of neck prolog Any muscle that is part of the cervical (neck) region. UMLS:C0027532 ncithesaurus:Neck_Muscle muscle organ of neck OBOL:automatic muscle organ of neck (volume) OBOL:automatic neck (volume) muscle organ OBOL:automatic neck muscle organ OBOL:automatic Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. BTO:0001261 EMAPA:35103 FMA:9620 GAID:89 MA:0000520 MESH:D000009 NCIT:C32040 OpenCyc:Mx4rvlygNJwpEbGdrcN5Y29ycA UMLS:C0000739 abdomen muscle abdomen muscle organ abdominal muscle abdominal wall muscle muscle organ of abdomen uberon abdominal wall musculature UBERON:0002378 muscle of abdomen prolog Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. UMLS:C0000739 ncithesaurus:Abdominal_Muscle abdomen muscle organ OBOL:automatic muscle organ of abdomen OBOL:automatic abdominal wall musculature EMAPA:35103 Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 EFO:0000952 EMAPA:35251 FMA:9640 GAID:100 MA:0000011 MAT:0000301 MESH:D003238 MIAA:0000301 NCIT:C12374 OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA TAO:0001641 UMLS:C0009780 VSAO:0000017 XAO:0001017 ZFA:0001632 galen:ConnectiveTissue portion of connective tissue textus connectivus uberon Bindegewebe UBERON:0002384 connective tissue Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. GO_REF:0000034 PSPUB:0000170 VSAO:0000017 One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] 2012-06-20 AAO:0000098 AAO AAO:LAP Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] 2012-08-14 TAO:0001641 TAO TAO:wd Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] 2012-08-14 VSAO:0000017 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 MA also has set of connective tissues MA UMLS:C0009780 ncithesaurus:Connective_Tissue portion of connective tissue FMA:9640 Bindegewebe BTO:0000421 Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 EHDAA2:0003122 EMAPA:32715 FMA:9641 MA:0002437 MESH:D009132 NCIT:C12435 UMLS:C2328219 galen:MuscleTissue muscular tissue portion of muscle tissue textus muscularis uberon UBERON:0002385 Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. muscle tissue Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. GO:0060537 One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] 2012-06-20 AAO:0000306 AAO AAO:LAP UMLS:C2328219 ncithesaurus:Muscle_Tissue muscular tissue portion of muscle tissue FMA:9641 The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants. The middle forelimb region. [Evolution, Fourth_Edition_(2006)_Boston_etc.:_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.321, see_Kardong_KV][VHOG] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here BTO:0001447 CALOHA:TS-2205 EFO:0003053 EHDAA2:0000553 EHDAA:4172 EHDAA:6218 EMAPA:17417 FMA:9663 GAID:55 MA:0000034 MESH:D005542 NCIT:C32628 OpenCyc:Mx4rvVjnmpwpEbGdrcN5Y29ycA UMLS:C0016536 VHOG:0000341 VSAO:0005058 galen:Forearm antebrachial region antebrachium antibrachium arm middle limb segment arm zeugopod brachial region middle limb segment brachial region zeugopod forearm forelimb epipodium forelimb zeugopodium forelimb zygopod intermediate segment of free upper limb lower arm lower segment of arm middle limb segment of arm middle limb segment of brachial region middle limb segment of forelimb middle limb segment of proximal segment of free upper limb regio antebrachialis zeugopod of arm zeugopod of brachial region zeugopod of forelimb zeugopod of proximal segment of free upper limb wing zeugopod uberon antebrachium fore epipodium UBERON:0002386 forelimb zeugopod Forearm:labeled.png http://upload.wikimedia.org/wikipedia/commons/3/3b/Veins.jpg MA The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants. PHENOSCAPE:curators The middle forelimb region. [Evolution, Fourth_Edition_(2006)_Boston_etc.:_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.321, see_Kardong_KV][VHOG] 2012-09-17 VHOG:0000341 VHOG Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000341 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 UMLS:C0016536 ncithesaurus:Forearm antebrachium antebrachium VSAO:0005058 arm middle limb segment OBOL:automatic arm zeugopod OBOL:automatic brachial region middle limb segment OBOL:automatic brachial region zeugopod OBOL:automatic lower arm MA:0000034 middle limb segment of arm OBOL:automatic middle limb segment of brachial region OBOL:automatic middle limb segment of forelimb middle limb segment of proximal segment of free upper limb OBOL:automatic regio antebrachialis FMA:9663 FMA:TA zeugopod of brachial region OBOL:automatic zeugopod of proximal segment of free upper limb OBOL:automatic wing zeugopod NCBITaxon:8782 OBOL:automatic antebrachium distal portion of the hind limb, including tarsal region, metatarsal region and digits. pedal BTO:0000476 CALOHA:TS-0377 EFO:0003065 EHDAA2:0000546 EMAPA:17459 FMA:9664 GAID:40 MA:0000044 MESH:D005528 NCIT:C32622 OpenCyc:Mx4rvVi-k5wpEbGdrcN5Y29ycA UMLS:C0016504 VHOG:0000350 galen:Foot foot hindlimb autopod hindlimb autopodium hindlimb distal free limb segment pes terminal segment of free lower limb hind foot hind paw hind-paw hindfeet hindfoot hindfoot of quadruped hindpaw uberon hind limb autopodium UBERON:0002387 pes http://upload.wikimedia.org/wikipedia/commons/a/ae/Male_Right_Foot_1.jpg distal portion of the hind limb, including tarsal region, metatarsal region and digits. UMLS:C0016504 ncithesaurus:Foot foot MA:0000044 hindlimb autopod OBOL:automatic hindlimb autopodium OBOL:automatic hindlimb distal free limb segment OBOL:automatic pes hind paw EMAPA:17428 OBOL:automatic hind-paw EMAPA:17428 hindfeet hindpaw MA:0000044 hind limb autopodium VHOG:0000350 A digit that is part of a manus (hand). One of the fingers of the manus.[AAO] UBERON:0000028 AAO:0000857 BTO:0004669 EHDAA2:0000404 EMAPA:32642 FMA:9666 GAID:57 MA:0000041 MESH:D005385 NCIT:C32608 NLXANAT:20090602 OpenCyc:Mx4rvVi_f5wpEbGdrcN5Y29ycA UMLS:C0016129 XAO:0003036 galen:Finger digit of hand digit of manus digitus manus finger fore digit forelimb digit hand digit manual digit (phalangeal portion) plus soft tissue uberon UBERON:0002389 manual digit PHENOSCAPE:ni A digit that is part of a manus (hand). One of the fingers of the manus.[AAO] 2012-06-20 AAO:0000857 AAO AAO:LAP UMLS:C0016129 ncithesaurus:Finger digit of hand FMA:9666 finger FMA:9666 fore digit AAO:0000857 XAO:0003036 hand digit MA:0000041 manual digit (phalangeal portion) plus soft tissue Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] hematopoietic In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 EFO:0000798 EMAPA:35402 EV:0100045 FMA:9667 GAID:1008 MA:0002434 MAT:0000022 MESH:D006413 MIAA:0000022 NCIT:C12909 TAO:0005023 UMLS:C0018957 VHOG:0001624 XAO:0000122 ZFA:0005023 haematological system haemopoietic system organa haemopoietica uberon Blutbildungssystem haematopoietic system hematological system hematolymphoid system hemopoietic system UBERON:0002390 hematopoietic system FMA definitional Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] 2012-06-20 AAO:0011002 AAO AAO:EJS Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] 2012-09-17 VHOG:0001624 VHOG DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes WP UMLS:C0018957 ncithesaurus:Hematopoietic_System Blutbildungssystem BTO:0000570 Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. BTO:0000855 CALOHA:TS-0580 EFO:0000871 ENVO:02000041 EV:0100049 FMA:9671 GAID:1186 MA:0002520 MAT:0000055 MESH:A12.207.630 MIAA:0000055 NCIT:C13252 OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA UMLS:C0024202 VHOG:0001590 ZFA:0005658 galen:Lymph uberon lympha UBERON:0002391 lymph http://upload.wikimedia.org/wikipedia/commons/1/19/Illu_lymph_capillary.png Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. UMLS:C0024202 ncithesaurus:Lymph lympha the paired channels leading from the lacrimal sacs to the inferior meatus of the nose, through which tears are conducted through the nasal cavity The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG] the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue nasolacrimal duct - posterior naris AAO:0000643 EHDAA2:0001237 EHDAA:7849 EHDAA:9094 EMAPA:17853 FMA:9703 GAID:902 MA:0001299 MESH:D009301 NCIT:C33161 OpenCyc:Mx4rv6PJy5wpEbGdrcN5Y29ycA UMLS:C0027437 VHOG:0000664 uberon d. nasolacrimalis tear duct UBERON:0002392 nasolacrimal duct http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png the paired channels leading from the lacrimal sacs to the inferior meatus of the nose, through which tears are conducted through the nasal cavity ISBN:0-683-40008-8 MP:0008969 The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG] 2012-09-17 VHOG:0000664 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256 nasolacrimal duct - posterior naris VHOG:0000664 UMLS:C0027437 ncithesaurus:Nasolacrimal_Duct d. nasolacrimalis tear duct Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. A duct that carries bile from the liver to the intestine. Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG] (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA AAO:0011019 BTO:0000122 CALOHA:TS-0075 EHDAA2:0000741 EMAPA:35171 EV:0100091 FMA:9706 GAID:280 MA:0000354 MESH:D001652 NCIT:C12376 OpenCyc:Mx4rvdCds5wpEbGdrcN5Y29ycA TAO:0001100 UMLS:C0005400 VHOG:0000212 XAO:0000134 ZFA:0001100 uberon bile tube biliary duct gall duct hepatic duct UBERON:0002394 bile duct http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png EMAPA MA XAO Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. A duct that carries bile from the liver to the intestine. ZFA:0001100, ZFA:curator Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG] 2012-09-17 VHOG:0000212 VHOG (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] 2012-09-17 VHOG:0000212 VHOG DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000) we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA ZFA UMLS:C0005400 ncithesaurus:Bile_Duct biliary duct FMA:9706 gall duct BTO:0000122 hepatic duct ZFA:0001100 distal segment of the fore limb, including carpal region, metacarpal region and digits. like all limb segments, this class encompasses both the unformed hand region of the embryo to the fully formed structure complete with skeleton manual AAO:0010803 BTO:0004668 CALOHA:TS-2213 EHDAA2:0000728 EMAPA:17428 FMA:9712 GAID:56 MA:0000037 MESH:D006225 NCIT:C32712 NLXANAT:20090603 OpenCyc:Mx4rvViGVZwpEbGdrcN5Y29ycA UMLS:C0018563 VHOG:0000344 galen:Hand forelimb autopod forelimb autopodium hand hand region terminal segment of free upper limb fore foot fore paw fore-paw forefeet forefoot forefoot of quadruped forepaw uberon UBERON:0002398 manus http://upload.wikimedia.org/wikipedia/commons/7/76/LeftHand0.jpg distal segment of the fore limb, including carpal region, metacarpal region and digits. UMLS:C0018563 ncithesaurus:Hand forelimb autopod OBOL:automatic forelimb autopodium OBOL:automatic hand MA:0000037 hand region EHDAA2:0000728 fore foot fore paw EMAPA:17428 OBOL:automatic fore-paw EMAPA:17428 forefeet forefoot forepaw MA:0000037 The outer serous membrane of the pulmonary pleural. EMAPA:16776 FMA:9733 MA:0002488 NCIT:C33273 OpenCyc:Mx4rvv2Uq5wpEbGdrcN5Y29ycA UMLS:C0225777 VHOG:0001495 uberon pleura parietalis UBERON:0002400 the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax parietal pleura The outer serous membrane of the pulmonary pleural. UBERON:cjm UMLS:C0225777 ncithesaurus:Parietal_Pleura pleura parietalis The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs. Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]. FMA treats this as part of the lungs EHDAA2:0002205 EMAPA:16777 FMA:9734 MA:0002489 NCIT:C33881 OpenCyc:Mx4rwNFqppwpEbGdrcN5Y29ycA UMLS:C0225776 VHOG:0001496 pleura pulmonalis pleura visceralis pleura visceralis (pulmonalis) pulmonary visceral pleura uberon lung mesothelium lung pleura pulmonary pleura UBERON:0002401 visceral pleura FMA The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs. UBERON:cjm Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]. FMA treats this as part of the lungs FMA UMLS:C0225776 ncithesaurus:Visceral_Pleura pleura pulmonalis FMA:9734 FMA:TA pleura visceralis lung mesothelium EHDAA2:0002205 pulmonary pleura FMA:9734 The fluid-filled cavity that lies between the visceral and parietal pleurae. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86 BTO:0004422 EHDAA2:0001475 EMAPA:16773 EMAPA:16774 FMA:9740 GAID:95 MA:0000055 MESH:A01.911.800.650 NCIT:C12840 OpenCyc:Mx4rwCKAppwpEbGdrcN5Y29ycA UMLS:C0178802 VHOG:0000581 cavitas pleuralis uberon cavitum pleuralae cavitum pleurale UBERON:0002402 pleural cavity http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png Wikipedia The fluid-filled cavity that lies between the visceral and parietal pleurae. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000581 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86 EHDAA2 UMLS:C0178802 ncithesaurus:Pleural_Cavity cavitas pleuralis cavitum pleuralae cavitum pleurale Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 BTO:0005810 FMA:9825 GAID:328 MA:0002711 MESH:D007107 NCIT:C12735 OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA TAO:0001159 UMLS:C0020962 VHOG:0001247 XAO:0003152 ZFA:0001159 uberon UBERON:0002405 immune system Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] 2012-09-17 VHOG:0001247 VHOG PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010) UMLS:C0020962 ncithesaurus:Immune_System a double-walled sac containing the heart and the roots of the great vessels. FMA:9868 RETIRED_EHDAA2:0001443 TAO:0000054 uberon pericardium UBERON:0002406 pericardial sac http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png FMA a double-walled sac containing the heart and the roots of the great vessels. The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. Peritoneum that surrounds the heart.[AAO] pericardial In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO) we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium AAO:0010817 BSA:0000090 BTO:0000717 CALOHA:TS-0761 EFO:0000820 EHDAA:5376 EMAPA:16133 EV:0100023 FMA:9869 GAID:569 MA:0000099 MAT:0000454 MESH:D010496 NCIT:C13005 OpenCyc:Mx4rvoCLgJwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001443 TAO:0000054 UMLS:C0031050 VHOG:0001280 XAO:0004182 ZFA:0000054 galen:Pericardium uberon UBERON:0002407 pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png MA The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. Peritoneum that surrounds the heart.[AAO] 2012-06-20 AAO:0010817 AAO AAO:JMG In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity FMA this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO) ZFA we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium FMA UMLS:C0031050 ncithesaurus:Pericardium Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. EHDAA:3422 EHDAA:5378 EMAPA:19031 FMA:9870 MA:0000483 NCIT:C94500 UMLS:C0225969 VHOG:0000537 lamina parietalis (pericardii serosum) lamina parietalis pericardii parietal layer of serous pericardium parietal pericardium uberon pericardial sac UBERON:0002408 parietal serous pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. UMLS:C0225969 ncithesaurus:Parietal_Pericardium lamina parietalis pericardii FMA:9870 FMA:TA parietal pericardium VHOG:0000537 pericardial sac Transudate contained in the pericardial cavity.[FMA] BTO:0001016 FMA:9887 MA:0002530 uberon UBERON:0002409 pericardial fluid FMA Transudate contained in the pericardial cavity.[FMA] FMA:9887 The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib AAO:0000033 BIRNLEX:1123 BTO:0002507 CALOHA:TS-2001 EHDA:10095 EHDAA2:0000158 EHDAA:3767 EMAPA:16984 FMA:65553 GAID:706 MA:0000219 MESH:D001341 NCIT:C12673 TAO:0001574 UMLS:C0004388 UMLS:C1305381 VHOG:0000396 ZFA:0001574 autonomic division of peripheral nervous system autonomic part of peripheral nervous system divisio autonomica systematis nervosi peripherici pars autonomica systematis nervosi peripherici peripheral autonomic nervous system visceral nervous system uberon ANS divisio autonomica systematis nervosi peripherici UBERON:0002410 autonomic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png cjm EMAPA MA NIFSTD ZFA-modified-from-isa The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. GO:0048483 Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000396 VHOG Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] 2012-06-20 AAO:0000033 AAO AAO:BJB From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] 2012-09-17 VHOG:0000396 VHOG DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000) FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib FMA UMLS:C0004388 BIRNLEX:1123 UMLS:C0004388 ncithesaurus:Autonomic_Nervous_System UMLS:C1305381 BIRNLEX:1123 autonomic division of peripheral nervous system FMA:65553 autonomic part of peripheral nervous system FMA:65553 divisio autonomica systematis nervosi peripherici FMA:TA pars autonomica systematis nervosi peripherici FMA:TA peripheral autonomic nervous system FMA:65553 ANS divisio autonomica systematis nervosi peripherici the small, erectile body located at the anterior end of the vulva clitoral BTO:0002020 EHDAA2:0000255 EHDAA:9360 EMAPA:30819 FMA:9909 GAID:385 MA:0000382 MESH:D002987 NCIT:C12308 OpenCyc:Mx4rvVjr6ZwpEbGdrcN5Y29ycA UMLS:C0008984 VHOG:0000700 galen:Clitoris uberon UBERON:0002411 clitoris http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg Wikipedia MA EHDAA2 Wikipedia the small, erectile body located at the anterior end of the vulva ISBN:0-683-40008-8 MP:0003127 UMLS:C0008984 ncithesaurus:Clitoris The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. Consider changing name to make distinction from inferred superclass 'vertebral element' clear we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO] Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO] AAO:0000691 CALOHA:TS-2352 EFO:0001371 EMAPA:32740 FMA:9914 MA:0000309 NCIT:C12933 OpenCyc:Mx4rvt2Dh5wpEbGdrcN5Y29ycA TAO:0001189 UMLS:C0549207 XAO:0004019 ZFA:0001189 galen:Vertebra vertebra bone vertebrae uberon UBERON:0002412 vertebra FMA The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO] 2012-08-14 TAO:0001189 TAO ZFIN:curator Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO] 2012-06-20 AAO:0000691 AAO AAO:Pugener_and_Maglia_2008 UMLS:C0549207 ncithesaurus:Vertebra vertebrae PHENOSCAPE:ad A vertebra that is located in the cervical region of the vertebral column. In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery. EMAPA:17674 FMA:9915 GAID:235 MA:0000311 MESH:D002574 NCIT:C12693 XAO:0003076 galen:CervicalVertebra cervical vertebrae uberon vertebrae cervicales UBERON:0002413 cervical vertebra http://upload.wikimedia.org/wikipedia/commons/f/f8/Illu_vertebral_column.jpg true A vertebra that is located in the cervical region of the vertebral column. cervical vertebrae vertebrae cervicales Large vertebra of the movable part of the vertebral column, characterized by the absence of the foramen transversarium within the transverse process, and by the absence of facets on the sides of the body. Whereas all rats had six lumbar vertebrae, variable patterns in mice included mostly five vertebrae in DBA/2J, mostly six vertebrae in C57BL/6J, and a mix in B6129PF2/J CALOHA:TS-2364 EMAPA:18007 FMA:9921 GAID:240 MA:0000312 MESH:D008159 NCIT:C12744 OpenCyc:Mx4rvaOek5wpEbGdrcN5Y29ycA UMLS:C0024091 galen:LumbarVertebra uberon UBERON:0002414 lumbar vertebra http://upload.wikimedia.org/wikipedia/commons/c/c8/Gray93.png Large vertebra of the movable part of the vertebral column, characterized by the absence of the foramen transversarium within the transverse process, and by the absence of facets on the sides of the body. Whereas all rats had six lumbar vertebrae, variable patterns in mice included mostly five vertebrae in DBA/2J, mostly six vertebrae in C57BL/6J, and a mix in B6129PF2/J PMCID:PMC2700063 UMLS:C0024091 ncithesaurus:Lumbar_Vertebra An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin AEO:0000109 BILA:0000117 BTO:0001348 EFO:0000963 EHDAA:9198 GAID:1245 MAT:0000094 MESH:D013623 MIAA:0000094 OpenCyc:Mx4rvVjiC5wpEbGdrcN5Y29ycA WBbt:0005741 caudal subdivision uberon UBERON:0002415 tail An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail AEO:0000109 caudal subdivision Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] UBERON:0007029 AEO:0000154 BILA:0000118 CALOHA:TS-1299 CARO:0002001 EFO:0000807 EHDAA2:0000836 EHDAA2_RETIRED:0003154 EHDAA:6520 EMAPA:17524 EV:0100151 FBbt:00004969 FMA:72979 HAO:0000421 MA:0000014 MAT:0000033 MESH:D034582 MIAA:0000033 NCIT:C12907 TADS:0000108 UMLS:C0037267 VHOG:0000403 XAO:0000176 galen:Surface integumentary system uberon body surface dermal system external covering of organism integumentum commune organism surface surface UBERON:0002416 integumental system Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. CARO:0002001 (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] 2012-09-17 VHOG:0000403 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) UMLS:C0037267 ncithesaurus:Integumentary_System integumentary system FMA:72979 dermal system MIAA:0000033 integumentum commune organism surface EHDAA2:0003154 surface BILA:0000118 The abdominal segment of the torso. EMAPA:35104 FMA:259211 MA:0000021 uberon abdomen/pelvis/perineum lower body lower trunk lumbar region UBERON:0002417 abdominal segment of trunk FMA The abdominal segment of the torso. abdomen/pelvis/perineum MA:0000021 lower body MA:0000021 lower trunk FMA:259211 lumbar region Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] AAO:0000060 AEO:0000087 BTO:0000206 EFO:0000949 EHDAA2:0003087 EMAPA:32730 EV:0100141 FMA:37377 GAID:99 MA:0000104 MAT:0000189 MESH:D002356 MIAA:0000189 NCIT:C12373 NCIT:C32268 OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA TAO:0001501 UMLS:C0007301 VHOG:0001207 VSAO:0000040 XAO:0000170 ZFA:0005622 galen:Cartilage cartilage tissue cartilaginous tissue chondrogenic tissue uberon cartilage cartilages portion of cartilage tissue UBERON:0002418 Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W] cartilage tissue http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000040 A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] 2012-06-20 AAO:0000060 AAO AAO:LAP Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] 2012-08-14 TAO:0001501 TAO ZFIN:curator Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] 2012-08-14 VSAO:0000040 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000060 AAO Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] 2012-09-17 VHOG:0001207 VHOG DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012) UMLS:C0007301 ncithesaurus:Cartilage cartilage tissue FMA:37377 chondrogenic tissue VSAO:0000040 cartilages VHOG:0001207 portion of cartilage tissue FMA:37377 A gland that is part of a skin of body [Automatically generated definition]. check FMA, use plural for now as general class not there EMAPA:35774 FMA:71878 MA:0000146 glandulae cutis uberon set of skin glands skin glands skin glands set UBERON:0002419 skin gland A gland that is part of a skin of body [Automatically generated definition]. OBOL:automatic glandulae cutis FMA:71878 FMA:TA set of skin glands FMA:71878 skin glands skin glands set Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures. Fluid-filled brain cavity. Kimmel et al, 1995.[TAO] Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO] The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592]. The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] AAO:0011043 BAMS:4V BAMS:V4 BIRNLEX:1256 BM:Pons-4V BTO:0003426 CALOHA:TS-2015 DHBA:10669 DHBA:12805 DMBA:126651782 EHDAA2:0000100 EHDAA:896 EMAPA:16917 EV:0100310 FMA:78469 GAID:610 HBA:9421 MA:0000196 MBA:145 MESH:D020546 NCIT:C12828 OpenCyc:Mx4rv-7Q6pwpEbGdrcN5Y29ycA TAO:0000110 UMLS:C0149556 VHOG:0000006 XAO:0003099 ZFA:0000110 ventricle IV rhombencephalic vesicle uberon 4th ventricle IVth ventricle fourth ventricle proper hindbrain ventricle rhombencephalic ventricle ventricle of hindbrain ventricle of rhombencephalon ventriculus quartus UBERON:0002422 fourth ventricle http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png EHDAA2 Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures. BIRNLEX:1256 Fluid-filled brain cavity. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000110 TAO ZFIN:curator Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO] 2012-06-20 AAO:0011043 AAO UBERON:0002422 The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592]. GO:0021592 The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000006 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 UMLS:C0149556 ncithesaurus:Fourth_Ventricle_of_the_Brain ventricle IV ZFA:0000110 rhombencephalic vesicle ZFA:0000110 4th ventricle MA:0000196 IVth ventricle VHOG:0000006 fourth ventricle proper BAMS:V4 hindbrain ventricle VHOG:0000006 rhombencephalic ventricle VHOG:0000006 ventricle of hindbrain BTO:0003426 ventricle of rhombencephalon BTO:0003426 ventriculus quartus The part of the digestive system that contains the liver and the biliary system System responsible for the production and movement of bile[ZFIN:curator]. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008] AAO:0011056 CALOHA:TS-1308 EFO:0000800 EHDAA2:0000998 EHDAA:2189 EMAPA:16840 EV:0100088 MA:0000324 MAT:0000024 MIAA:0000024 NCIT:C43612 TAO:0000036 UMLS:C1711359 VHOG:0000294 XAO:0000132 ZFA:0000036 hepaticobiliary system liver and biliary system uberon liver/biliary system UBERON:0002423 hepatobiliary system The part of the digestive system that contains the liver and the biliary system System responsible for the production and movement of bile[ZFIN:curator]. ZFIN:curator UMLS:C1711359 ncithesaurus:Hepatobiliary_System hepaticobiliary system GO:0061008 An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme AAO:0010357 BTO:0001775 CALOHA:TS-0715 EHDAA2:0001325 EHDAA:2187 EMAPA:16839 EMAPA:26942 FMA:265152 MA:0000344 NCIT:C49595 TAO:0000816 UMLS:C1709332 VHOG:0000187 XAO:0003201 ZFA:0000816 epithelium of mucosa of mouth epithelium of oral mucosa uberon UBERON:0002424 oral epithelium AAO-modified An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. ZFA:0000816 the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme UMLS:C1709332 ncithesaurus:Oral_Cavity_Epithelium epithelium of mucosa of mouth FMA:265152 epithelium of oral mucosa FMA:265152 Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]. EMAPA:16589 EMAPA:19032 FMA:84882 MA:0000484 VHOG:0000538 lamina visceralis pericardii serosi serous visceral pericardium visceral lamina of serous pericardium visceral layer of serous pericardium visceral pericardium uberon epicardium pericardium visceral mesothelium UBERON:0002425 visceral serous pericardium cjm FMA Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]. lamina visceralis pericardii serosi visceral pericardium VHOG:0000538 epicardium MA:0000484 pericardium visceral mesothelium EMAPA:16589 Any muscle organ that is part of a chest [Automatically generated definition]. BTO:0000508 CALOHA:TS-1037 EMAPA:17747 EMAPA:17748 FMA:9619 MA:0000548 anterior thoracic region muscle organ anterolateral part of thorax muscle organ chest muscle organ front of thorax muscle organ muscle of thorax muscle organ of anterior thoracic region muscle organ of anterolateral part of thorax muscle organ of chest muscle organ of front of thorax musculus thoracicus thoracic muscle uberon UBERON:0002426 chest muscle Any muscle organ that is part of a chest [Automatically generated definition]. OBOL:automatic anterior thoracic region muscle organ OBOL:automatic anterolateral part of thorax muscle organ OBOL:automatic chest muscle organ OBOL:automatic front of thorax muscle organ OBOL:automatic muscle of thorax FMA:9619 muscle organ of anterior thoracic region OBOL:automatic muscle organ of anterolateral part of thorax OBOL:automatic muscle organ of chest OBOL:automatic muscle organ of front of thorax OBOL:automatic A zone of skin that is part of an arm [Automatically generated definition]. EMAPA:37350 MA:0000596 NCIT:C52754 UMLS:C0222204 skin of arm uberon brachial region skin UBERON:0002427 arm skin A zone of skin that is part of an arm [Automatically generated definition]. OBOL:automatic EMAPA:37350 MA:th UMLS:C0222204 ncithesaurus:Arm_Skin skin of arm OBOL:automatic brachial region skin OBOL:automatic A bone that is part of a limb [Automatically generated definition]. the formal definition is very inclusive, and includes sesamoids NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle EFO:0000945 MAT:0000151 MIAA:0000151 NCIT:C32223 UMLS:C0582791 bone of extremity bone of limb free limb bone uberon UBERON:0002428 limb bone A bone that is part of a limb [Automatically generated definition]. OBOL:automatic NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle NCIT UMLS:C0582791 ncithesaurus:Bone_of_the_Extremity bone of limb OBOL:automatic free limb bone UBERONREF:0000003 Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted]. FMA:61213 MA:0000736 NCIT:C32298 UMLS:C0588054 lymph node of neck uberon UBERON:0002429 cervical lymph node http://upload.wikimedia.org/wikipedia/commons/4/4c/Lymph_node_regions.jpg Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted]. UMLS:C0588054 ncithesaurus:Cervical_Lymph_Node A blood vessel that is part of a choroid [Automatically generated definition]. EMAPA:17828 FMA:76550 MA:0001237 blood vessel of choroid blood vessel of choroid coat blood vessel of choroidea blood vessel of posterior uvea choroid blood vessel choroid blood vessels choroid blood vessels set choroid coat blood vessel choroidea blood vessel posterior uvea blood vessel vasa sanguinea choroideae uberon set of choroid blood vessels UBERON:0002443 cannot find singular in FMA, using Set class choroidal blood vessel A blood vessel that is part of a choroid [Automatically generated definition]. OBOL:automatic blood vessel of choroid OBOL:automatic blood vessel of choroid coat OBOL:automatic blood vessel of choroidea OBOL:automatic blood vessel of posterior uvea OBOL:automatic choroid blood vessel OBOL:automatic choroid coat blood vessel OBOL:automatic choroidea blood vessel OBOL:automatic posterior uvea blood vessel OBOL:automatic vasa sanguinea choroideae FMA:76550 FMA:TA set of choroid blood vessels FMA:76550 The mucous secreting gland associated with the mucuous membrane lining the uterus. simple or branched tubular BTO:0003433 BTO:0004518 EMAPA:29919 MA:0001726 NCIT:C33842 UMLS:C1183035 endometrial gland endometrial mucuous gland endometrium gland glandulae uterinae uterine gland uberon glandulae uterinae UBERON:0002451 endometrial gland http://upload.wikimedia.org/wikipedia/commons/2/28/Gray1169.png MP The mucous secreting gland associated with the mucuous membrane lining the uterus. UMLS:C1183035 ncithesaurus:Uterine_Gland endometrial gland BTO:0003433 glandulae uterinae FMA:71647 FMA:TA glandulae uterinae An artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted]. MA has both mammary and thoracic EHDAA2:0000880 EHDAA:8585 EMAPA:18617 FMA:3960 MA:0001982 MA:0001984 NCIT:C52941 OpenCyc:Mx4rMe0MIao8EduQrwACs5b6Bw UMLS:C0226276 internal mammary artery internal thoracic mammary artery uberon arteria mammaria interna arteria thoracica interna mammary artery UBERON:0002456 internal thoracic artery http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray522.png An artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted]. MA has both mammary and thoracic MA UMLS:C0226276 ncithesaurus:Internal_Mammary_Artery internal mammary artery MA:0001982 arteria mammaria interna arteria thoracica interna mammary artery EMAPA:18617 The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061]. Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG] UBERON:0006001 EHDAA2:0000882 EHDAA:4340 EMAPA:17616 MA:0001985 TAO:0001061 VHOG:0000225 XAO:0004165 ZFA:0001061 intersegmental artery uberon intersegmental arteries UBERON:0002457 intersomitic artery The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries MP:0010662 Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061]. ZFA:0001061 Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG] 2012-09-17 VHOG:0000225 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612 intersegmental artery ZFA:0001061 intersegmental arteries ZFA:0001061 Arteries that supply the spinal cord. EHDAA2:0001890 EHDAA:4355 EMAPA:18241 MA:0002043 NCIT:C33587 TAO:0000682 UMLS:C0447043 ZFA:0000682 spinal arteries uberon UBERON:0002458 spinal artery Arteries that supply the spinal cord. UMLS:C0447043 ncithesaurus:Spinal_Artery spinal arteries ZFA:0000682 A tributary of the iliac vein that drains the urinary bladder. EMAPA:37205 MA:0002263 venae vesicales vesical veins vesical veins set uberon UBERON:0002460 vesical vein http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png A tributary of the iliac vein that drains the urinary bladder. UBERON:cjm EMAPA:37205 MA:th venae vesicales FMA:70911 FMA:TA vesical veins Segment of neural tree organ which consists of nerve fiber bundles aggregated to form a cable-like structure that branches off to different nerves; together with all nerves of the same tree. Example: trunk of cranial nerve, trunk of spinal nerve, trunk of peripheral nerve[FMA:5913]. UBERON:0001147 BTO:0000927 EHDAA:4675 EMAPA:16986 FMA:14383 FMA:5913 MA:0000229 MA:0002408 peripheral nerve trunk trunk of nerve trunk of peripheral nerve uberon UBERON:0002464 nerve trunk Segment of neural tree organ which consists of nerve fiber bundles aggregated to form a cable-like structure that branches off to different nerves; together with all nerves of the same tree. Example: trunk of cranial nerve, trunk of spinal nerve, trunk of peripheral nerve[FMA:5913]. FMA:5913 peripheral nerve trunk EMAPA:16986 The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] lymphoid The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013] The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013] We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments. UBERON:0002096 EHDAA2:0001043 EHDAA:8677 EMAPA:37664 FMA:74594 GAID:931 MA:0002435 MAT:0000197 MIAA:0000197 NCIT:C12746 OpenCyc:Mx4rwQAKT5wpEbGdrcN5Y29ycA TAO:0000385 UMLS:C0024235 VHOG:0000842 XAO:0003199 ZFA:0000385 lymphatic system uberon lymphatic circulatory system lymphatic drainage system systema lymphoideum UBERON:0002465 lymphoid system http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg FMA The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] 2012-06-20 AAO:0010522 AAO AAO:BJB Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] 2012-09-17 VHOG:0000842 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627 We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments. EMAPA:37664 MA:th UMLS:C0024235 ncithesaurus:Lymphatic_System lymphatic system ZFA:0000385 lymphatic circulatory system lymphatic drainage system systema lymphoideum Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. BTO:0000644 FMA:62974 GAID:1162 MA:0002515 MESH:D007419 NCIT:C32875 UMLS:C0021849 intestinal secretion succus entericus uberon intestinal juice UBERON:0002466 intestine secretion Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. UMLS:C0021849 ncithesaurus:Intestinal_Secretion intestinal secretion FMA:62974 succus entericus intestinal juice BTO:0000644 A mucosa that is part of a esophagus [Automatically generated definition]. UBERON:0003345 BTO:0002859 EMAPA:26981 FMA:62996 MA:0002680 NCIT:C32538 UMLS:C0227176 esophageal mucosa esophageal mucous membrane esophagus mucosa esophagus mucous membrane lamina muscularis mucosae oesophageae mucosa of esophagus mucosa of oesophagus mucous membrane of esophagus mucous membrane of oesophagus oesophageal mucosa oesophagus mucosa oesophagus mucous membrane tunica mucosa esophagi tunica mucosa oesophageae tunica mucosa oesophagi uberon muscularis mucosae of oesophagus tunica mucosa oesophagi UBERON:0002469 esophagus mucosa A mucosa that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C0227176 ncithesaurus:Esophageal_Mucosa esophagus mucosa FMA:62996 esophagus mucous membrane OBOL:automatic lamina muscularis mucosae oesophageae FMA:62996 FMA:TA mucosa of esophagus OBOL:automatic mucosa of oesophagus OBOL:automatic mucous membrane of oesophagus FMA:62996 oesophageal mucosa FMA:62996 oesophagus mucous membrane OBOL:automatic tunica mucosa oesophageae FMA:62996 FMA:TA muscularis mucosae of oesophagus FMA:62996 tunica mucosa oesophagi BTO:0002859 Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton. autopod BTO:0004359 EFO:0000877 EMAPA:32722 FMA:83015 MA:0002714 MAT:0000091 MIAA:0000091 NCIT:C77660 UMLS:C0687080 autopodial limb segment autopodial segment autopodium autopodium region distal free limb segment distal segment of free limb uberon autopodial element distal segment of limb manus/pes paw paw/hand/foot/hoof pod UBERON:0002470 autopod region definitional Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot autopod MA:0002714 UMLS:C0687080 ncithesaurus:Paw autopodial limb segment MA:th distal free limb segment FMA:83015 distal segment of free limb FMA:83015 distal segment of limb EMAPA:32722 The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus). zeugopodial middle part of limb EFO:0000878 FMA:83016 MA:0002716 MAT:0000092 MIAA:0000092 epipodium middle free limb segment middle limb segment zeugopod limb segment zeugopodial limb segment zeugopodium zygopod zygopodium uberon middle segment of free limb UBERON:0002471 There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators] zeugopod The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus). PHENOSCAPE:curators epipodium MA:th middle free limb segment FMA:83016 zeugopod limb segment MA:th zeugopodial limb segment MA:th middle segment of free limb FMA:83016 The proximal free limb segment. Includes as parts the stylopod skeleton. stylopodial Naming conventions for pod terms under discussion within phenoscape group proximal part of limb EFO:0000879 FMA:83014 MA:0002717 MAT:0000093 MIAA:0000093 propodium proximal free limb segment stylopodial limb segment stylopodium uberon proximal segment of free limb UBERON:0002472 stylopod The proximal free limb segment. Includes as parts the stylopod skeleton. propodium MA:th proximal free limb segment FMA:83014 stylopodial limb segment MA:th proximal segment of free limb FMA:83014 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. see https://github.com/obophenotype/uberon/issues/27 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] CALOHA:TS-2011 EMAPA:35179 FMA:224804 MA:0002780 MESH:D001842 NCIT:C13076 UMLS:C0391978 VSAO:0000047 XAO:0004040 ZFA:0005621 galen:BoneTissue calcium tissue osseous tissue osteogenic tissue mineralized bone tissue uberon bone portion of bone tissue UBERON:0002481 bone tissue VSAO Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000047 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] 2012-08-14 VSAO:0000047 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 UMLS:C0391978 ncithesaurus:Bone_Tissue osteogenic tissue VSAO:curator mineralized bone tissue XAO:0004040 bone MESH:A02.835.232 portion of bone tissue FMA:224804 The minute canals that pass the prostatic secretions to the urethra. EMAPA:36568 FMA:19580 MA:0002785 NCIT:C13102 UMLS:C0227965 duct of prostate duct of prostate gland prostate duct prostate gland duct prostatic duct uberon UBERON:0002485 prostate duct The minute canals that pass the prostatic secretions to the urethra. MP:0009734 UMLS:C0227965 ncithesaurus:Prostatic_Duct Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd]. BTO:0004256 EMAPA:35503 FMA:7474 MA:0002802 NCIT:C33003 OpenCyc:Mx4rv6axr5wpEbGdrcN5Y29ycA UMLS:C0222647 galen:LongBone uberon os longum UBERON:0002495 Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251] long bone Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd]. VSAO:wd UMLS:C0222647 ncithesaurus:Long_Bone os longum BTO:0004256 An epithelium that is part of a iris [Automatically generated definition]. EMAPA:35447 FMA:58517 MA:0002826 epithelial tissue of iris epithelium of iris epithelium pigmentosum (iris) epithelium pigmentosum iridis iris epithelial tissue iris epithelium pigmented epithelium of iris uberon iris pigmented epithelium UBERON:0002506 iris epithelium FMA MA An epithelium that is part of a iris [Automatically generated definition]. OBOL:automatic epithelial tissue of iris OBOL:automatic epithelium of iris OBOL:automatic epithelium pigmentosum (iris) FMA:58517 epithelium pigmentosum iridis FMA:58517 FMA:TA iris epithelial tissue OBOL:automatic iris epithelium FMA:58517 pigmented epithelium of iris FMA:58517 iris pigmented epithelium MA:0002826 A lymph node that is part of an abdomen [Automatically generated definition]. EMAPA:35992 FMA:12787 MA:0002827 abdomen lymph node lymph node of abdomen uberon parietal abdominal lymph node UBERON:0002507 abdominal lymph node A lymph node that is part of an abdomen [Automatically generated definition]. OBOL:automatic abdomen lymph node OBOL:automatic parietal abdominal lymph node FMA:12787 The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. BTO:0000767 EMAPA:35561 FMA:12795 MA:0002829 NCIT:C77641 UMLS:C0229792 mesenteric node uberon nodi lymphoidei mesenterici UBERON:0002509 mesenteric lymph node FMA The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group. MP:0005232 UMLS:C0229792 ncithesaurus:Mesenteric_Lymph_Node nodi lymphoidei mesenterici BTO:0000767 Replacement bone that forms within cartilage. placement in this class to be inferred Replacement bone that forms within cartilage.[VSAO] some structures, e.g. in ZFA are both intramembrane and endochondral AAO:0010776 AEO:0000083 BTO:0002157 EHDAA2:0003083 FMA:24321 TAO:0001591 VSAO:0000145 XAO:0004018 ZFA:0001591 ossified chondrogenic bone uberon cartilaginous bone endochondral bones UBERON:0002513 endochondral bone https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg VSAO VSAO Replacement bone that forms within cartilage. GO:0001958 GO_REF:0000034 VSAO:0000145 Replacement bone that forms within cartilage.[VSAO] 2012-08-14 VSAO:0000145 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 some structures, e.g. in ZFA are both intramembrane and endochondral ZFA ossified chondrogenic bone VSAO:0000145 cartilaginous bone BTO:0002157 endochondral bones ZFA:0001591 The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof. basicranial FMA:52801 MA:0002840 MESH:D019291 MFMO:0000044 NCIT:C12493 UMLS:C0149543 base of cranium base of skull basis cranii cranial base uberon UBERON:0002517 The skull base is formed from a series of cartilages either side of, and rostral to, the notochord, whose tip lies just caudal to the pituitary gland. It is closely associated with the sensory capsules, which partially or completely sur- round the olfactory epithelium, the eye, and the inner ear[PMID:11523816] basicranium http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof. UMLS:C0149543 ncithesaurus:Base_of_the_Skull base of skull FMA:52801 basis cranii FMA:52801 FMA:TA cranial base FMA:52801 MA:0002840 Connective tissue composed of elastic fibers. FMA:20113 GAID:926 MA:0002853 MESH:D004547 NCIT:C32495 elastic connective tissue textus connectivus elasticus elastic fiber uberon UBERON:0002521 elastic tissue http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png Connective tissue composed of elastic fibers. textus connectivus elasticus The middle layer of an artery or vein. [WP,unvetted]. BTO:0002011 EMAPA:36298 FMA:55590 GAID:170 MA:0002855 MESH:D017540 NCIT:C33821 UMLS:C0162867 uberon tunica media vasorum UBERON:0002522 May be composed of smooth muscle and elastic tissue tunica media Illu:artery.jpg MA cjm cjm The middle layer of an artery or vein. [WP,unvetted]. UMLS:C0162867 ncithesaurus:Tunica_Media tunica media vasorum tunica media vasorum BTO:0002011 The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] BTO:0002012 EMAPA:36297 FMA:55589 GAID:523 MA:0002861 MESH:D017539 NCIT:C33820 UMLS:C0162864 uberon Bichat's tunic intima tunica intima vasorum UBERON:0002523 tunica intima Illu:artery.jpg FMA check for exceptions, e.g. capillaries ISBN:0073040584 The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. ISBN:0073040584 NCIT:C33820 The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] Wikipedia UMLS:C0162864 ncithesaurus:Tunica_Intima Bichat's tunic BTO:0002012 intima BTO:0002012 tunica intima vasorum BTO:0002012 A lymph node that is part of a pancreas [Automatically generated definition]. FMA:16626 MA:0002881 NCIT:C77642 UMLS:C0229783 lymph node of pancreas pancreas lymph node pancreatic node uberon aJCC level 19 node pyloric lymph node UBERON:0002527 pancreatic lymph node A lymph node that is part of a pancreas [Automatically generated definition]. OBOL:automatic UMLS:C0229783 ncithesaurus:Pancreatic_Lymph_Node lymph node of pancreas OBOL:automatic pancreas lymph node OBOL:automatic aJCC level 19 node FMA:16626 pyloric lymph node MA:0002881 A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles. TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z FMA:241863 MA:0002889 NCIT:C38630 UMLS:C1268195 free limb segment segment of limb subdivision of limb uberon extremity part limb region region of limb UBERON:0002529 limb segment A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles. FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z FMA UMLS:C1268195 ncithesaurus:Extremity_Part free limb segment FMA:241863 an organ that functions as a secretory or excretory organ glandular UBERON:MIAA_0000021 AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 EHDAA:4475 EHDAA:6522 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 NCIT:C13319 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA UMLS:C1285092 WikipediaCategory:Glands galen:Gland glandular organ uberon Druese glandula UBERON:0002530 gland http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png an organ that functions as a secretory or excretory organ MGI:csmith MP:0002163 UMLS:C1285092 ncithesaurus:Gland glandular organ Druese BTO:0000522 glandula glandula BTO:0000522 In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 MIAA:0000067 VHOG:0000243 epiblast uberon blastocyst ectoblast epiblastus primitive ectoderm UBERON:0002532 epiblast (generic) http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] ZFIN:curator In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] 2012-09-17 VHOG:0000243 VHOG DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) epiblast VHOG:0000243 ectoblast MP:0003886 epiblastus primitive ectoderm VHOG:0000243 The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] AAO:0011104 BTO:0001445 EFO:0002748 EHDAA2:0001976 EHDAA:1595 EMAPA:16580 MAT:0000070 MIAA:0000070 TAO:0000077 VHOG:0000201 XAO:0000107 ZFA:0000077 tail bud tailbud uberon end bud tail bud mesenchyme UBERON:0002533 post-anal tail bud The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. BTO:0001445 Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] 2012-06-20 AAO:0011104 AAO ISBN:0815318960 OMD:tail+bud (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] 2012-09-17 VHOG:0000201 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 tail bud ZFA:0000077 end bud BTO:0001445 tail bud mesenchyme ZFA:0000077 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering AAO:0010359 BTO:0001785 EFO:0000959 EHDAA:571 EMAPA:16117 FMA:293015 GAID:1292 MAT:0000242 MESH:A16.254.160 MIAA:0000242 NCIT:C34249 TAO:0001306 UMLS:C0080322 VHOG:0000155 XAO:0000096 ZFA:0001306 pharyngeal arches branchial arch uberon arcus pharyngei visceral arch UBERON:0002539 pharyngeal arch http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png EHDAA2 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. ZFA:yb One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010359 AAO NLM:branchial+arch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] 2012-09-17 VHOG:0000155 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) UMLS:C0080322 ncithesaurus:Pharyngeal_Arch pharyngeal arches branchial arch BTO:0001785 MP:0002884 arcus pharyngei A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG] digital AAO:0011126 EFO:0000881 EMAPA:32725 FMA:85518 MA:0000690 MAT:0000285 MIAA:0000285 NCIT:C40186 OpenCyc:Mx4rvzLD_ZwpEbGdrcN5Y29ycA UMLS:C0582802 VHOG:0000944 XAO:0003032 galen:Digit acropodial unit digit (phalangeal portion) plus soft tissue limb digit uberon UBERON:0002544 digit A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG] 2012-09-17 VHOG:0000944 VHOG DOI:10.1038/nature07339 Boisvert CA, Mark-Kurik E and Ahlberg PE, The pectoral fin of Panderichthys and the origin of digits. Nature (2008) FMA:85518 GAT UMLS:C0582802 ncithesaurus:Digit digit (phalangeal portion) plus soft tissue limb digit MA:0000690 Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass ectodermal placode placode AAO:0010466 EFO:0001650 FMA:293966 MAT:0000369 MIAA:0000369 XAO:0000305 ectodermal cranial placode uberon cranial placodes UBERON:0002546 cranial placode cjm Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons ectodermal placode FMA:293966 placode ectodermal cranial placode UBERON:cjm cranial placodes XAO:0000305 Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. cavity BIRNLEX:1011 EMAPA:37442 FMA:67552 MA:0002447 NCIT:C34007 galen:Cavity uberon UBERON:0002553 anatomical cavity Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. FMA:67552 EMAPA:37442 MA:th BIRNLEX:1019 FMA:12237 cavity of organ uberon UBERON:0002558 organ cavity cavity of organ FMA:12237 The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube BIRNLEX:1029 FMA:75007 cavity of neuraxis cavity of ventricular system of neuraxis neuraxis cavity neuraxis lumen uberon UBERON:0002561 lumen of central nervous system The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube cavity of neuraxis FMA:75007 cavity of ventricular system of neuraxis FMA:75007 neuraxis cavity FMA:75007 Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. BIRNLEX:1167 FMA:55676 NCIT:C13031 UMLS:C0445620 anatomical structure of brain biological structure of brain brain anatomical structure brain biological structure brain part neuraxis segment neuroanatomical region segment of brain uberon UBERON:0002616 regional part of brain Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. BIRNLEX:1167 UMLS:C0445620 ncithesaurus:Brain_Part anatomical structure of brain OBOL:automatic biological structure of brain OBOL:automatic brain anatomical structure OBOL:automatic brain biological structure OBOL:automatic neuraxis segment FMA:55676 segment of brain BIRNLEX:1167 A spinal cord segment that adjacent_to a cervical region. BIRNLEX:1499 FMA:71166 MA:0003081 NCIT:C12892 UMLS:C0581619 UMLS:C1278837 cervical segment of spinal cord cervical segments of spinal cord [1-8] cervical spinal cord pars cervicalis medullae spinalis segmenta cervicalia medullae spinalis [1-8 uberon UBERON:0002726 cervical spinal cord A spinal cord segment that adjacent_to a cervical region. OBOL:automatic UMLS:C0581619 BIRNLEX:1499 UMLS:C0581619 ncithesaurus:Cervical_Spinal_Cord UMLS:C1278837 BIRNLEX:1499 cervical segment of spinal cord FMA:71166 cervical segments of spinal cord [1-8] FMA:71166 cervical spinal cord FMA:71166 pars cervicalis medullae spinalis FMA:71166 FMA:TA segmenta cervicalia medullae spinalis [1-8 FMA:71166 FMA:TA A regional part of brain that is part of a cerebellar cortex [Automatically generated definition]. BIRNLEX:1571 FMA:76924 cerebellar cortical segment segment of cerebellar cortex uberon UBERON:0002749 regional part of cerebellar cortex A regional part of brain that is part of a cerebellar cortex [Automatically generated definition]. OBOL:automatic cerebellar cortical segment FMA:76924 segment of cerebellar cortex BIRNLEX:1571 . BIRNLEX:1704 FMA:71168 MA:0003083 NCIT:C12895 UMLS:C0581620 UMLS:C0581621 UMLS:C1278838 lumbar segment of spinal cord lumbar segments of spinal cord [1-5] lumbar spinal cord pars lumbalis medullae spinalis segmenta lumbalia medullae spinalis [1-5] spinal cord lumbar segment uberon UBERON:0002792 lumbar spinal cord . UMLS:C0581620 BIRNLEX:1704 UMLS:C0581621 ncithesaurus:Lumbar_Spinal_Cord UMLS:C1278838 BIRNLEX:1704 lumbar segment of spinal cord FMA:71168 lumbar segments of spinal cord [1-5] FMA:71168 lumbar spinal cord FMA:71168 pars lumbalis medullae spinalis FMA:71168 FMA:TA segmenta lumbalia medullae spinalis [1-5] FMA:71168 FMA:TA spinal cord lumbar segment MA:0003083 Parietal lobe of the left hemisphere of the brain BIRNLEX:1728 FMA:72974 UMLS:C1281960 uberon UBERON:0002802 left parietal lobe Parietal lobe of the left hemisphere of the brain BIRNLEX:1728 UMLS:C1281960 BIRNLEX:1728 Parietal lobe of the right hemisphere of the brain BIRNLEX:1729 FMA:72973 UMLS:C1281959 uberon UBERON:0002803 right parietal lobe Parietal lobe of the right hemisphere of the brain BIRNLEX:1729 UMLS:C1281959 BIRNLEX:1729 A temporal lobe that is part of a left cerebral hemisphere. BIRNLEX:1784 FMA:72972 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rwQLi-ZwpEbGdrcN5Y29ycA UMLS:C1281971 uberon UBERON:0002808 left temporal lobe A temporal lobe that is part of a left cerebral hemisphere. OBOL:automatic UMLS:C1281971 BIRNLEX:1784 A temporal lobe that is part of a right cerebral hemisphere. BIRNLEX:1785 FMA:72971 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rwQLi-ZwpEbGdrcN5Y29ycA UMLS:C1281970 uberon UBERON:0002809 right temporal lobe A temporal lobe that is part of a right cerebral hemisphere. OBOL:automatic UMLS:C1281970 BIRNLEX:1785 A frontal cortex that is part of a right cerebral hemisphere. BIRNLEX:1786 FMA:72969 UMLS:C1281954 uberon UBERON:0002810 right frontal lobe A frontal cortex that is part of a right cerebral hemisphere. OBOL:automatic UMLS:C1281954 BIRNLEX:1786 A frontal cortex that is part of a left cerebral hemisphere. BIRNLEX:1787 FMA:72970 UMLS:C1281955 uberon UBERON:0002811 left frontal lobe A frontal cortex that is part of a left cerebral hemisphere. OBOL:automatic UMLS:C1281955 BIRNLEX:1787 A cerebral hemisphere that is in the left side of a brain. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern BIRNLEX:1795 FMA:61819 NCIT:C32955 UMLS:C0228176 left hemisphere uberon UBERON:0002812 left cerebral hemisphere A cerebral hemisphere that is in the left side of a brain. OBOL:automatic UMLS:C0228176 ncithesaurus:Left_Cerebral_Hemisphere left hemisphere BIRNLEX:1795 A cerebral hemisphere that is in the right side of a brain. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern BIRNLEX:1797 FMA:67292 NCIT:C33472 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvigx5ZwpEbGdrcN5Y29ycA UMLS:C0228175 right hemisphere uberon UBERON:0002813 right cerebral hemisphere A cerebral hemisphere that is in the right side of a brain. OBOL:automatic UMLS:C0228175 ncithesaurus:Right_Cerebral_Hemisphere right hemisphere BIRNLEX:1797 Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453) BAMS:12 BAMS:12N BAMS:XII BIRNLEX:2644 BM:XII DHBA:12545 EHDAA2:0004635 EMAPA:35416 EV:0100286 FMA:54505 HBA:9557 MA:0001039 MBA:773 NCIT:C12899 UMLS:C0228802 VHOG:0001358 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 ncithesaurus:Nucleus_of_the_Hypoglossal_Nerve hypoglossal XII nucleus hypoglossal nerve nucleus hypoglossal nucleus nucleus nervi hypoglossi nucleus of hypoglossal nerve twelfth cranial nerve nucleus uberon nucleus hypoglossalis nucleus nervi hypoglossi UBERON:0002871 hypoglossal nucleus http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453) BIRNLEX:2644 UMLS:C0228802 BIRNLEX:2644 UMLS:C0228802 ncithesaurus:Hypoglossal_Nucleus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 BIRNLEX:2644 hypoglossal XII nucleus MA:0001039 hypoglossal nerve nucleus FMA:54505 hypoglossal nucleus FMA:54505 nucleus nervi hypoglossi FMA:54505 FMA:TA nucleus of hypoglossal nerve FMA:54505 twelfth cranial nerve nucleus FMA:54505 nucleus hypoglossalis NeuroNames:757 nucleus nervi hypoglossi The deep groove which separates the two hemispheres of the vertebrate brain. The falx cerebri, a dural brain covering, lies within the medial longitudinal fissure. [WP,unvetted]. LF BAMS:lf BAMS:lfh BIRNLEX:4041 DHBA:10622 FMA:83727 HBA:9401 NCIT:C33005 OpenCyc:Mx4rwJlWu5wpEbGdrcN5Y29ycA UMLS:C0228186 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=35 fissura interhemispherica fissura longitudinalis cerebrales fissura longitudinalis cerebri fissura longitudinalis magna hemispheric sulcus interhemispheric fissure longitudinal cerebral fissure longitudinal fissure of hemisphere longitudinal fissure of the cerebrum longitudinal sulcus medial longitudinal fissure sagittal fissure uberon UBERON:0002921 longitudinal fissure http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png FMA The deep groove which separates the two hemispheres of the vertebrate brain. The falx cerebri, a dural brain covering, lies within the medial longitudinal fissure. [WP,unvetted]. LF BIRNLEX:4041 NIFSTD:NeuroNames_abbrevSource UMLS:C0228186 BIRNLEX:4041 UMLS:C0228186 ncithesaurus:Longitudinal_Fissure http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=35 BIRNLEX:4041 fissura interhemispherica BIRNLEX:4041 fissura longitudinalis cerebrales BIRNLEX:4041 fissura longitudinalis cerebri BIRNLEX:4041 fissura longitudinalis magna BIRNLEX:4041 hemispheric sulcus FMA:83727 interhemispheric fissure FMA:83727 longitudinal cerebral fissure FMA:83727 longitudinal fissure of hemisphere BIRNLEX:4041 longitudinal fissure of the cerebrum BIRNLEX:4041 longitudinal sulcus FMA:83727 medial longitudinal fissure FMA:83727 sagittal fissure FMA:83727 A nucleus of brain that is part of a trigeminal nuclear complex. massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. BM:V BTO:0001074 CALOHA:TS-2077 EMAPA:35883 EV:0100271 FMA:71247 GAID:604 MA:0001028 MESH:D014278 NCIT:C12807 UMLS:C0040999 VHOG:0001353 nucleus of trigeminal nuclear complex trigeminal V nucleus trigeminal nuclear complex nucleus trigeminal nucleus uberon nucleus mesencephalicus nervi trigemini nucleus mesencephalicus trigeminalis nucleus tractus mesencephali nervi trigeminalis UBERON:0002925 trigeminal nucleus A nucleus of brain that is part of a trigeminal nuclear complex. OBOL:automatic massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. GO https://github.com/obophenotype/mouse-anatomy-ontology/issues/58 UMLS:C0040999 ncithesaurus:Trigeminal_Nucleus nucleus of trigeminal nuclear complex FMA:71247 trigeminal V nucleus MA:0001028 trigeminal nuclear complex nucleus FMA:71247 trigeminal nucleus FMA:71248 nucleus mesencephalicus nervi trigemini BTO:0001074 nucleus mesencephalicus trigeminalis BTO:0001074 nucleus tractus mesencephali nervi trigeminalis BTO:0001074 A sensory epithelium that is part of a gustatory system. FMA:62412 uberon UBERON:0002926 gustatory epithelium NIFSTD A sensory epithelium that is part of a gustatory system. OBOL:automatic Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum] BAMS:PTg BIRNLEX:923 DHBA:12416 FMA:71108 HBA:9135 UMLS:C0228426 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=557 dorsal pons dorsal portion of pons tegmental portion of pons tegmentum of pons tegmentum pontis uberon pars dorsalis pontis pars posterior pontis tegmentum pontis UBERON:0003023 pontine tegmentum Brainstem:Abducens.png Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). BIRNLEX:923 UMLS:C0228426 BIRNLEX:923 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=557 BIRNLEX:923 dorsal portion of pons FMA:71108 tegmental portion of pons FMA:71108 tegmentum of pons FMA:71108 tegmentum pontis FMA:71108 FMA:TA pars dorsalis pontis NeuroNames:557 pars posterior pontis NeuroNames:557 tegmentum pontis A wall, dividing a cavity or structure into smaller ones[WP]. septal AAO:0011127 FMA:86461 OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ septa uberon UBERON:0003037 general anatomical term in FMA septum A wall, dividing a cavity or structure into smaller ones[WP]. septa The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. BIRNLEX:966 FMA:71167 MA:0003082 NCIT:C12894 UMLS:C0581620 pars thoracica medullae spinalis segmenta thoracica medullae spinalis [1-12] thoracic region of spinal cord thoracic segment of spinal cord thoracic segments of spinal cord [1-12] thoracic spinal cord uberon UBERON:0003038 thoracic spinal cord http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. UMLS:C0581620 BIRNLEX:966 UMLS:C0581620 ncithesaurus:Thoracic_Spinal_Cord pars thoracica medullae spinalis FMA:71167 FMA:TA segmenta thoracica medullae spinalis [1-12] FMA:71167 FMA:TA thoracic region of spinal cord FMA:71167 thoracic segment of spinal cord FMA:71167 thoracic segments of spinal cord [1-12] FMA:71167 thoracic spinal cord FMA:71167 A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] AAO:0011076 EFO:0003420 EHDAA2:0001232 EHDAA:1504 EMAPA:16543 FMA:293971 TAO:0000048 VHOG:0000186 XAO:0000005 ZFA:0000048 olfactory placodes placoda nasalis placoda olfactoria uberon nasal I placode nasal placode UBERON:0003050 Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic olfactory placode NCBIBook:NBK53171 ZFA EHDAA2 A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. XAO:0000005 We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] 2012-09-17 VHOG:0000186 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 olfactory placodes placoda nasalis placoda olfactoria An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP] Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG] The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG] MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305 UBERON:0004373 AAO:0011080 BTO:0002661 EHDAA2:0001342 EMAPA:16669 FMA:302920 NCIT:C34240 TAO:0000051 UMLS:C1518678 VHOG:0001148 XAO:0000006 ZFA:0000051 otic vesicle uberon OV acoustic vesicle auditory vesicle otocyst UBERON:0003051 ear vesicle http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray40.png An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP] MP:0009806 Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000051 TAO ZFIN:curator One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG] 2012-09-17 VHOG:0001148 VHOG The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG] 2012-09-17 VHOG:0001148 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413 MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305 MP UMLS:C1518678 ncithesaurus:Otic_Vesicle otic vesicle MP:0004311 acoustic vesicle VHOG:0001148 auditory vesicle BTO:0002661 otocyst MP:0004311 The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] AAO:0011064 DMBA:16810 EHDAA2:0004395 EHDAA:5789 EMAPA:32857 NCIT:C93172 TAO:0000042 VHOG:0000649 XAO:0000016 ZFA:0000042 MHB mid-hindbrain boundary mid-hindbrain junction midbrain hindbrain boundary uberon isthmic organizer territory isthmo-cerebellar region isthmus isthmus/MHB UBERON:0003052 midbrain-hindbrain boundary ZFA ZFA ZFA The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. GO:0021555 Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] 2012-09-17 VHOG:0000649 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) isthmic organizer territory XAO:0000016 isthmo-cerebellar region VHOG:0000649 isthmus/MHB Geisha:syn NCBITaxon:8782 A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP] In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html) EHDAA2:0001846 EHDAA:6538 FMA:295662 NCIT:C34247 TAO:0001185 UMLS:C1518973 VHOG:0001680 XAO:0000029 ZFA:0001185 skin periderm uberon EVL epidermis epithelial layer epidermis outer layer epitrichium periderm UBERON:0003055 periderm EHDAA2 EHDAA2 ZFA A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. ISBN:9780878932504 The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001185 TAO ZFIN:curator relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] 2012-08-14 TAO:0001185 TAO UMLS:C1518973 ncithesaurus:Periderm skin periderm EHDAA2:0001846 EVL ZFA:0001185 epitrichium MP:0013530 The portion of neural plate anterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011084 TAO:0007016 VHOG:0001200 XAO:0000045 ZFA:0007016 uberon anterior neural plate UBERON:0003056 pre-chordal neural plate The portion of neural plate anterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001200 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 The portion of neural plate posterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] TAO:0007017 VHOG:0001201 XAO:0000046 ZFA:0007017 uberon posterior neural plate UBERON:0003057 chordal neural plate The portion of neural plate posterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001201 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 EMAPA:16752 TAO:0000279 VHOG:0000559 XAO:0000057 ZFA:0000279 segmental plate unsegmented paraxial mesoderm uberon PSM presumptive somite mesoderm somitogenic mesoderm somitomeric mesoderm unsegmented mesenchyme UBERON:0003059 presomitic mesoderm Bgee:AN Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000279 TAO ZFIN:curator It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] 2012-09-17 VHOG:0000559 VHOG DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) unsegmented paraxial mesoderm somitomeric mesoderm GO:0002075 unsegmented mesenchyme VHOG:0000559 In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0011088 NCIT:C34279 TAO:0000150 UMLS:C1283945 VHOG:0000082 XAO:0000063 ZFA:0000150 uberon archinephric duct ductus pronephricus pronephric ducts UBERON:0003060 The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct GO Wikipedia XAO In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000150 TAO ZFIN:curator The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000082 VHOG (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] 2012-09-17 VHOG:0000082 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 UMLS:C1283945 ncithesaurus:Pronephric_Duct archinephric duct VHOG:0000082 ductus pronephricus pronephric ducts ZFA:0000150 Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 EHDAA:207 NCIT:C34113 TAO:0000094 TE:E5.11.2.0.0.0.4 UMLS:C1511224 VHOG:0000085 XAO:0000067 ZFA:0000094 blood islands uberon VBI caudal hematopoietic tissue posterior ICM posterior blood island ventral blood island UBERON:0003061 blood island Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000094 TAO ZFIN:curator Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] 2012-06-20 AAO:0011006 AAO AAO:EJS relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] 2012-08-14 TAO:0000094 TAO Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000085 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac EHDAA2 UMLS:C1511224 ncithesaurus:Blood_Island blood islands A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue TODO - check; developmental relationship to anterior hypoblast in ZFA? Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] UBERON:0004881 head mesenchyme head mesoderm AAO:0011085 EHDAA2:0001493 EHDAA:181 FMA:295532 TAO:0000060 VHOG:0000086 XAO:0000079 ZFA:0000060 uberon UBERON:0003063 prechordal plate ZFA PMID:16313393 A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue ISBN:0838580343 MP:0004387 Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000060 TAO ZFIN:curator Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] 2012-09-17 VHOG:0000086 VHOG There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] 2012-09-17 VHOG:0000086 VHOG DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008) head mesenchyme XAO:0000079 head mesoderm XAO:0000079 The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). AAO:0010575 EMAPA:16056 EMAPA:16178 FMA:293147 NCIT:C34193 TAO:0001206 UMLS:C1284010 VHOG:0000087 XAO:0000085 ZFA:0001206 uberon IM intermediate mesenchyme intermediate plate intermediate plate mesoderm mesenchyma intermedium UBERON:0003064 intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png AAO EMAPA XAO The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. GOC:curators Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] 2012-06-20 AAO:0010575 AAO AAO:EJS (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] 2012-09-17 VHOG:0000087 VHOG Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43 all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). ZFA UMLS:C1284010 ncithesaurus:Intermediate_Mesoderm intermediate mesenchyme intermediate plate EMAPA:16178 intermediate plate mesoderm mesenchyma intermedium The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, develops from visceral pouch 2 2 AAO:0010363 EHDAA2:0000050 EHDAA:611 EMAPA:16272 FMA:293017 NCIT:C34288 TAO:0001596 VHOG:0000297 XAO:0000098 ZFA:0001611 2nd pharyngeal arch arcus pharyngeus secundus branchial arch 2 hyoid arch pharyngeal arch 2 second branchial arch second pharyngeal arch second visceral arch visceral arch 2 uberon 2nd arch 2nd visceral arch hyoid bars pharyngeal arches 2 UBERON:0003066 pharyngeal arch 2 http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. ZFIN:yb The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010363 AAO XAO:EJS A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000297 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) in XAO, develops from visceral pouch 2 XAO arcus pharyngeus secundus branchial arch 2 hyoid arch XAO:0000098 second branchial arch second visceral arch visceral arch 2 2nd arch EHDAA2:0000050 2nd visceral arch VHOG:0000297 pharyngeal arches 2 VHOG:0000297 Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] TAO:0001310 VHOG:0000103 XAO:0000187 ZFA:0001310 dorsolateral placodes uberon UBERON:0003067 The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode dorsolateral placode NCBIBook:NBK53175 Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. ZFIN:curator In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000103 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) dorsolateral placodes ZFA:0001310 The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 VHOG:0000107 XAO:0000205 ZFA:0001204 uberon chordamesoderm UBERON:0003068 axial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. GO:0048318 The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000107 VHOG chordamesoderm A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK] Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). AAO:0011079 EFO:0003429 EHDAA2:0001339 EHDAA:506 EMAPA:16195 FMA:293973 NCIT:C34239 TAO:0000138 UMLS:C1518677 VHOG:0000235 XAO:0000223 ZFA:0000138 placoda otica uberon auditory placode ear placode ear/otic placode octaval VIII placode octaval placode UBERON:0003069 otic placode invaginates NCBIBook:NBK53175 A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK] NCBIBook:NBK53175 Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] 2012-08-14 TAO:0000138 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] 2012-09-17 VHOG:0000235 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). NCBIBook:NBK53175 UMLS:C1518677 ncithesaurus:Otic_Placodes placoda otica octaval VIII placode ISBN:0471888893 octaval placode ISBN:0471888893 A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...' EFO:0003433 EHDAA2:0004209 TAO:0000162 VHOG:0000109 XAO:0000225 ZFA:0000162 trigeminal V placode trigeminal placode uberon profundus V placode profundus placode trigeminal placodes UBERON:0003070 trigeminal placode complex ISBN:0471888893 A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] XAO The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000162 TAO ZFIN:curator The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000109 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) trigeminal placode EHDAA2:0004209 VHOG:0000109 XAO:0000225 ZFA:0000162 profundus V placode ISBN:0471888893 profundus placode ISBN:0471888893 trigeminal placodes ZFA:0000162 Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. UBERON:0005060 AAO:0011038 EFO:0003541 EHDAA2:0004431 TAO:0000570 XAO:0000227 XAO:0004090 ZFA:0000570 eye placode occular primordium ocular primordium optic placode optic placode of camera-type eye optic primordium uberon eye anlage eye field optic field optic placodes UBERON:0003071 eye primordium EHDAA2 XAO Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. GO:0046619 ZFA:0000570 TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. GO eye placode OBOL:automatic optic placode GO:0046619 optic placode of camera-type eye GO:0046619 eye anlage XAO:0000227 optic placodes Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] BTO:0005351 EHDAA2:0001303 EHDAA:2912 EMAPA:16674 NCIT:C34233 TAO:0001202 UMLS:C0231109 VHOG:0000167 ZFA:0001202 uberon eye cup eyecup ocular cup ophtalmic cup UBERON:0003072 optic cup ZFA ZFA Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. MP:0004269 ZFA:0001202 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] 2012-09-17 VHOG:0000167 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C0231109 ncithesaurus:Optic_Cup eyecup BTO:0005351 ocular cup VHOG:0000167 ophtalmic cup BTO:0005351 A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) AAO:0011055 EFO:0003494 EHDAA2:0000982 EHDAA:2908 EMAPA:16672 FMA:296767 NCIT:C34202 TAO:0000122 UMLS:C1517770 VHOG:0000166 XAO:0000240 ZFA:0000122 uberon lens placodes placoda lentis UBERON:0003073 lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png NCBIBook:NBK53175 A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. ZFIN:curator Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000122 TAO ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000166 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) NCBIBook:NBK53175 UMLS:C1517770 ncithesaurus:Lens_Placodes lens placodes ZFA:0000122 placoda lentis Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts. AAO:0000637 EHDAA2:0001243 EHDAA:1590 EMAPA:16577 GAID:1315 MESH:A16.254.940 NCIT:C26469 TAO:0000546 UMLS:C0043204 VHOG:0000082 XAO:0000242 ZFA:0000546 Wolffian duct uberon Leydig's duct archinephric duct ductus mesonephricus; ductus Wolffi renal duct UBERON:0003074 mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png GO EHDAA2 Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. ZFIN:curator Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] 2012-06-20 AAO:0000637 AAO AAO:BJB The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000082 VHOG (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] 2012-09-17 VHOG:0000082 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 UMLS:C0043204 ncithesaurus:Mesonephric_Duct Wolffian duct GOC:yaf ZFA:0000546 Leydig's duct archinephric duct VHOG:0000082 ductus mesonephricus; ductus Wolffi A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 DMBA:15565 EHDAA:346 EHDAA:902 EMAPA:35593 FMA:293879 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 UMLS:C0920623 VHOG:0000068 XAO:0000249 ZFA:0000132 uberon lamina neuralis presumptive central nervous system UBERON:0003075 neural plate Neural:Crest.png Wikipedia Bgee:AN A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] ISBN:0815318960 OMD:neural+plate ZFIN:curator The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000132 TAO ZFIN:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000068 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 UMLS:C0920623 ncithesaurus:Neural_Plate lamina neuralis (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011082 TAO:0007037 VHOG:0001383 XAO:0000250 ZFA:0007037 uberon UBERON:0003076 posterior neural tube lexical (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001383 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 EMAPA:16751 FMA:293145 NCIT:C34244 TAO:0000255 UMLS:C1284009 VHOG:0000114 XAO:0000259 ZFA:0000255 paraxial mesenchyme somitic mesoderm uberon mesoderma paraxiale UBERON:0003077 paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 Bgee:AN The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] GO:0048339 Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] 2012-06-20 AAO:0010568 AAO AAO:EJS Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] 2012-09-17 VHOG:0000114 VHOG DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) ZFA UMLS:C1284009 ncithesaurus:Paraxial_Mesoderm paraxial mesenchyme ZFA:0000255 somitic mesoderm ISBN:9780878932504 mesoderma paraxiale Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group AAO:0011036 EFO:0003455 FMA:293968 TAO:0001294 VHOG:0000117 XAO:0000284 ZFA:0001294 epibranchial placodes uberon ventrolateral placode UBERON:0003078 epibranchial placode NCBIBook:NBK53175 ZFA ZFA EHDAA2-abduced Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. VHOG:0000117 Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] 2012-09-17 VHOG:0000117 VHOG These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000117 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001) Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively NCBIBook:NBK53175 in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group XAO epibranchial placodes ZFA:0001294 ventrolateral placode ISBN:0471888893 TODO - add grouping class for the anterior end of the neural tube at all stages (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011012 TAO:0007038 VHOG:0001384 XAO:0000307 ZFA:0007038 uberon UBERON:0003080 anterior neural tube lexical (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001384 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 EMAPA:16179 FMA:293149 NCIT:C34199 TAO:0000121 UMLS:C1517749 VHOG:0000118 XAO:0000311 ZFA:0000121 LPM lateral mesoderm uberon lateral plate lateral plate mesenchyme mesoderma laminae lateralis UBERON:0003081 lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 EHDAA2 VHOG Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. MP:0010117 Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] 2012-06-20 AAO:0010574 AAO AAO:EJS The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000118 VHOG A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] 2012-09-17 VHOG:0000118 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) subclass of mesoderm in ZFA. ZFA UMLS:C1517749 ncithesaurus:Lateral_Mesoderm LPM ZFA:0000121 lateral mesoderm GO:0048368 lateral plate mesenchyme EHDAA2:0000919 mesoderma laminae lateralis A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] AAO:0011067 AEO:0001018 BTO:0000742 EHDAA2_RETIRED:0003431 EHDAA:1721 EHDAA:1727 EHDAA:1733 EHDAA:1739 EMAPA:32841 FMA:295658 NCIT:C34214 TAO:0001056 UMLS:C1513802 VHOG:0001244 XAO:0000315 ZFA:0001056 myomeres uberon muscle plate myomere myotome region myotomes myotomus UBERON:0003082 myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. AEO:0001018 Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001056 TAO ZFIN:curator In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] 2012-09-17 VHOG:0001244 VHOG DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003) UMLS:C1513802 ncithesaurus:Myotome_Region myomeres TAO:0001056 myotomus Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010582 EFO:0003605 EHDAA2:0001901 TAO:0001024 VHOG:0000062 XAO:0000319 ZFA:0001024 TNC uberon trunk crest UBERON:0003083 trunk neural crest Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. ISBN:0815318960 Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] 2012-06-20 AAO:0010582 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000062 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 TNC XAO:0000319 Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 TAO:0000028 UMLS:C1514450 XAO:0000336 ZFA:0000028 uberon cardiac field fused heart primordium UBERON:0003084 heart primordium Obol ZFA ZFA XAO Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] 2012-08-14 TAO:0000028 TAO ZFIN:curator The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] 2012-06-20 AAO:0011044 AAO XAO:curator relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] 2012-08-14 TAO:0000028 TAO UMLS:C1514450 ncithesaurus:Primordium_of_the_Heart cardiac field ZFA:0000028 Extension of the dorsal aorta in the tail. Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO] The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO] AAO:0011023 EFO:0003472 TAO:0000011 VHOG:0000123 XAO:0000364 ZFA:0000011 uberon CA UBERON:0003086 caudal artery Extension of the dorsal aorta in the tail. ZFIN:curator Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000011 TAO ZFIN:curator The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO] 2012-06-20 AAO:0011023 AAO ISBN:0-226-55763-4 Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] part_of somite in XAO AAO:0010571 AEO:0000212 EHDAA2:0003439 EMAPA:31159 FMA:295652 NCIT:C34287 TAO:0001080 UMLS:C0183176 VHOG:0000680 XAO:0000397 ZFA:0001080 sclerotomes uberon sclerotomus UBERON:0003089 sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png EHDAA2 EHDAA2 ZFA Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. XB:curator Skeletogenic portion of somites.[AAO] 2012-06-20 AAO:0010571 AAO AAO:EJS The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] 2012-09-17 VHOG:0000680 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) part_of somite in XAO XAO UMLS:C0183176 ncithesaurus:Sclerotome sclerotomes TAO:0001080 sclerotomus The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus. Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]. In all vertebrates the thyroid arises from the ventral aspect of the second pouch Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm AAO:0011106 BTO:0004709 EHDAA2:0002033 EHDAA:952 EMAPA:16361 NCIT:C34312 TAO:0001081 UMLS:C1519512 XAO:0000444 ZFA:0001081 uberon thyroid primordia UBERON:0003091 thyroid primordium ZFA ZFA VHOG ISBN:0073040584 The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus. Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]. ZFIN:curator In all vertebrates the thyroid arises from the ventral aspect of the second pouch Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm EHDAA2 UMLS:C1519512 ncithesaurus:Thyroid_Primordium thyroid primordia ZFA:0001081 neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] Neural crest that is part of the head.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010580 EFO:0003645 EHDAA2:0004420 EMAPA:16091 TAO:0001194 VHOG:0000063 XAO:0001001 ZFA:0001194 CNC cephalic neural crest cranial NCC population head NCC population uberon crista neuralis cranialis head crest head neural crest UBERON:0003099 cranial neural crest neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. MGI:anna Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] 2012-06-20 AAO:0010580 AAO AAO:EJS Neural crest that is part of the head.[TAO] 2012-08-14 TAO:0001194 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000063 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 CNC XAO:0001001 cephalic neural crest EMAPA:16091 crista neuralis cranialis Gonochoristic organism that can produce female gametes. AAO:0010030 BILA:0000028 CARO:0000028 FBbt:00007011 FMA:67812 HAO:0000028 TAO:0000303 TGMA:0001839 XAO:0003005 ZFA:0000303 female human body uberon female UBERON:0003100 female organism Gonochoristic organism that can produce female gametes. CARO:0000028 female human body FMA:67812 female TAO:0000303 Gonochoristic organism that can produce male gametes. AAO:0010033 BILA:0000027 CARO:0000027 FBbt:00007004 FMA:67811 HAO:0000027 TAO:0000242 TGMA:0001838 WBbt:0007850 XAO:0003006 ZFA:0000242 male human body uberon male UBERON:0003101 male organism Gonochoristic organism that can produce male gametes. CARO:0000027 male human body FMA:67811 male TAO:0000242 Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. consider obsoleting. See issue/1305 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] AAO:0010337 AEO_RETIRED:0000010 EHDAA2_RETIRED:0003010 TAO:0000292 VSAO:0000001 XAO:0003028 ZFA:0000292 galen:SurfaceRegion anatomical surface feature uberon surface feature surface region surface structures UBERON:0003102 surface structure Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] 2012-08-14 TAO:0000292 TAO ZFIN:curator anatomical surface feature EHDAA2:0003010 surface structures ZFA:0000292 Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 CARO:0000024 EHDAA2:0003024 HAO:0000024 TADS:0000598 TAO:0000496 TGMA:0001837 VHOG:0001723 XAO:0003041 ZFA:0000496 uberon organ UBERON:0003103 compound organ Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. CARO:0000024 Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 CALOHA:TS-0620 EHDAA2:0003145 EV:0100007 NCIT:C13301 TAO:0000393 UMLS:C0162415 VHOG:0000170 XAO:0003046 ZFA:0000393 mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue uberon mesenchyma UBERON:0003104 mesenchyme http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. BTO:0001393 ZFIN:curator A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000393 TAO ZFIN:curator Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] 2012-06-20 AAO:0010427 AAO AAO:EJS UMLS:C0162415 ncithesaurus:Mesenchyme mesenchyma Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ. Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO] Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO] AAO:0010206 EFO:0003525 NCIT:C98765 TAO:0000351 XAO:0003172 ZFA:0000351 uberon ethmoid region UBERON:0003112 olfactory region Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ. TAO:0000351 Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO] 2012-08-14 TAO:0000351 TAO TAO:MAH Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO] 2012-06-20 AAO:0010206 AAO AAO:EJS ethmoid region ZFA:0000351 Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] AAO:0010154 TAO:0000863 VHOG:0001665 XAO:0003169 ZFA:0000863 dendrocranium exocranium dermal skull roof dermatocranial cover roof of skull skull roof uberon dermal bone cranium dermal part of skull dermal skull bones roofing bones of the skull skull exoskeleton UBERON:0003113 dermatocranium Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. ZFA:0000863 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] 2012-08-14 TAO:0000863 TAO ZFIN:curator Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] 2012-06-20 AAO:0010154 AAO AAO:BJB dendrocranium TAO:0000863 exocranium UBERONREF:0000007 dermal skull roof roof of skull skull roof dermal bone cranium ZFA:0000863 roofing bones of the skull The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, called branchial arch 1 and df VP3 3 AAO:0010365 EHDAA2:0000069 EHDAA:1080 EMAPA:16399 FMA:293029 TAO:0001598 VHOG:0000298 XAO:0000447 ZFA:0001606 3rd pharyngeal arch first gill arch gill arch 1 third pharyngeal arch third visceral arch visceral arch 3 uberon 3rd arch 3rd visceral arch branchial arch 1 first branchial arch UBERON:0003114 pharyngeal arch 3 The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. MP:0006339 The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO] 2012-06-20 AAO:0010365 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000298 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) in XAO, called branchial arch 1 and df VP3 XAO first gill arch ZFA:0001606 gill arch 1 ZFA:0001606 3rd arch EHDAA2:0000069 3rd visceral arch VHOG:0000298 branchial arch 1 AAO:0010365 ZFA:0001606 first branchial arch ZFA:0001606 contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, called branchial arch 2 and df VP4 4 AAO:0010366 EHDAA2:0000086 EHDAA:1663 EMAPA:16760 FMA:293035 TAO:0001599 VHOG:0000299 XAO:0000449 ZFA:0001607 4th branchial arch 4th pharyngeal arch 4th visceral arch fourth pharyngeal arch gill arch 2 second gill arch visceral arch 4 uberon 4th arch branchial arch 2 fourth visceral arch second branchial arch UBERON:0003115 pharyngeal arch 4 contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus MP:0006340 The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] 2012-06-20 AAO:0010366 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000299 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) in XAO, called branchial arch 2 and df VP4 XAO 4th branchial arch gill arch 2 ZFA:0001607 second gill arch ZFA:0001607 4th arch EHDAA2:0000086 branchial arch 2 AAO:0010366 ZFA:0001607 fourth visceral arch VHOG:0000299 second branchial arch ZFA:0001607 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 6 UBERON:0004349 AAO:0010368 EHDAA2:0004075 EMAPA:32766 FMA:293047 TAO:0001601 VHOG:0001205 XAO:0000453 ZFA:0001609 6th arch gill arch 4 sixth branchial arch visceral arch 6 uberon 6th pharyngeal arch 6th visceral arch branchial arch 4 fourth branchial arch sixth pharyngeal arch sixth visceral arch UBERON:0003117 pharyngeal arch 6 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles MP:0006347 The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] 2012-06-20 AAO:0010368 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0001205 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) 6th arch EHDAA2:0004075 gill arch 4 ZFA:0001609 visceral arch 6 ZFA:0001609 6th pharyngeal arch VHOG:0001205 6th visceral arch VHOG:0001205 branchial arch 4 AAO:0010368 ZFA:0001609 fourth branchial arch sixth pharyngeal arch VHOG:0001205 sixth visceral arch XAO:0000453 The vessels formed within the first pair of branchial arches in embryogenesis Disappears early in development in tetrapods ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas UBERON:0004371 AAO:0010415 EHDAA2:0000007 EMAPA:16202 EMAPA:16685 TAO:0005005 VHOG:0000149 XAO:0000342 ZFA:0005005 1st arch artery AA1 aortic arch 1 first aortic arch first branchial arch artery mandibular aortic arch uberon 1st aortic arch artery 1st branchial arch artery 1st pharyngeal arch artery first arch artery UBERON:0003118 pharyngeal arch artery 1 The vessels formed within the first pair of branchial arches in embryogenesis MP:0010355 ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas ZFA 1st arch artery EMAPA:16685 AA1 ZFA:0005005 aortic arch 1 ZFA:0005005 first aortic arch XAO:0000342 mandibular aortic arch ZFA:0005005 1st aortic arch artery EMAPA:16685 1st branchial arch artery EMAPA:16685 1st pharyngeal arch artery EMAPA:16685 first arch artery EMAPA:16685 The vessels formed within the second pair of branchial arches in embryogenesis The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]. The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO] UBERON:0004372 AAO:0010418 EHDAA2:0000051 EMAPA:16203 EMAPA:16686 TAO:0005006 VHOG:0000148 XAO:0000343 ZFA:0005006 2nd arch artery AA2 aortic arch 2 hyoid aortic arch second aortic arch second branchial arch artery uberon 2nd aortic arch artery 2nd branchial arch artery 2nd pharyngeal arch artery UBERON:0003119 pharyngeal arch artery 2 The vessels formed within the second pair of branchial arches in embryogenesis MP:0010356 The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]. The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO] 2012-06-20 AAO:0010418 AAO ISBN:0-02-377110-0 2nd arch artery EHDAA2:0000051 AA2 ZFA:0005006 aortic arch 2 ZFA:0005006 hyoid aortic arch ZFA:0005006 second aortic arch XAO:0000343 2nd aortic arch artery EMAPA:16686 2nd branchial arch artery EMAPA:16686 2nd pharyngeal arch artery EMAPA:16686 The vessels formed within the third pair of branchial arches in embryogenesis Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]. The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] UBERON:0004352 AAO:0010419 EHDAA2:0000070 EMAPA:16687 TAO:0005007 VHOG:0000147 XAO:0000344 ZFA:0005007 3rd arch artery AA3 aortic arch 3 carotid arch third aortic arch third branchial arch artery uberon 3rd aortic arch artery 3rd branchial arch artery 3rd pharyngeal arch artery UBERON:0003120 pharyngeal arch artery 3 The vessels formed within the third pair of branchial arches in embryogenesis MP:0006356 Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005007 TAO ZFIN:curator The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]. The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] 2012-06-20 AAO:0010419 AAO ISBN:0-02-377110-0 3rd arch artery EHDAA2:0000070 AA3 ZFA:0005007 aortic arch 3 ZFA:0005007 carotid arch third aortic arch XAO:0000344 3rd aortic arch artery EMAPA:16687 3rd branchial arch artery EMAPA:16687 3rd pharyngeal arch artery EMAPA:16687 The vessels formed within the fourth pair of branchial arches in embryogenesis Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta UBERON:0004350 AAO:0010420 EHDAA2:0000087 EMAPA:17004 TAO:0005008 XAO:0000355 ZFA:0005008 4th arch artery AA4 aortic arch 4 fourth aortic arch fourth branchial arch artery uberon 4th aortic arch artery 4th branchial arch artery 4th pharyngeal arch artery systemic arch UBERON:0003121 proximal right subclavian pharyngeal arch artery 4 The vessels formed within the fourth pair of branchial arches in embryogenesis MP:0006354 Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005008 TAO ZFIN:curator The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] 2012-06-20 AAO:0010420 AAO ISBN:0-02-377110-0 The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. 4th arch artery EHDAA2:0000087 AA4 ZFA:0005008 aortic arch 4 ZFA:0005008 fourth aortic arch XAO:0000355 4th aortic arch artery EMAPA:17004 4th branchial arch artery EMAPA:17004 4th pharyngeal arch artery EMAPA:17004 systemic arch ISBN:0073040584 XAO:0000355 The vessels formed within the sixth pair of branchial arches in embryogenesis The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries UBERON:0004351 AAO:0010422 EHDAA2:0000102 EMAPA:17005 TAO:0005016 VHOG:0000144 XAO:0000353 ZFA:0005016 6th arch artery AA6 aortic arch 6 sixth aortic arch sixth branchial arch artery uberon 6th aortic arch artery 6th branchial arch artery 6th pharyngeal arch artery pulmonary arch UBERON:0003123 pharyngeal arch artery 6 The vessels formed within the sixth pair of branchial arches in embryogenesis MP:0006355 The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005016 TAO ZFIN:curator The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] 2012-06-20 AAO:0010422 AAO ISBN:0-02-377110-0 The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries 6th arch artery EMAPA:17005 AA6 ZFA:0005016 aortic arch 6 ZFA:0005016 sixth aortic arch XAO:0000353 6th aortic arch artery EMAPA:17005 6th branchial arch artery EMAPA:17005 6th pharyngeal arch artery EMAPA:17005 pulmonary arch ISBN:0073040584 the outermost extraembryonic membrane The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG] The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252]. Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] chorionic The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN:0073040584] Extra-embryonic ectoderm BTO:0000252 CALOHA:TS-0144 EFO:0002780 EHDAA2:0000245 EHDAA:150 EMAPA:16112 EV:0100121 FMA:80224 GAID:1299 MESH:A16.254.403.473 NCIT:C34122 NCIT:C34124 UMLS:C0008503 UMLS:C1516505 VHOG:0000200 chorion chorion (vertebrates) embryonic chorion fetal chorion uterine chorion uberon chorion frondosum chorionic sac UBERON:0003124 chorion membrane http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png ISBN:0073040584 the outermost extraembryonic membrane MESH:A10.615.284.473 MP:0002836 The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG] 2012-09-17 VHOG:0000200 VHOG The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252]. BTO:0000252 Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] 2012-09-17 VHOG:0000200 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 Extra-embryonic ectoderm UMLS:C0008503 ncithesaurus:Chorion UMLS:C1516505 ncithesaurus:Chorionic_Sac uterine chorion ZFIN:curator chorion frondosum chorionic sac The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. An elongated tube which carries air to and from the lungs.[AAO] The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] tracheal In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx. in mouse 15-18 C-rings, 15-20 in human. AAO:0010140 BTO:0001388 CALOHA:TS-1060 EFO:0000935 EHDAA2:0002066 EHDAA:3078 EMAPA:16853 EV:0100040 FMA:7394 GAID:361 MA:0000441 MAT:0000137 MESH:D014132 MIAA:0000137 NCIT:C12428 OpenCyc:Mx4rvViOX5wpEbGdrcN5Y29ycA UMLS:C0040578 VHOG:0000371 XAO:0000118 cartilaginous trachea vertebrate trachea windpipe uberon tracheal tubule UBERON:0003126 trachea http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg EHDAA2 The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. GO:0060438 An elongated tube which carries air to and from the lungs.[AAO] 2012-06-20 AAO:0010140 AAO AAO:BJB The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000371 VHOG In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] 2012-09-17 VHOG:0000371 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409 in mouse 15-18 C-rings, 15-20 in human. ISBN:0123813611 UMLS:C0040578 ncithesaurus:Trachea vertebrate trachea tracheal tubule BTO:0001388 Upper portion of the skull that excludes the mandible (when present in the organism). cranial the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton BTO:0001328 EFO:0000831 EHDAA:6029 EMAPA:17680 FMA:71325 MA:0000316 MAT:0000340 MIAA:0000340 OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA VHOG:0000334 bones of cranium ossa cranii set of bones of cranium skull minus mandible upper part of skull uberon calvarium epicranial plate skeletal system of head UBERON:0003128 cranium FMA-inferred Upper portion of the skull that excludes the mandible (when present in the organism). the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium FMA The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton WP bones of cranium FMA:71325 ossa cranii FMA:71325 FMA:TA set of bones of cranium FMA:71325 calvarium BTO:0001328 Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates BTO:0001295 CALOHA:TS-2344 EHDAA2:0000325 EMAPA:17680 FMA:46565 GAID:82 MESH:D012886 NCIT:C12789 OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA UMLS:C0037303 WikipediaCategory:Skull galen:Skull uberon cranial skeleton skeletal system of head UBERON:0003129 skull FMA Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. FMA A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates WP UMLS:C0037303 ncithesaurus:Skull An organ involved in reproduction GO uses genitalia for the singular organ EMAPA:17381 EMAPA:37731 MA:0001752 MESH:D005835 NCIT:C25177 OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA TGMA:0000591 UMLS:C0017420 WBbt:0008422 genital organ reproductive system organ sex organ uberon genitalia UBERON:0003133 reproductive organ An organ involved in reproduction UBERON:xp GO uses genitalia for the singular organ GO EMAPA:37731 MA:th UMLS:C0017420 ncithesaurus:Genitalia genitalia A female organ involved in reproduction EMAPA:28540 MA:0000544 female organism reproductive organ female organism reproductive structure female organism reproductive system organ female organism sex organ female reproductive gland/organ female reproductive system organ female sex organ reproductive organ of female organism reproductive structure of female organism reproductive system organ of female organism sex organ of female organism uberon UBERON:0003134 female reproductive organ A female organ involved in reproduction UBERON:xp female organism reproductive organ OBOL:automatic female organism reproductive structure OBOL:automatic female organism reproductive system organ OBOL:automatic female organism sex organ OBOL:automatic female reproductive gland/organ MA:0000544 reproductive organ of female organism OBOL:automatic reproductive structure of female organism OBOL:automatic reproductive system organ of female organism OBOL:automatic sex organ of female organism OBOL:automatic A male organ involved in reproduction MA:0000545 male organism reproductive organ male organism reproductive structure male organism reproductive system organ male organism sex organ male reproductive gland/organ male reproductive system organ male sex organ reproductive organ of male organism reproductive structure of male organism reproductive system organ of male organism sex organ of male organism uberon UBERON:0003135 male reproductive organ A male organ involved in reproduction UBERON:xp male organism reproductive organ OBOL:automatic male organism reproductive structure OBOL:automatic male organism reproductive system organ OBOL:automatic male organism sex organ OBOL:automatic male reproductive gland/organ MA:0000545 reproductive organ of male organism OBOL:automatic reproductive structure of male organism OBOL:automatic reproductive system organ of male organism OBOL:automatic sex organ of male organism OBOL:automatic Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBbt:00005159 FMA:77853 gustatory organ system organ gustatory system organ organ of gustatory organ system organ of gustatory system organ of taste system taste organ taste system organ uberon UBERON:0003212 gustatory organ Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBC:auto_generated_definition gustatory organ system organ OBOL:automatic gustatory system organ OBOL:automatic organ of gustatory organ system OBOL:automatic organ of gustatory system OBOL:automatic organ of taste system OBOL:automatic taste system organ OBOL:automatic Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. uberon UBERON:0003218 ovary septum Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. GO:0080126 one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO] A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] EHDAA2:0004062 EHDAA:4041 EHDAA:5021 EHDAA:5915 EMAPA:17375 VHOG:0000540 metanephric blastema metanephric mesoderm metanephrogenic mesenchyme metanephros associated mesenchyme uberon UBERON:0003220 Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme ISBN:9780878932504 one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO] GO:0072075 A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] 2012-09-17 VHOG:0000540 VHOG When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] 2012-09-17 VHOG:0000540 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462 metanephric blastema metanephric mesoderm metanephrogenic mesenchyme EHDAA:5021 metanephros associated mesenchyme RETIRED_EHDAA2:0001139 Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits. phalangeal In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three CALOHA:TS-2211 EMAPA:32614 FMA:321661 MA:0000304 NCIT:C33317 OpenCyc:Mx4rvolPZpwpEbGdrcN5Y29ycA UMLS:C0222682 VSAO:0000199 galen:Phalanx digit long bone long bone of digit phalange phalanges phalanx bone uberon UBERON:0003221 phalanx Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits. VSAO:0000199 In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three WP UMLS:C0222682 ncithesaurus:Phalanx digit long bone OBOL:automatic long bone of digit OBOL:automatic phalanges phalanx bone An epithelium that is part of a elbow [Automatically generated definition]. EHDAA2:0000430 EHDAA:4168 EHDAA:6214 EMAPA:17415 VHOG:0001044 cubital region epithelial tissue cubital region epithelium elbow epithelial tissue elbow epithelium epithelial tissue of cubital region epithelial tissue of elbow epithelium of cubital region uberon UBERON:0003229 epithelium of elbow EHDAA2 An epithelium that is part of a elbow [Automatically generated definition]. OBOL:automatic cubital region epithelial tissue OBOL:automatic cubital region epithelium OBOL:automatic elbow epithelial tissue OBOL:automatic elbow epithelium OBOL:automatic epithelial tissue of cubital region OBOL:automatic epithelial tissue of elbow OBOL:automatic epithelium of cubital region OBOL:automatic An epithelium that is part of a wrist [Automatically generated definition]. EHDAA2:0000219 EHDAA:5198 carpal region epithelial tissue carpal region epithelium epithelial tissue of carpal region epithelial tissue of wrist epithelium of wrist wrist epithelial tissue wrist epithelium uberon UBERON:0003230 epithelium of carpal region EHDAA2 EHDAA2 An epithelium that is part of a wrist [Automatically generated definition]. OBOL:automatic carpal region epithelial tissue OBOL:automatic carpal region epithelium OBOL:automatic epithelial tissue of carpal region OBOL:automatic epithelial tissue of wrist OBOL:automatic epithelium of wrist OBOL:automatic wrist epithelial tissue OBOL:automatic wrist epithelium OBOL:automatic An epithelium that is part of a hip [Automatically generated definition]. EHDAA2:0000784 EHDAA:5155 EHDAA:6180 EMAPA:17491 VHOG:0000779 epithelial tissue of hip epithelial tissue of hip region epithelial tissue of regio coxae epithelium of hip region epithelium of regio coxae hip epithelial tissue hip epithelium hip region epithelial tissue hip region epithelium regio coxae epithelial tissue regio coxae epithelium uberon UBERON:0003231 epithelium of hip EHDAA2 An epithelium that is part of a hip [Automatically generated definition]. OBOL:automatic epithelial tissue of hip OBOL:automatic epithelial tissue of hip region OBOL:automatic epithelial tissue of regio coxae OBOL:automatic epithelium of hip region OBOL:automatic epithelium of regio coxae OBOL:automatic hip epithelial tissue OBOL:automatic hip epithelium OBOL:automatic hip region epithelial tissue OBOL:automatic hip region epithelium OBOL:automatic regio coxae epithelial tissue OBOL:automatic regio coxae epithelium OBOL:automatic An epithelium that is part of a shoulder [Automatically generated definition]. EHDAA2:0001835 EHDAA:4182 EHDAA:6230 EMAPA:17422 VHOG:0000761 epithelial tissue of shoulder shoulder epithelial tissue shoulder epithelium uberon UBERON:0003233 epithelium of shoulder EHDAA2 An epithelium that is part of a shoulder [Automatically generated definition]. OBOL:automatic epithelial tissue of shoulder OBOL:automatic shoulder epithelial tissue OBOL:automatic shoulder epithelium OBOL:automatic An epithelium that is part of a lower jaw [Automatically generated definition]. EHDAA2:0001019 EHDAA:7999 EMAPA:35516 VHOG:0000802 epithelial tissue of lower jaw epithelial tissue of ventral mandibular arch epithelium of ventral mandibular arch lower jaw epithelial tissue lower jaw epithelium ventral mandibular arch epithelial tissue ventral mandibular arch epithelium uberon UBERON:0003236 epithelium of lower jaw An epithelium that is part of a lower jaw [Automatically generated definition]. OBOL:automatic epithelial tissue of lower jaw OBOL:automatic epithelial tissue of ventral mandibular arch OBOL:automatic epithelium of ventral mandibular arch OBOL:automatic lower jaw epithelial tissue OBOL:automatic lower jaw epithelium OBOL:automatic ventral mandibular arch epithelial tissue OBOL:automatic ventral mandibular arch epithelium OBOL:automatic An epithelium that is part of a lower arm [Automatically generated definition]. EHDAA2:0000554 EHDAA:4174 EHDAA:6220 EMAPA:17418 VHOG:0001096 forearm epithelium uberon UBERON:0003247 epithelium of forearm EHDAA2 An epithelium that is part of a lower arm [Automatically generated definition]. OBOL:automatic An epithelium that is part of a footplate. EHDAA2:0000548 EHDAA:5145 EHDAA:6144 EMAPA:32655 foot plate epithelium footplate epithelium uberon UBERON:0003248 epithelium of footplate EHDAA2 EHDAA2 An epithelium that is part of a footplate. OBOL:automatic footplate epithelium EHDAA2:0000548 An epithelium that is part of a otic placode [Automatically generated definition]. check ZFA, placemeant, appears to refer to both adult structures and primordium EHDAA2:0001341 EHDAA:510 EMAPA:16197 VHOG:0000636 ZFA:0007068 epithelial tissue of otic placode otic epithelium otic placode epithelial tissue otic placode epithelium uberon UBERON:0003249 epithelium of otic placode An epithelium that is part of a otic placode [Automatically generated definition]. OBOL:automatic epithelial tissue of otic placode OBOL:automatic otic epithelium otic placode epithelial tissue OBOL:automatic otic placode epithelium OBOL:automatic Subdivision of skeletal system that consists of all ribs in an organism connected to the sternum and the vertebrae. Some vertebrates have abdominal ribs (gastrialia), not connected to the vertebrate - these are not considered part of the rib case. Anatomical cluster that consists of more than one rib in an individual.[TAO] FMA:7480 galen:RibCage cavea thoracis rib cage thoracic cage uberon cavea thoracis UBERON:0003252 thoracic rib cage http://upload.wikimedia.org/wikipedia/commons/8/88/Gray112.png Subdivision of skeletal system that consists of all ribs in an organism connected to the sternum and the vertebrae. Some vertebrates have abdominal ribs (gastrialia), not connected to the vertebrate - these are not considered part of the rib case. Anatomical cluster that consists of more than one rib in an individual.[TAO] 2012-08-14 TAO:0002100 TAO TAO:wd cavea thoracis FMA:7480 FMA:TA rib cage FMA:7480 thoracic cage FMA:7480 cavea thoracis The neck of the rib is the flattened portion which extends lateralward from the head; it is about 2.5 cm. long, and is placed in front of the transverse process of the lower of the two vertebrC& with which the head articulates. Its anterior surface is flat and smooth, its posterior rough for the attachment of the ligament of the neck, and perforated by numerous foramina. Of its two borders the superior presents a rough crest (crista colli costE) for the attachment of the anterior costotransverse ligament; its inferior border is rounded. On the posterior surface at the junction of the neck and body, and nearer the lower than the upper border, is an eminencebthe tubercle; it consists of an articular and a non-articular portion. The articular portion, the lower and more medial of the two, presents a small, oval surface for articulation with the end of the transverse process of the lower of the two vertebrC& to which the head is connected. The non-articular portion is a rough elevation, and affords attachment to the ligament of the tubercle. The tubercle is much more prominent in the upper than in the lower ribs. EMAPA:37826 FMA:7576 collum costae rib neck uberon collum costae UBERON:0003253 neck of rib http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray122.png The neck of the rib is the flattened portion which extends lateralward from the head; it is about 2.5 cm. long, and is placed in front of the transverse process of the lower of the two vertebrC& with which the head articulates. Its anterior surface is flat and smooth, its posterior rough for the attachment of the ligament of the neck, and perforated by numerous foramina. Of its two borders the superior presents a rough crest (crista colli costE) for the attachment of the anterior costotransverse ligament; its inferior border is rounded. On the posterior surface at the junction of the neck and body, and nearer the lower than the upper border, is an eminencebthe tubercle; it consists of an articular and a non-articular portion. The articular portion, the lower and more medial of the two, presents a small, oval surface for articulation with the end of the transverse process of the lower of the two vertebrC& to which the head is connected. The non-articular portion is a rough elevation, and affords attachment to the ligament of the tubercle. The tubercle is much more prominent in the upper than in the lower ribs. EMAPA:37826 MA:th collum costae rib neck FMA:7576 collum costae The portion of the yolk sac that is derived from endoderm and lines the yolk sac. EHDAA2:0002215 EHDAA:166 EMAPA:16086 VHOG:0000626 uberon UBERON:0003257 yolk sac endoderm EHDAA2 The portion of the yolk sac that is derived from endoderm and lines the yolk sac. UBERON:cjm An endoderm that is part of a foregut [Automatically generated definition]. TODO - check EHDAA2:0004568 EHDAA:524 foregut endoderm uberon UBERON:0003258 endoderm of foregut An endoderm that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut endoderm OBOL:automatic An endoderm that is part of a midgut [Automatically generated definition]. TODO - check EHDAA:987 EMAPA:16257 RETIRED_EHDAA2:0001194 VHOG:0001080 midgut endoderm uberon UBERON:0003259 endoderm of midgut An endoderm that is part of a midgut [Automatically generated definition]. OBOL:automatic midgut endoderm OBOL:automatic An endoderm that is part of a hindgut [Automatically generated definition]. TODO - check EHDAA:979 RETIRED_EHDAA2:0000781 hindgut endoderm uberon UBERON:0003260 endoderm of hindgut An endoderm that is part of a hindgut [Automatically generated definition]. OBOL:automatic hindgut endoderm OBOL:automatic An endoderm that is part of a thyroid primordium. UBERON:0005235 EHDAA:956 EMAPA:25357 RETIRED_EHDAA2:0002035 VHOG:0001089 endoderm of thyroid primordium uberon UBERON:0003261 thyroid primordium endoderm ZFA-propagated An endoderm that is part of a thyroid primordium. OBOL:automatic endoderm of thyroid primordium OBOL:automatic A mesenchyme that is part of a chorion. TODO - check UBERON:0003423 EHDAA2:0003245 EHDAA:154 EMAPA:16114 EMAPA:16266 RETIRED_EHDAA2:0000247 VHOG:0000620 chorion mesenchyme chorion mesoderm chorionic mesenchyme mesenchyme of chorion mesenchyme of chorion (vertebrates) uberon UBERON:0003265 chorionic mesenchyme EHDAA2 EHDAA2 ISBN:0073040584 A mesenchyme that is part of a chorion. OBOL:automatic chorion mesenchyme OBOL:automatic chorion mesoderm RETIRED_EHDAA2:0000247 chorionic mesenchyme EHDAA2:0003245 mesenchyme of chorion (vertebrates) OBOL:automatic A calcareous tooth that is part of the lower jaw region. In mammals, the lower jaw teeth are attached to the mandible (dentary). EHDAA2:0001029 EHDAA:8009 EMAPA:17917 FMA:321647 MA:0001907 NCIT:C49582 UMLS:C1708757 calcareous tooth of lower jaw lower jaw calcareous tooth lower jaw dentine containing tooth lower jaw tooth lower jaw vertebrate tooth mandibular tooth uberon UBERON:0003268 tooth of lower jaw A calcareous tooth that is part of the lower jaw region. In mammals, the lower jaw teeth are attached to the mandible (dentary). UMLS:C1708757 ncithesaurus:Lower_Jaw_Tooth calcareous tooth of lower jaw OBOL:automatic lower jaw calcareous tooth OBOL:automatic lower jaw dentine containing tooth OBOL:automatic lower jaw tooth OBOL:automatic lower jaw vertebrate tooth OBOL:automatic mandibular tooth NCBITaxon:40674 A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. EHDAA2:0000486 EHDAA:2923 EMAPA:17844 eye skeletal muscle eye skeletal muscle tissue skeletal muscle tissue of eye uberon eye skeletal muscle group UBERON:0003269 skeletal muscle tissue of eye A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. OBOL:automatic eye skeletal muscle OBOL:automatic eye skeletal muscle tissue OBOL:automatic skeletal muscle tissue of eye OBOL:automatic eye skeletal muscle group EHDAA2:0000486 A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 lower jaw mandible AAO:0000274 EHDAA2:0004606 EHDAA:8005 EMAPA:17906 EMAPA:17910 FMA:54398 MA:0001906 TAO:0001273 VHOG:0000428 XAO:0003084 ZFA:0001273 lower jaw skeleton uberon mandibles mandibular series UBERON:0003278 skeleton of lower jaw EHDAA2 VHOG-modified A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] 2012-08-14 TAO:0001273 TAO ZFIN:curator The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] 2012-09-17 VHOG:0000428 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101 Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 FMA lower jaw MA:0001906 lower jaw ZFA:0001273 mandible ZFA:0001273 lower jaw skeleton AAO:0000274 mandibles TAO:0001273 mandibular series ZFA:0001273 An endothelium that is part of a trachea. EHDAA:3082 RETIRED_EHDAA2:0002068 endothelium of windpipe trachea endothelium windpipe endothelium uberon UBERON:0003279 endothelium of trachea An endothelium that is part of a trachea. OBOL:automatic endothelium of windpipe OBOL:automatic trachea endothelium OBOL:automatic windpipe endothelium OBOL:automatic The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. TODO - check primitive vs developed The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG] EHDAA2:0001922 EHDAA:2999 EMAPA:17024 MA:0001617 VHOG:0000358 mesentery of ventriculus mesogaster mesogastium mesogastrium stomach mesentery ventriculus mesentery uberon UBERON:0003281 mesentery of stomach MA MA The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG] 2012-09-17 VHOG:0000358 VHOG mesentery of ventriculus OBOL:automatic mesogaster mesogastium MA:0001617 mesogastrium stomach mesentery Obol:obol ventriculus mesentery OBOL:automatic A mesentery that surrounds the heart. EHDAA:432 EMAPA:16212 RETIRED_EHDAA2:0000739 VHOG:0000353 heart mesentery uberon cardiac mesentery mesocardium UBERON:0003282 mesentery of heart A mesentery that surrounds the heart. MA:th heart mesentery OBOL:automatic cardiac mesentery EMAPA:16212 mesocardium MA:0000098 A mesentery that is part of a esophagus [Automatically generated definition]. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EHDAA2:0001288 EHDAA:2943 EMAPA:16836 MA:0001569 VHOG:0000415 esophagus mesentery gullet mesentery mesentery of esophagus mesentery of gullet meso-esophagus oesophagus mesentery uberon UBERON:0003283 mesentery of oesophagus A mesentery that is part of a esophagus [Automatically generated definition]. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000415 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 esophagus mesentery MA:0001569 gullet mesentery OBOL:automatic mesentery of esophagus OBOL:automatic mesentery of gullet OBOL:automatic oesophagus mesentery VHOG:0000415 A mesentery that is part of a midgut [Automatically generated definition]. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EHDAA2:0001202 EHDAA:3031 EMAPA:16721 EMAPA:17039 EMAPA:17197 VHOG:0000413 midgut mesentery uberon UBERON:0003284 mesentery of midgut A mesentery that is part of a midgut [Automatically generated definition]. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000413 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 midgut mesentery OBOL:automatic A meninx that is part of a midbrain [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001174 EHDAA:3708 EMAPA:17791 MA:0001058 RETIRED_EHDAA2:0001109 VHOG:0000012 meninges of midbrain midbrain meninges midbrain meninx uberon mesencephalon meninges UBERON:0003288 meninx of midbrain A meninx that is part of a midbrain [Automatically generated definition]. OBOL:automatic Meninges that are part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000012 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000012 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 meninges of midbrain OBOL:automatic midbrain meninges OBOL:automatic midbrain meninx OBOL:automatic mesencephalon meninges VHOG:0000012 A meninx that is part of a telencephalon [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the telencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001990 EHDAA:5476 EMAPA:17774 MA:0000979 VHOG:0000010 meninges of telencephalon telencephalon meninges telencephalon meninx uberon UBERON:0003289 meninx of telencephalon A meninx that is part of a telencephalon [Automatically generated definition]. OBOL:automatic Meninges that are part of the telencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000010 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000010 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 meninges of telencephalon OBOL:automatic telencephalon meninges OBOL:automatic telencephalon meninx OBOL:automatic A meninx that is part of a diencephalon [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000399 EHDAA:5458 EMAPA:17764 MA:0000826 VHOG:0000009 between brain meninges between brain meninx diencephalon meninges diencephalon meninx interbrain meninges interbrain meninx mature diencephalon meninges mature diencephalon meninx meninges of between brain meninges of diencephalon meninges of interbrain meninges of mature diencephalon meninx of between brain meninx of interbrain meninx of mature diencephalon uberon UBERON:0003290 meninx of diencephalon A meninx that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Meninges that are part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000009 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000009 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 between brain meninges OBOL:automatic between brain meninx OBOL:automatic diencephalon meninges OBOL:automatic diencephalon meninx OBOL:automatic interbrain meninges OBOL:automatic interbrain meninx OBOL:automatic mature diencephalon meninges OBOL:automatic mature diencephalon meninx OBOL:automatic meninges of between brain OBOL:automatic meninges of diencephalon OBOL:automatic meninges of interbrain OBOL:automatic meninges of mature diencephalon OBOL:automatic meninx of between brain OBOL:automatic meninx of interbrain OBOL:automatic meninx of mature diencephalon OBOL:automatic A meninx that is part of a hindbrain [Automatically generated definition]. consider changing genus to subdivision of meninx Meninges that are part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000770 EHDAA:3688 EMAPA:17783 MA:0000987 VHOG:0000011 hindbrain meninges hindbrain meninx meninges of hindbrain uberon rhomencephalon meninges UBERON:0003291 meninx of hindbrain definitional A meninx that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Meninges that are part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000011 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000011 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 hindbrain meninges OBOL:automatic hindbrain meninx OBOL:automatic meninges of hindbrain OBOL:automatic rhomencephalon meninges VHOG:0000011 A meninx that is part of a spinal cord [Automatically generated definition]. Meninges that are part of the spinal cord. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] CALOHA:TS-2148 EHDAA2:0001895 EHDAA:2865 EMAPA:17804 MA:0001130 NCIT:C12350 UMLS:C0037938 VHOG:0000443 menines of spinal cord meninges of spinal cord spinal cord meninges spinal cord meninx spinal meninges spinal meninx uberon UBERON:0003292 meninx of spinal cord A meninx that is part of a spinal cord [Automatically generated definition]. OBOL:automatic Meninges that are part of the spinal cord. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000443 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000443 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C0037938 ncithesaurus:Spinal_Meninges menines of spinal cord meninges of spinal cord OBOL:automatic spinal cord meninges OBOL:automatic spinal cord meninx OBOL:automatic spinal meninges A gland that is part of a foregut [Automatically generated definition]. EHDAA2:0000567 EHDAA:950 EMAPA:16557 VHOG:0000650 foregut gland uberon UBERON:0003294 gland of foregut A gland that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut gland OBOL:automatic Racemose mucous glands beneath the mucous membrane of the pharynx. BTO:0004849 EHDAA2:0001461 EHDAA:2967 FMA:55075 pharynx gland uberon glandulae pharyngeae UBERON:0003295 pharyngeal gland BTO Racemose mucous glands beneath the mucous membrane of the pharynx. pharynx gland EHDAA2:0001461 glandulae pharyngeae BTO:0004849 Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. EHDAA2:0000395 EHDAA:4475 EMAPA:16897 VHOG:0000653 diencephalon gland interbrain gland uberon UBERON:0003296 gland of diencephalon Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. diencephalon gland OBOL:automatic interbrain gland OBOL:automatic A gland that is part of a integumental system [Automatically generated definition]. EHDAA2:0000837 EHDAA:6522 EMAPA:17758 MA:0000144 VHOG:0000654 integumental gland integumental system gland integumentary gland uberon UBERON:0003297 gland of integumental system A gland that is part of a integumental system [Automatically generated definition]. OBOL:automatic integumental gland integumental system gland integumentary gland A blood island that is part of a mesoderm. in EHDAA2, gives rise to blood and dorsal aorta UBERON:0003305 EHDAA2:0003241 EHDAA:170 EMAPA:16115 mesoderm blood islands uberon mesenchyme blood island UBERON:0003304 mesoderm blood island EHDAA2 EHDAA2 A blood island that is part of a mesoderm. OBOL:automatic in EHDAA2, gives rise to blood and dorsal aorta EHDAA2 mesoderm blood islands EHDAA2:0003241 mesenchyme blood island OBOL:automatic Mesenchyme that is part of a developing testis [Automatically generated definition]. EHDAA2:0002010 EHDAA:8150 EMAPA:35858 VHOG:0001442 testis mesenchyme uberon UBERON:0003312 mesenchyme of testis Mesenchyme that is part of a developing testis [Automatically generated definition]. OBOL:automatic testis mesenchyme OBOL:automatic Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 EHDAA:2910 EMAPA:16673 VHOG:0001084 mesenchyme of eye uberon UBERON:0003314 eye mesenchyme EHDAA2 Mesenchyme that is part of a developing camera-type eye. OBOL:automatic mesenchyme of eye OBOL:automatic Mesenchyme that is part of a developing ovary [Automatically generated definition]. EHDAA2:0001362 EHDAA:8128 VHOG:0001441 female reproductive system gonad mesenchyme female reproductive system gonada mesenchyme gonad of female reproductive system mesenchyme gonada of female reproductive system mesenchyme mesenchyme of female reproductive system gonad mesenchyme of female reproductive system gonada mesenchyme of gonad of female reproductive system mesenchyme of gonada of female reproductive system ovary mesenchyme uberon UBERON:0003315 mesenchyme of ovary Mesenchyme that is part of a developing ovary [Automatically generated definition]. OBOL:automatic female reproductive system gonad mesenchyme OBOL:automatic female reproductive system gonada mesenchyme OBOL:automatic gonad of female reproductive system mesenchyme OBOL:automatic gonada of female reproductive system mesenchyme OBOL:automatic mesenchyme of female reproductive system gonad OBOL:automatic mesenchyme of female reproductive system gonada OBOL:automatic mesenchyme of gonad of female reproductive system OBOL:automatic mesenchyme of gonada of female reproductive system OBOL:automatic ovary mesenchyme OBOL:automatic The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme. UBERON:0003264 EHDAA2:0002216 EHDAA:168 EHDAA:205 EMAPA:16087 EMAPA:16267 VHOG:0000503 VHOG:0000617 yolk sac mesenchyme uberon UBERON:0003316 mesenchyme of yolk sac The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme. UBERON:cjm yolk sac mesenchyme OBOL:automatic Mesenchyme that is part of a developing elbow [Automatically generated definition]. EHDAA2:0000432 EHDAA:4170 EHDAA:6216 EMAPA:17416 VHOG:0001075 cubital region mesenchyme elbow mesenchyme mesenchyme of cubital region uberon UBERON:0003318 mesenchyme of elbow Mesenchyme that is part of a developing elbow [Automatically generated definition]. OBOL:automatic cubital region mesenchyme OBOL:automatic elbow mesenchyme OBOL:automatic mesenchyme of cubital region OBOL:automatic Mesenchyme of the carpal region that contributes to the carpal skeleton. EHDAA2:0000220 EHDAA:5200 EMAPA:19122 carpal region mesenchyme carpus mesenchyme mesenchyme of wrist wrist mesenchyme uberon UBERON:0003319 mesenchyme of carpal region Mesenchyme of the carpal region that contributes to the carpal skeleton. carpal region mesenchyme OBOL:automatic carpus mesenchyme OBOL:automatic mesenchyme of wrist OBOL:automatic wrist mesenchyme OBOL:automatic Mesenchyme that is part of a developing hip [Automatically generated definition]. EHDAA2:0000786 EHDAA:5157 EHDAA:6182 EMAPA:17492 VHOG:0001029 hip mesenchyme hip region mesenchyme mesenchyme of hip region mesenchyme of regio coxae regio coxae mesenchyme uberon UBERON:0003320 mesenchyme of hip Mesenchyme that is part of a developing hip [Automatically generated definition]. OBOL:automatic hip mesenchyme OBOL:automatic hip region mesenchyme OBOL:automatic mesenchyme of hip region OBOL:automatic mesenchyme of regio coxae OBOL:automatic regio coxae mesenchyme OBOL:automatic Mesenchyme that is part of a developing shoulder [Automatically generated definition]. EHDAA2:0001837 EHDAA:4184 EHDAA:6232 EMAPA:17423 VHOG:0001035 shoulder mesenchyme uberon UBERON:0003322 mesenchyme of shoulder Mesenchyme that is part of a developing shoulder [Automatically generated definition]. OBOL:automatic shoulder mesenchyme OBOL:automatic Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. EHDAA2:0001024 EHDAA:8003 EMAPA:17916 VHOG:0001069 lower jaw mesenchyme mesenchyme of ventral mandibular arch ventral mandibular arch mesenchyme uberon UBERON:0003324 mesenchyme of lower jaw EHDAA2 Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. OBOL:automatic lower jaw mesenchyme OBOL:automatic mesenchyme of ventral mandibular arch OBOL:automatic ventral mandibular arch mesenchyme OBOL:automatic Mesenchyme that is part of a developing pinna [Automatically generated definition]. EMAPA divides this spatially into condensation + rest, and temporally into mesenchyme and cartilage condensation EHDAA2:0001469 EHDAA:8981 EMAPA:17591 VHOG:0000747 auricle mesenchyme auricle of ear mesenchyme auricle of external ear mesenchyme auricula (auris externa) mesenchyme auricula mesenchyme mesenchyme of auricle mesenchyme of auricle of ear mesenchyme of auricle of external ear mesenchyme of auricula mesenchyme of auricula (auris externa) mesenchyme of pinna of ear pinna mesenchyme pinna of ear mesenchyme uberon UBERON:0003325 mesenchyme of pinna Mesenchyme that is part of a developing pinna [Automatically generated definition]. OBOL:automatic EMAPA divides this spatially into condensation + rest, and temporally into mesenchyme and cartilage condensation EMAPA auricle mesenchyme OBOL:automatic auricle of ear mesenchyme OBOL:automatic auricle of external ear mesenchyme OBOL:automatic auricula (auris externa) mesenchyme OBOL:automatic auricula mesenchyme OBOL:automatic mesenchyme of auricle OBOL:automatic mesenchyme of auricle of ear OBOL:automatic mesenchyme of auricle of external ear OBOL:automatic mesenchyme of auricula OBOL:automatic mesenchyme of auricula (auris externa) OBOL:automatic mesenchyme of pinna of ear OBOL:automatic pinna mesenchyme OBOL:automatic pinna of ear mesenchyme OBOL:automatic Mesenchyme that is part of a developing lower arm [Automatically generated definition]. EHDAA2:0000555 EHDAA:4176 EHDAA:6222 EMAPA:17419 VHOG:0000504 uberon UBERON:0003327 mesenchyme of forearm Mesenchyme that is part of a developing lower arm [Automatically generated definition]. OBOL:automatic Mesenchyme that is part of a footplate. We group two EMAPA classes here but these may need to be separated UBERON:0005260 EHDAA2:0000549 EHDAA:5149 EHDAA:6172 EMAPA:17252 EMAPA:17488 VHOG_RETIRED:0001055 foot plate mesenchyme uberon UBERON:0003328 mesenchyme of footplate EHDAA2 Mesenchyme that is part of a footplate. OBOL:automatic We group two EMAPA classes here but these may need to be separated EMAPA A submucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27217 EMAPA:27227 EMAPA:27535 FMA:85399 anal canal submucosa anal canal viewed anatomically submucosa anal region submucosa anatomical anal canal submucosa submucosa of anal canal viewed anatomically submucosa of anal region submucosa of anatomical anal canal uberon UBERON:0003329 submucosa of anal canal A submucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic anal canal submucosa OBOL:automatic anal canal viewed anatomically submucosa OBOL:automatic anal region submucosa OBOL:automatic anatomical anal canal submucosa OBOL:automatic submucosa of anal canal viewed anatomically OBOL:automatic submucosa of anal region OBOL:automatic submucosa of anatomical anal canal OBOL:automatic The submucous layer of the wall of the rectum. BTO:0002114 EMAPA:27083 FMA:15034 rectal submucosa rectum submucosa tela submucosa recti uberon UBERON:0003330 submucosa of rectum The submucous layer of the wall of the rectum. BTO:0002114 rectal submucosa FMA:15034 rectum submucosa OBOL:automatic tela submucosa recti BTO:0002114 A submucosa that is part of a colon [Automatically generated definition]. EMAPA:27379 FMA:14985 MA:0003200 colon submucosa colonic submucosa large bowel submucosa submucosa of large bowel uberon UBERON:0003331 submucosa of colon A submucosa that is part of a colon [Automatically generated definition]. OBOL:automatic colon submucosa OBOL:automatic colonic submucosa FMA:14985 large bowel submucosa OBOL:automatic submucosa of large bowel OBOL:automatic A submucosa that is part of a duodenum [Automatically generated definition]. EMAPA:27027 EMAPA:27097 EMAPA:27239 FMA:14943 MA:0003213 doudenal submucosa duodenal submucosa duodenum submucosa uberon UBERON:0003332 submucosa of duodenum A submucosa that is part of a duodenum [Automatically generated definition]. OBOL:automatic doudenal submucosa FMA:14943 duodenal submucosa FMA:14943 duodenum submucosa OBOL:automatic A serous membrane that is part of a rectum [Automatically generated definition]. EMAPA:27087 FMA:15039 rectal serosa rectum serosa rectum serous membrane serous membrane of rectum visceral peritoneum of rectum uberon UBERON:0003334 serosa of rectum A serous membrane that is part of a rectum [Automatically generated definition]. OBOL:automatic rectal serosa FMA:15039 rectum serosa OBOL:automatic rectum serous membrane OBOL:automatic serous membrane of rectum OBOL:automatic visceral peritoneum of rectum FMA:15039 A serous membrane that is part of a colon [Automatically generated definition]. EMAPA:27387 FMA:14990 MA:0003199 colon serosa colon serous membrane colonic serosa large bowel serosa large bowel serous membrane serosa of large bowel serous membrane of colon serous membrane of large bowel visceral peritoneum of colon uberon UBERON:0003335 serosa of colon A serous membrane that is part of a colon [Automatically generated definition]. OBOL:automatic colon serosa OBOL:automatic colon serous membrane OBOL:automatic colonic serosa FMA:14990 large bowel serosa OBOL:automatic large bowel serous membrane OBOL:automatic serosa of large bowel OBOL:automatic serous membrane of colon OBOL:automatic serous membrane of large bowel OBOL:automatic visceral peritoneum of colon FMA:14990 A serous membrane that is part of a duodenum [Automatically generated definition]. 1st part serosa, 2nd - 4th adventitia EMAPA:27247 FMA:14948 MA:0003212 doudenal serosa duodenal serosa duodenum serosa duodenum serous membrane serous membrane of duodenum visceral peritoneum of duodenum uberon UBERON:0003336 serosa of duodenum A serous membrane that is part of a duodenum [Automatically generated definition]. OBOL:automatic doudenal serosa FMA:14948 duodenal serosa FMA:14948 duodenum serosa OBOL:automatic duodenum serous membrane OBOL:automatic serous membrane of duodenum OBOL:automatic visceral peritoneum of duodenum FMA:14948 A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS BIRNLEX:2548 BTO:0001123 EMAPA:32814 MA:0001161 peripheral nervous system ganglion uberon UBERON:0003338 ganglion of peripheral nervous system A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). BIRNLEX:2548 we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS MA peripheral nervous system ganglion OBOL:automatic A ganglion that is part of a central nervous system [Automatically generated definition]. this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia EHDAA2:0000227 EMAPA:16658 FMA:83843 central nervous system ganglion ganglion of neuraxis neuraxis ganglion uberon UBERON:0003339 ganglion of central nervous system A ganglion that is part of a central nervous system [Automatically generated definition]. OBOL:automatic this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia FMA central nervous system ganglion OBOL:automatic ganglion of neuraxis OBOL:automatic neuraxis ganglion OBOL:automatic A mucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27531 FMA:74654 NCIT:C60784 UMLS:C0227414 anal canal mucosa anal canal mucosa of organ anal canal mucous membrane anal canal organ mucosa anal canal viewed anatomically mucosa anal canal viewed anatomically mucosa of organ anal canal viewed anatomically mucous membrane anal canal viewed anatomically organ mucosa anal mucosa anal mucous membrane anal region mucosa anal region mucosa of organ anal region mucous membrane anal region organ mucosa anatomical anal canal mucosa anatomical anal canal mucosa of organ anatomical anal canal mucous membrane anatomical anal canal organ mucosa mucosa of anal canal viewed anatomically mucosa of anal region mucosa of anatomical anal canal mucosa of organ of anal canal mucosa of organ of anal canal viewed anatomically mucosa of organ of anal region mucosa of organ of anatomical anal canal mucous membrane of anal canal mucous membrane of anal canal viewed anatomically mucous membrane of anal region mucous membrane of anatomical anal canal organ mucosa of anal canal organ mucosa of anal canal viewed anatomically organ mucosa of anal region organ mucosa of anatomical anal canal uberon UBERON:0003342 mucosa of anal canal A mucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic UMLS:C0227414 ncithesaurus:Anal_Mucosa anal canal mucosa OBOL:automatic anal canal mucosa of organ OBOL:automatic anal canal mucous membrane OBOL:automatic anal canal organ mucosa OBOL:automatic anal canal viewed anatomically mucosa OBOL:automatic anal canal viewed anatomically mucosa of organ OBOL:automatic anal canal viewed anatomically mucous membrane OBOL:automatic anal canal viewed anatomically organ mucosa OBOL:automatic anal mucosa FMA:74654 anal mucous membrane FMA:74654 anal region mucosa OBOL:automatic anal region mucosa of organ OBOL:automatic anal region mucous membrane OBOL:automatic anal region organ mucosa OBOL:automatic anatomical anal canal mucosa OBOL:automatic anatomical anal canal mucosa of organ OBOL:automatic anatomical anal canal mucous membrane OBOL:automatic anatomical anal canal organ mucosa OBOL:automatic mucosa of anal canal viewed anatomically OBOL:automatic mucosa of anal region OBOL:automatic mucosa of anatomical anal canal OBOL:automatic mucosa of organ of anal canal OBOL:automatic mucosa of organ of anal canal viewed anatomically OBOL:automatic mucosa of organ of anal region OBOL:automatic mucosa of organ of anatomical anal canal OBOL:automatic mucous membrane of anal canal OBOL:automatic mucous membrane of anal canal viewed anatomically OBOL:automatic mucous membrane of anal region OBOL:automatic mucous membrane of anatomical anal canal OBOL:automatic organ mucosa of anal canal OBOL:automatic organ mucosa of anal canal viewed anatomically OBOL:automatic organ mucosa of anal region OBOL:automatic organ mucosa of anatomical anal canal OBOL:automatic A mucosa that is part of a oral opening [Automatically generated definition]. EMAPA:26937 mucosa of oral opening mucosa of oral part of face mucosa of organ of oral opening mucosa of organ of oral part of face mucosa of organ of oral region mucosa of organ of subdivision of mouth mucosa of subdivision of mouth mucous membrane of oral opening mucous membrane of oral part of face mucous membrane of oral region mucous membrane of subdivision of mouth oral opening mucosa oral opening mucosa of organ oral opening mucous membrane oral opening organ mucosa oral part of face mucosa oral part of face mucosa of organ oral part of face mucous membrane oral part of face organ mucosa oral region mucosa oral region mucosa of organ oral region mucous membrane oral region organ mucosa organ mucosa of oral opening organ mucosa of oral part of face organ mucosa of oral region organ mucosa of subdivision of mouth subdivision of mouth mucosa subdivision of mouth mucosa of organ subdivision of mouth mucous membrane subdivision of mouth organ mucosa uberon UBERON:0003343 mucosa of oral region A mucosa that is part of a oral opening [Automatically generated definition]. OBOL:automatic mucosa of oral opening OBOL:automatic mucosa of oral part of face OBOL:automatic mucosa of organ of oral opening OBOL:automatic mucosa of organ of oral part of face OBOL:automatic mucosa of organ of oral region OBOL:automatic mucosa of organ of subdivision of mouth OBOL:automatic mucosa of subdivision of mouth OBOL:automatic mucous membrane of oral opening OBOL:automatic mucous membrane of oral part of face OBOL:automatic mucous membrane of oral region OBOL:automatic mucous membrane of subdivision of mouth OBOL:automatic oral opening mucosa OBOL:automatic oral opening mucosa of organ OBOL:automatic oral opening mucous membrane OBOL:automatic oral opening organ mucosa OBOL:automatic oral part of face mucosa OBOL:automatic oral part of face mucosa of organ OBOL:automatic oral part of face mucous membrane OBOL:automatic oral part of face organ mucosa OBOL:automatic oral region mucosa OBOL:automatic oral region mucosa of organ OBOL:automatic oral region mucous membrane OBOL:automatic oral region organ mucosa OBOL:automatic organ mucosa of oral opening OBOL:automatic organ mucosa of oral part of face OBOL:automatic organ mucosa of oral region OBOL:automatic organ mucosa of subdivision of mouth OBOL:automatic subdivision of mouth mucosa OBOL:automatic subdivision of mouth mucosa of organ OBOL:automatic subdivision of mouth mucous membrane OBOL:automatic subdivision of mouth organ mucosa OBOL:automatic A mucosa that is part of a rectum [Automatically generated definition]. CALOHA:TS-2107 EMAPA:27081 FMA:15033 MA:0003218 mucosa of organ of rectum mucous membrane of rectum organ mucosa of rectum rectal mucosa rectal mucous membrane rectum mucosa rectum mucosa of organ rectum mucous membrane rectum organ mucosa uberon UBERON:0003346 mucosa of rectum A mucosa that is part of a rectum [Automatically generated definition]. OBOL:automatic mucosa of organ of rectum OBOL:automatic mucous membrane of rectum OBOL:automatic organ mucosa of rectum OBOL:automatic rectal mucosa FMA:15033 rectal mucous membrane FMA:15033 rectum mucosa OBOL:automatic rectum mucosa of organ OBOL:automatic rectum mucous membrane OBOL:automatic rectum organ mucosa OBOL:automatic A layer of epithelial cells on the surface of the mucosa. BTO:0003752 uberon lamina epithelialis mucosa lamina epithelialis mucosae UBERON:0003350 lies on top of lamina propria epithelium of mucosa A layer of epithelial cells on the surface of the mucosa. BTO:0003752 lamina epithelialis mucosa BTO:0003752 lamina epithelialis mucosae BTO:0003752 An epithelium that is part of a pharynx [Automatically generated definition]. Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] BSA:0000112 BTO:0005240 EMAPA:16708 MA:0002725 RETIRED_EHDAA2:0001460 TAO:0001174 XAO:0003202 ZFA:0001174 epithelial tissue of pharynx epithelium of pharynx pharynx epithelial tissue pharynx epithelium uberon UBERON:0003351 pharyngeal epithelium ZFA ZFA An epithelium that is part of a pharynx [Automatically generated definition]. OBOL:automatic Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] 2012-08-14 TAO:0001174 TAO ZFIN:curator epithelial tissue of pharynx OBOL:automatic epithelium of pharynx OBOL:automatic pharynx epithelial tissue OBOL:automatic pharynx epithelium OBOL:automatic An epithelium that is part of a midgut. BTO:0005053 EHDAA2:0001195 EMAPA:16569 MA:0003205 epithelial tissue of midgut midgut epithelial tissue midgut epithelium uberon UBERON:0003352 epithelium of midgut BTO An epithelium that is part of a midgut. OBOL:automatic epithelial tissue of midgut OBOL:automatic midgut epithelial tissue OBOL:automatic midgut epithelium BTO:0005053 midgut epithelium OBOL:automatic An epithelium that is part of a hindgut [Automatically generated definition]. EHDAA2:0000782 EMAPA:16717 MA:0003206 epithelial tissue of hindgut hindgut epithelial tissue hindgut epithelium uberon UBERON:0003353 epithelium of hindgut An epithelium that is part of a hindgut [Automatically generated definition]. OBOL:automatic epithelial tissue of hindgut OBOL:automatic hindgut epithelial tissue OBOL:automatic hindgut epithelium OBOL:automatic An epithelium that is part of a rectum [Automatically generated definition]. CALOHA:TS-2066 EHDAA2:0001594 EMAPA:17898 FMA:17510 MA:0003219 VHOG:0001037 epithelial tissue of rectum rectal epithelium rectum epithelial tissue rectum epithelium uberon UBERON:0003354 epithelium of rectum An epithelium that is part of a rectum [Automatically generated definition]. OBOL:automatic epithelial tissue of rectum OBOL:automatic rectal epithelium FMA:17510 rectum epithelial tissue OBOL:automatic rectum epithelium OBOL:automatic An epithelium that is part of a tongue [Automatically generated definition]. BTO:0000992 CALOHA:TS-1051 EHDAA2:0004598 EMAPA:17881 FMA:284658 MA:0001592 NCIT:C49300 UMLS:C1710436 epithelial tissue of tongue tongue epithelial tissue tongue epithelium uberon lingual epithelium UBERON:0003357 examples: tongue squamous epithelium, keratined, non-keratinized and parakeratinized epithelium, as well as gustatory epithelium. Note that not all these subtypes are named in individual anatomy ontologies. epithelium of tongue An epithelium that is part of a tongue [Automatically generated definition]. OBOL:automatic UMLS:C1710436 ncithesaurus:Tongue_Epithelium epithelial tissue of tongue OBOL:automatic tongue epithelial tissue OBOL:automatic tongue epithelium OBOL:automatic lingual epithelium BTO:0000992 An epithelium that is part of a submandibular gland [Automatically generated definition]. BTO:0004557 EMAPA:18813 VHOG:0000989 epithelial tissue of submandibular gland submandibular gland epithelial tissue submandibular gland epithelium uberon submandibular duct epithelium submandibular gland duct epithelium submaxillary gland epithelium UBERON:0003359 epithelium of submandibular gland An epithelium that is part of a submandibular gland [Automatically generated definition]. OBOL:automatic epithelial tissue of submandibular gland OBOL:automatic submandibular gland epithelial tissue OBOL:automatic submandibular gland epithelium OBOL:automatic submandibular duct epithelium BTO:0004557 submandibular gland duct epithelium BTO:0004557 submaxillary gland epithelium EMAPA:18813 An epithelium that is part of a right lung [Automatically generated definition]. EMAPA:17663 MA:0003132 epithelial tissue of right lung right lung epithelial tissue right lung epithelium uberon UBERON:0003364 epithelium of right lung An epithelium that is part of a right lung [Automatically generated definition]. OBOL:automatic epithelial tissue of right lung OBOL:automatic right lung epithelial tissue OBOL:automatic right lung epithelium OBOL:automatic An epithelium that is part of a left lung [Automatically generated definition]. EMAPA:17655 MA:0003131 epithelial tissue of left lung left lung epithelial tissue left lung epithelium uberon UBERON:0003365 epithelium of left lung An epithelium that is part of a left lung [Automatically generated definition]. OBOL:automatic epithelial tissue of left lung OBOL:automatic left lung epithelial tissue OBOL:automatic left lung epithelium OBOL:automatic An unilaminar epithelium that surrounds a pelvic appendage bud. UBERON:0005232 EHDAA2:0001034 EMAPA:16780 VHOG:0001048 hindlimb ectoderm hindlimb bud ectoderm hindlimb ectoderm lower limb bud ectoderm pelvic fin bud ectoderm uberon leg ectoderm UBERON:0003371 pelvic appendage bud ectoderm EHDAA2 EHDAA2 An unilaminar epithelium that surrounds a pelvic appendage bud. OBOL:automatic hindlimb ectoderm VHOG:0001048 hindlimb bud ectoderm EMAPA:16780 hindlimb bud ectoderm hindlimb ectoderm VHOG:0001048 lower limb bud ectoderm EHDAA2:0001034 pelvic fin bud ectoderm leg ectoderm OBOL:automatic An unilaminar epithelium that surrounds a pectoral appendage bud. UBERON:0005231 UBERON:0005663 EHDAA2:0002134 EMAPA:16407 VHOG:0001047 forelimb bud ectoderm forelimb ectoderm pectoral fin bud ectoderm upper limb bud ectoderm wing ectoderm uberon arm ectoderm UBERON:0003372 pectoral appendage bud ectoderm EHDAA2 EHDAA2 An unilaminar epithelium that surrounds a pectoral appendage bud. OBOL:automatic forelimb bud ectoderm EMAPA:16407 forelimb bud ectoderm forelimb ectoderm VHOG:0001047 pectoral fin bud ectoderm upper limb bud ectoderm EHDAA2:0002134 wing ectoderm Geisha:syn NCBITaxon:8782 arm ectoderm OBOL:automatic An ectoderm that is part of a footplate. EMAPA:17250 uberon UBERON:0003373 ectoderm of footplate An ectoderm that is part of a footplate. OBOL:automatic A extraembryonic structure that develops_from a ectoderm and is part of a chorion. BTO:0005145 EMAPA:16113 chorion ectoderm uberon chorion epithelium chorionic epithelium UBERON:0003374 chorionic ectoderm ISBN:0073040584 A extraembryonic structure that develops_from a ectoderm and is part of a chorion. OBOL:automatic chorion ectoderm OBOL:automatic chorionic epithelium BTO:0005145 A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]. EHDAA2:0004155 EMAPA:17326 FMA:7282 VHOG:0001227 cardiac muscle of cardiac right atrium cardiac muscle of heart right atrium cardiac muscle tissue of heart right atrium cardiac muscle tissue of right atrium cardiac muscle tissue of right atrium of heart myocardium of right atrium right atrium heart muscle right atrium myocardium textus muscularis of myocardium of right atrium textus muscularis of myocardium of right atrium of heart textus muscularis of myocardium of right cardiac atrium uberon UBERON:0003379 cardiac muscle of right atrium A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]. OBOL:automatic cardiac muscle of cardiac right atrium OBOL:automatic cardiac muscle of heart right atrium OBOL:automatic cardiac muscle tissue of heart right atrium OBOL:automatic cardiac muscle tissue of right atrium OBOL:automatic cardiac muscle tissue of right atrium of heart OBOL:automatic right atrium heart muscle EHDAA2:0004155 right atrium myocardium VHOG:0001227 textus muscularis of myocardium of right atrium OBOL:automatic textus muscularis of myocardium of right atrium of heart OBOL:automatic textus muscularis of myocardium of right cardiac atrium OBOL:automatic A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]. EHDAA2:0004154 EMAPA:17320 FMA:7285 VHOG:0001225 cardiac left atrium cardiac muscle cardiac left atrium cardiac muscle tissue cardiac muscle of cardiac left atrium cardiac muscle of heart left atrium cardiac muscle of left atrium of heart left atrium heart muscle left atrium myocardium myocardium of left atrium textus muscularis of myocardium of cardiac left atrium textus muscularis of myocardium of heart left atrium textus muscularis of myocardium of left atrium textus muscularis of myocardium of left atrium of heart textus muscularis of myocardium of left cardiac atrium uberon UBERON:0003380 cardiac muscle of left atrium A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]. OBOL:automatic cardiac left atrium cardiac muscle OBOL:automatic cardiac left atrium cardiac muscle tissue OBOL:automatic cardiac muscle of cardiac left atrium OBOL:automatic cardiac muscle of heart left atrium OBOL:automatic cardiac muscle of left atrium of heart OBOL:automatic left atrium heart muscle EHDAA2:0004154 left atrium myocardium VHOG:0001225 textus muscularis of myocardium of cardiac left atrium OBOL:automatic textus muscularis of myocardium of heart left atrium OBOL:automatic textus muscularis of myocardium of left atrium OBOL:automatic textus muscularis of myocardium of left atrium of heart OBOL:automatic textus muscularis of myocardium of left cardiac atrium OBOL:automatic A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. EMAPA:17342 FMA:83452 VHOG:0001236 cardiac muscle tissue of right ventricle right ventricular cardiac muscle tissue uberon right ventricle cardiac muscle UBERON:0003381 cardiac muscle of right ventricle A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of right ventricle FMA:83452 right ventricular cardiac muscle tissue GO:0003221 right ventricle cardiac muscle VHOG:0001236 A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. EMAPA:17339 FMA:83453 VHOG:0001234 cardiac muscle tissue of left ventricle left ventricular cardiac muscle tissue uberon left ventricle cardiac muscle UBERON:0003382 cardiac muscle of left ventricle A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of left ventricle FMA:83453 left ventricular cardiac muscle tissue GO:0003220 left ventricle cardiac muscle VHOG:0001234 A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. EHDAA2:0004158 EMAPA:17335 FMA:84084 VHOG:0000999 cardiac muscle of interventricular septum cardiac muscle tissue of interventricular septum interventricular septum cardiac muscle interventricular septum heart muscle interventricular septum myocardium uberon interventricular septum muscle UBERON:0003383 cardiac muscle tissue of interventricular septum A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of interventricular septum FMA:84084 interventricular septum cardiac muscle VHOG:0000999 interventricular septum heart muscle EHDAA2:0004158 interventricular septum myocardium VHOG:0000999 interventricular septum muscle A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. EMAPA:18963 pharynx skeletal muscle pharynx skeletal muscle tissue skeletal muscle tissue of pharynx uberon UBERON:0003384 skeletal muscle tissue of pharynx A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. OBOL:automatic pharynx skeletal muscle OBOL:automatic pharynx skeletal muscle tissue OBOL:automatic skeletal muscle tissue of pharynx OBOL:automatic any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle EMAPA:18807 MA:0001268 ocular smooth muscle uberon UBERON:0003386 smooth muscle of eye any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi MGI:cwg MP:0005247 ocular smooth muscle MA:0001268 A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]. UBERON:0004244 BTO:0001391 EMAPA:19192 FMA:262010 MA:0001863 NCIT:C49306 UMLS:C1710458 trachea smooth muscle tracheal smooth muscle uberon UBERON:0003387 smooth muscle of trachea A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]. OBOL:automatic UMLS:C1710458 ncithesaurus:Trachea_Smooth_Muscle_Tissue trachea smooth muscle MA:0001863 tracheal smooth muscle BTO:0001391 A mesothelium that is part of a pericardium [Automatically generated definition]. RETIRED_EHDAA2:0001436 cavity of pericardial sac meso-epithelium cavity of pericardial sac mesothelium meso-epithelium of cavity of pericardial sac meso-epithelium of pericardial cavity mesothelium of cavity of pericardial sac pericardial cavity meso-epithelium pericardial cavity mesothelium uberon UBERON:0003388 mesothelium of pericardial cavity A mesothelium that is part of a pericardium [Automatically generated definition]. OBOL:automatic cavity of pericardial sac meso-epithelium OBOL:automatic cavity of pericardial sac mesothelium OBOL:automatic meso-epithelium of cavity of pericardial sac OBOL:automatic meso-epithelium of pericardial cavity OBOL:automatic mesothelium of cavity of pericardial sac OBOL:automatic pericardial cavity meso-epithelium OBOL:automatic pericardial cavity mesothelium OBOL:automatic A mesothelium that is part of a diaphragm [Automatically generated definition]. EMAPA:18429 diaphragm meso-epithelium diaphragm mesothelium meso-epithelium of diaphragm meso-epithelium of thoracic diaphragm mesothelium of thoracic diaphragm thoracic diaphragm meso-epithelium thoracic diaphragm mesothelium uberon UBERON:0003389 mesothelium of diaphragm A mesothelium that is part of a diaphragm [Automatically generated definition]. OBOL:automatic diaphragm meso-epithelium OBOL:automatic diaphragm mesothelium OBOL:automatic meso-epithelium of diaphragm OBOL:automatic meso-epithelium of thoracic diaphragm OBOL:automatic mesothelium of thoracic diaphragm OBOL:automatic thoracic diaphragm meso-epithelium OBOL:automatic thoracic diaphragm mesothelium OBOL:automatic A mesothelium that is part of a pleural cavity [Automatically generated definition]. BTO:0003155 EHDAA2:0001476 EMAPA:16775 FMA:18148 meso-epithelium of pleural cavity mesothelium of pleura pleural cavity meso-epithelium pleural cavity mesothelium pleural mesothelium uberon pleura UBERON:0003390 mesothelium of pleural cavity A mesothelium that is part of a pleural cavity [Automatically generated definition]. OBOL:automatic meso-epithelium of pleural cavity OBOL:automatic mesothelium of pleura FMA:18148 pleural cavity meso-epithelium OBOL:automatic pleural cavity mesothelium OBOL:automatic pleural mesothelium EMAPA:16775 pleura EMAPA:16775 A mesentery that is part of a urinary system [Automatically generated definition]. EMAPA:17367 MA:0003233 excretory system mesentery mesentery of excretory system mesentery of renal system mesentery of systema urinaria renal system mesentery systema urinaria mesentery urinary system mesentery uberon UBERON:0003393 mesentery of urinary system A mesentery that is part of a urinary system [Automatically generated definition]. OBOL:automatic excretory system mesentery OBOL:automatic mesentery of excretory system OBOL:automatic mesentery of renal system OBOL:automatic mesentery of systema urinaria OBOL:automatic renal system mesentery OBOL:automatic systema urinaria mesentery OBOL:automatic urinary system mesentery OBOL:automatic A mesentery that is part of a hindgut [Automatically generated definition]. EMAPA:16718 hindgut mesentery uberon UBERON:0003394 mesentery of hindgut A mesentery that is part of a hindgut [Automatically generated definition]. OBOL:automatic hindgut mesentery OBOL:automatic A mesentery that is part of a rectum [Automatically generated definition]. EMAPA:18664 rectum mesentery uberon UBERON:0003395 mesentery of rectum A mesentery that is part of a rectum [Automatically generated definition]. OBOL:automatic rectum mesentery OBOL:automatic A mesentery that is part of a colon [Automatically generated definition]. EMAPA:18942 FMA:14645 colon mesentery large bowel mesentery large intestinal mesentery mesentery of large bowel mesentery of large intestine mesocolon uberon UBERON:0003396 mesentery of colon FMA A mesentery that is part of a colon [Automatically generated definition]. OBOL:automatic colon mesentery OBOL:automatic large bowel mesentery OBOL:automatic large intestinal mesentery FMA:14645 mesentery of large bowel OBOL:automatic mesentery of large intestine FMA:14645 mesocolon A mesentery that is part of a duodenum [Automatically generated definition]. EMAPA:19081 duodenum mesentery uberon UBERON:0003397 mesentery of duodenum A mesentery that is part of a duodenum [Automatically generated definition]. OBOL:automatic duodenum mesentery OBOL:automatic A zone of skin that is part of a lower arm [Automatically generated definition]. EMAPA:18056 FMA:38265 MA:0000602 forearm skin lower arm skin lower segment of arm skin skin of antebrachial region skin of lower arm skin of lower segment of arm skin of zeugopod of arm uberon UBERON:0003403 skin of forearm A zone of skin that is part of a lower arm [Automatically generated definition]. OBOL:automatic forearm skin FMA:38265 lower arm skin OBOL:automatic lower segment of arm skin OBOL:automatic skin of antebrachial region OBOL:automatic skin of lower arm OBOL:automatic skin of lower segment of arm OBOL:automatic skin of zeugopod of arm OBOL:automatic A cartilage element that is part of a respiratory system [Automatically generated definition]. EMAPA:18694 MA:0001818 apparatus respiratorius cartilage cartilage of apparatus respiratorius respiratory system cartilage uberon UBERON:0003406 cartilage of respiratory system A cartilage element that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius cartilage OBOL:automatic cartilage of apparatus respiratorius OBOL:automatic respiratory system cartilage OBOL:automatic A gland that is part of a digestive tract [Automatically generated definition]. EMAPA:18815 MA:0003202 digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland uberon UBERON:0003408 gland of digestive tract A gland that is part of a digestive tract [Automatically generated definition]. OBOL:automatic digestive tract gland OBOL:automatic gland of digestive tract OBOL:automatic gland of lower gastrointestinal tract OBOL:automatic gut gland MA:0003202 lower gastrointestinal tract gland OBOL:automatic Any of the mucous, serous, or mixed glands that empty their secretions onto the surface of the tongue. EMAPA:25097 lingual gland tongue gland uberon UBERON:0003409 gland of tongue Any of the mucous, serous, or mixed glands that empty their secretions onto the surface of the tongue. lingual gland OBOL:automatic tongue gland OBOL:automatic A gland that is part of a oropharynx [Automatically generated definition]. EMAPA:25095 gland of oral part of pharynx gland of oropharynx oral part of pharynx gland oropharynx gland uberon UBERON:0003410 oropharyngeal gland A gland that is part of a oropharynx [Automatically generated definition]. OBOL:automatic gland of oral part of pharynx OBOL:automatic gland of oropharynx EMAPA:25095 oral part of pharynx gland OBOL:automatic oropharynx gland OBOL:automatic Mesenchyme that is part of a pelvic appendage bud. Mesoderm part of pelvic fin bud.[TAO] EHDAA2:0001035 EMAPA:16781 TAO:0001386 ZFA:0001386 leg mesenchyme lower limb bud mesenchyme hindlimb bud mesenchyme mesoderm pelvic fin bud pelvic fin bud mesenchyme uberon UBERON:0003412 pelvic appendage bud mesenchyme Mesenchyme that is part of a pelvic appendage bud. OBOL:automatic Mesoderm part of pelvic fin bud.[TAO] 2012-08-14 TAO:0001386 TAO ZFIN:curator leg mesenchyme OBOL:automatic lower limb bud mesenchyme EHDAA2:0001035 hindlimb bud mesenchyme EMAPA:16781 mesoderm pelvic fin bud ZFA:0001386 pelvic fin bud mesenchyme Mesenchyme that is part of a pectoral appendage bud. Mesoderm that is part of the pectoral fin bud.[TAO] UBERON:0005703 EHDAA2:0002135 EHDAA:1703 EMAPA:16408 TAO:0000789 ZFA:0000789 arm mesenchyme forelimb bud mesenchyme mesoderm pectoral fin bud pectoral fin bud mesenchyme upper limb bud mesenchyme wing mesenchyme uberon UBERON:0003413 pectoral appendage bud mesenchyme Mesenchyme that is part of a pectoral appendage bud. OBOL:automatic Mesoderm that is part of the pectoral fin bud.[TAO] 2012-08-14 TAO:0000789 TAO ZFIN:curator arm mesenchyme OBOL:automatic forelimb bud mesenchyme EMAPA:16408 mesoderm pectoral fin bud ZFA:0000789 pectoral fin bud mesenchyme upper limb bud mesenchyme EHDAA2:0002135 wing mesenchyme OBOL:automatic Mesenchyme that is part of a developing tongue [Automatically generated definition]. TODO - develops_from EHDAA2:0004614 EMAPA:17882 tongue mesenchyme uberon UBERON:0003416 mesenchyme of tongue Mesenchyme that is part of a developing tongue [Automatically generated definition]. OBOL:automatic tongue mesenchyme EHDAA2:0004614 Mesenchyme that is part of a developing submandibular gland [Automatically generated definition]. EMAPA:18814 VHOG:0001110 submandibular gland mesenchyme uberon submaxillary gland mesenchyme UBERON:0003418 mesenchyme of submandibular gland Mesenchyme that is part of a developing submandibular gland [Automatically generated definition]. OBOL:automatic submandibular gland mesenchyme OBOL:automatic submaxillary gland mesenchyme EMAPA:18814 A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP] TODO - check EMAPA:26127 EMAPA:35925 Wharton's jelly umbilical cord mesenchyme uberon UBERON:0003422 mesenchyme of umbilical cord A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP] Wharton's jelly EMAPA:26127 umbilical cord mesenchyme OBOL:automatic A lymph node that is located in a kidney [Automatically generated definition]. Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland FMA:276799 MA:0002882 NCIT:C77646 UMLS:C2699031 kidney lymph node lymph node of kidney uberon UBERON:0003425 renal lymph node A lymph node that is located in a kidney [Automatically generated definition]. OBOL:automatic Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland NCBITaxon:10090 UMLS:C2699031 ncithesaurus:Renal_Lymph_Node kidney lymph node OBOL:automatic lymph node of kidney OBOL:automatic An adipose tissue that is part of a dermis [Automatically generated definition]. MA:0000798 adipose tissue of dermis dermis fat tissue dermis fatty tissue fat tissue of dermis fatty tissue of dermis uberon UBERON:0003426 dermis adipose tissue An adipose tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic adipose tissue of dermis OBOL:automatic dermis fat tissue OBOL:automatic dermis fatty tissue OBOL:automatic fat tissue of dermis OBOL:automatic fatty tissue of dermis OBOL:automatic A nerve that is part of an abdomen [Automatically generated definition]. MA:0000521 nerve of abdomen uberon UBERON:0003429 abdomen nerve A nerve that is part of an abdomen [Automatically generated definition]. OBOL:automatic nerve of abdomen OBOL:automatic A nerve that is part of a neck [Automatically generated definition]. EMAPA:37263 MA:0000588 neck (volume) nerve nerve of neck nerve of neck (volume) uberon UBERON:0003430 neck nerve A nerve that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37263 MA:th neck (volume) nerve OBOL:automatic nerve of neck OBOL:automatic nerve of neck (volume) OBOL:automatic A nerve that is part of a leg [Automatically generated definition]. EMAPA:37343 MA:0000673 nerve of leg uberon UBERON:0003431 leg nerve A nerve that is part of a leg [Automatically generated definition]. OBOL:automatic EMAPA:37343 MA:th nerve of leg OBOL:automatic A nerve that is part of a chest [Automatically generated definition]. EMAPA:37266 MA:0000551 anterior thoracic region nerve anterolateral part of thorax nerve front of thorax nerve nerve of anterior thoracic region nerve of anterolateral part of thorax nerve of chest nerve of front of thorax uberon UBERON:0003432 chest nerve A nerve that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37266 MA:th anterior thoracic region nerve OBOL:automatic anterolateral part of thorax nerve OBOL:automatic front of thorax nerve OBOL:automatic nerve of anterior thoracic region OBOL:automatic nerve of anterolateral part of thorax OBOL:automatic nerve of chest OBOL:automatic nerve of front of thorax OBOL:automatic A nerve that is part of an arm [Automatically generated definition]. EMAPA:37336 MA:0000595 brachial region nerve nerve of arm nerve of brachial region uberon UBERON:0003433 arm nerve A nerve that is part of an arm [Automatically generated definition]. OBOL:automatic EMAPA:37336 MA:th brachial region nerve OBOL:automatic nerve of arm OBOL:automatic nerve of brachial region OBOL:automatic A nerve that is part of a wrist [Automatically generated definition]. EMAPA:37339 MA:0000637 carpal region nerve nerve of carpal region nerve of wrist uberon UBERON:0003434 wrist nerve A nerve that is part of a wrist [Automatically generated definition]. OBOL:automatic EMAPA:37339 MA:th carpal region nerve OBOL:automatic nerve of carpal region OBOL:automatic nerve of wrist OBOL:automatic A nerve that is part of a toe [Automatically generated definition]. EMAPA:37348 MA:0000649 digit of foot nerve digit of terminal segment of free lower limb nerve digitus pedis nerve foot digit nerve hind limb digit nerve nerve of digit of foot nerve of digit of terminal segment of free lower limb nerve of digitus pedis nerve of foot digit nerve of terminal segment of free lower limb digit nerve of toe terminal segment of free lower limb digit nerve toe nerve foot digit nerve uberon UBERON:0003435 pedal digit nerve A nerve that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37348 MA:th digit of foot nerve OBOL:automatic digit of terminal segment of free lower limb nerve OBOL:automatic digitus pedis nerve OBOL:automatic foot digit nerve MA:0000649 hind limb digit nerve OBOL:accepted nerve of digit of foot OBOL:automatic nerve of digit of terminal segment of free lower limb OBOL:automatic nerve of digitus pedis OBOL:automatic nerve of foot digit OBOL:automatic nerve of terminal segment of free lower limb digit OBOL:automatic nerve of toe OBOL:automatic terminal segment of free lower limb digit nerve OBOL:automatic toe nerve OBOL:automatic foot digit nerve NCBITaxon:9606 OBOL:accepted A nerve that is part of a shoulder [Automatically generated definition]. EMAPA:37335 MA:0000634 nerve of shoulder uberon UBERON:0003436 shoulder nerve A nerve that is part of a shoulder [Automatically generated definition]. OBOL:automatic EMAPA:37335 MA:th nerve of shoulder OBOL:automatic Any nerve that innervates the iris. added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea EMAPA:35449 MA:0001291 nerve of iris ciliary nerve uberon UBERON:0003438 iris nerve Any nerve that innervates the iris. UBERON:cjm nerve of iris OBOL:automatic A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). EMAPA:37264 MA:0000515 nerve of torso nerve of trunk torso nerve uberon trunk nerve UBERON:0003439 nerve of trunk region A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). EMAPA:37264 MA:th nerve of torso OBOL:automatic nerve of trunk OBOL:automatic torso nerve OBOL:automatic trunk nerve MA:0000515 A nerve that is part of a limb [Automatically generated definition]. EMAPA:37291 MA:0000693 nerve of limb uberon UBERON:0003440 limb nerve A nerve that is part of a limb [Automatically generated definition]. OBOL:automatic EMAPA:37291 MA:th nerve of limb OBOL:automatic A nerve that is part of a forelimb [Automatically generated definition]. EMAPA:37334 MA:0000616 fore limb nerve nerve of fore limb nerve of forelimb nerve of superior member nerve of upper extremity wing nerve uberon UBERON:0003441 forelimb nerve A nerve that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37334 MA:th fore limb nerve OBOL:automatic nerve of fore limb OBOL:automatic nerve of forelimb OBOL:automatic nerve of superior member OBOL:automatic nerve of upper extremity OBOL:automatic wing nerve NCBITaxon:8782 OBOL:automatic A nerve that is part of a hindlimb [Automatically generated definition]. EMAPA:37342 MA:0000664 hind limb nerve nerve of hind limb nerve of hindlimb nerve of inferior member nerve of lower extremity uberon UBERON:0003442 hindlimb nerve A nerve that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37342 MA:th hind limb nerve OBOL:automatic nerve of hind limb OBOL:automatic nerve of hindlimb OBOL:automatic nerve of inferior member OBOL:automatic nerve of lower extremity OBOL:automatic A nerve that is located in a thoracic cavity [Automatically generated definition]. consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve EMAPA:37267 MA:0000556 cavity of chest nerve cavity of thorax nerve chest cavity nerve nerve of cavity of chest nerve of cavity of thorax nerve of chest cavity nerve of pectoral cavity nerve of thoracic cavity pectoral cavity nerve uberon UBERON:0003443 thoracic cavity nerve A nerve that is located in a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37267 MA:th cavity of chest nerve OBOL:automatic cavity of thorax nerve OBOL:automatic chest cavity nerve OBOL:automatic nerve of cavity of chest OBOL:automatic nerve of cavity of thorax OBOL:automatic nerve of chest cavity OBOL:automatic nerve of pectoral cavity OBOL:automatic nerve of thoracic cavity OBOL:automatic pectoral cavity nerve OBOL:automatic A nerve that is part of a pelvis [Automatically generated definition]. EMAPA:37269 MA:0000542 nerve of pelvis uberon UBERON:0003444 pelvis nerve A nerve that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37269 MA:th nerve of pelvis OBOL:automatic A nerve that is part of a foot [Automatically generated definition]. EMAPA:37347 MA:0000653 foot nerve nerve of foot uberon UBERON:0003445 pes nerve A nerve that is part of a foot [Automatically generated definition]. OBOL:automatic EMAPA:37347 MA:th foot nerve MA:0000653 nerve of foot OBOL:automatic A nerve that is part of an ankle [Automatically generated definition]. FMA placement dubious EMAPA:37346 MA:0000640 nerve of ankle tarsal region nerve uberon neural network of ankle UBERON:0003446 ankle nerve A nerve that is part of an ankle [Automatically generated definition]. OBOL:automatic FMA placement dubious FMA EMAPA:37346 MA:th nerve of ankle OBOL:automatic tarsal region nerve neural network of ankle FMA:86901 A nerve that is part of a finger [Automatically generated definition]. EMAPA:37341 MA:0000625 digit of hand nerve digit of terminal segment of free upper limb nerve digitus manus nerve finger nerve hand digit nerve nerve of digit of hand nerve of digit of terminal segment of free upper limb nerve of digitus manus nerve of finger nerve of hand digit nerve of terminal segment of free upper limb digit terminal segment of free upper limb digit nerve uberon UBERON:0003447 digit nerve of manus A nerve that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37341 MA:th digit of hand nerve OBOL:automatic digit of terminal segment of free upper limb nerve OBOL:automatic digitus manus nerve OBOL:automatic finger nerve OBOL:automatic hand digit nerve MA:0000625 nerve of digit of hand OBOL:automatic nerve of digit of terminal segment of free upper limb OBOL:automatic nerve of digitus manus OBOL:automatic nerve of finger OBOL:automatic nerve of hand digit OBOL:automatic nerve of terminal segment of free upper limb digit OBOL:automatic terminal segment of free upper limb digit nerve OBOL:automatic A nerve that is part of a manus [Automatically generated definition]. EMAPA:37340 MA:0000629 hand nerve nerve of hand nerve of manus uberon UBERON:0003448 manus nerve A nerve that is part of a manus [Automatically generated definition]. OBOL:automatic EMAPA:37340 MA:th hand nerve MA:0000629 nerve of hand UBERON:cjm nerve of manus OBOL:automatic An intervertebral disk that is part of a tail [Automatically generated definition]. EMAPA:19592 MA:0000698 intervertebral disc of post-ventral region intervertebral disc of tail intervertebral disk of post-ventral region intervertebral disk of tail tail intervertebral disk tail spinal disc uberon UBERON:0003449 tail intervertebral disc An intervertebral disk that is part of a tail [Automatically generated definition]. OBOL:automatic intervertebral disc of post-ventral region UBERON:cjm intervertebral disc of tail OBOL:automatic intervertebral disk of post-ventral region OBOL:automatic intervertebral disk of tail OBOL:automatic tail intervertebral disk OBOL:automatic tail spinal disc OBOL:automatic A lymphatic vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:37580 MA:0001824 apparatus respiratorius lymph vessel apparatus respiratorius lymphatic vessel lymph vessel of apparatus respiratorius lymph vessel of respiratory system lymphatic vessel of apparatus respiratorius lymphatic vessel of respiratory system respiratory system lymph vessel uberon UBERON:0003456 respiratory system lymphatic vessel A lymphatic vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37580 MA:th apparatus respiratorius lymph vessel OBOL:automatic apparatus respiratorius lymphatic vessel OBOL:automatic lymph vessel of apparatus respiratorius OBOL:automatic lymph vessel of respiratory system OBOL:automatic lymphatic vessel of apparatus respiratorius OBOL:automatic lymphatic vessel of respiratory system OBOL:automatic respiratory system lymph vessel OBOL:automatic A bone that is part of a head [Automatically generated definition]. EMAPA:35996 MA:0000576 adult head bone adult head bone organ bone of adult head bone of head bone organ of adult head bone organ of head head bone organ uberon craniofacial bone UBERON:0003457 Different sources vary regarding which bones are craniofacial; e.g. hyoid bone head bone A bone that is part of a head [Automatically generated definition]. OBOL:automatic adult head bone OBOL:automatic adult head bone organ OBOL:automatic bone of adult head OBOL:automatic bone of head OBOL:automatic bone organ of adult head OBOL:automatic bone organ of head OBOL:automatic head bone organ OBOL:automatic craniofacial bone A bone that is part of a neck [Automatically generated definition]. EMAPA:37246 MA:0000584 OpenCyc:Mx4rvnpJSJwpEbGdrcN5Y29ycA bone of neck bone of neck (volume) bone organ of neck bone organ of neck (volume) neck (volume) bone neck (volume) bone organ neck bone organ uberon UBERON:0003458 neck bone A bone that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37246 MA:th bone of neck OBOL:automatic bone of neck (volume) OBOL:automatic bone organ of neck OBOL:automatic bone organ of neck (volume) OBOL:automatic neck (volume) bone OBOL:automatic neck (volume) bone organ OBOL:automatic neck bone organ OBOL:automatic A bone that is part of a chest [Automatically generated definition]. EMAPA:18025 MA:0000547 anterior thoracic region bone anterior thoracic region bone organ anterolateral part of thorax bone anterolateral part of thorax bone organ bone of anterior thoracic region bone of anterolateral part of thorax bone of chest bone of front of thorax bone organ of anterior thoracic region bone organ of anterolateral part of thorax bone organ of chest bone organ of front of thorax chest bone organ front of thorax bone front of thorax bone organ uberon UBERON:0003459 chest bone A bone that is part of a chest [Automatically generated definition]. OBOL:automatic anterior thoracic region bone OBOL:automatic anterior thoracic region bone organ OBOL:automatic anterolateral part of thorax bone OBOL:automatic anterolateral part of thorax bone organ OBOL:automatic bone of anterior thoracic region OBOL:automatic bone of anterolateral part of thorax OBOL:automatic bone of chest OBOL:automatic bone of front of thorax OBOL:automatic bone organ of anterior thoracic region OBOL:automatic bone organ of anterolateral part of thorax OBOL:automatic bone organ of chest OBOL:automatic bone organ of front of thorax OBOL:automatic chest bone organ OBOL:automatic front of thorax bone OBOL:automatic front of thorax bone organ OBOL:automatic A bone that is part of the region of the forelimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia EMAPA:37303 MA:0000592 OpenCyc:Mx4rwKTXoJwpEbGdrcN5Y29ycA arm bone organ bone of arm bone organ of arm uberon bone of upper extremity UBERON:0003460 arm bone A bone that is part of the region of the forelimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia EMAPA:37303 MA:th arm bone organ OBOL:automatic bone of arm OBOL:automatic bone organ of arm OBOL:automatic bone of upper extremity GAID:178 A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods. this is a forelimb bone in MA, but this would lead to part-disjointness violations. MA:0000631 bone of shoulder shoulder-articulating bone uberon UBERON:0003461 shoulder bone UBERONREF:0000003 MA A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods. this is a forelimb bone in MA, but this would lead to part-disjointness violations. MA bone of shoulder OBOL:automatic A bone that is part of a facial skeleton [Automatically generated definition]. test whether 'facial bone' is an exact synonym EMAPA:19019 EMAPA:35924 MA:0001482 MA:0003159 NCIT:C63706 UMLS:C0015455 bone of facial skeleton facial bone facial skeleton bone uberon bone of viscerocranium viscerocranium bone UBERON:0003462 facial bone MA A bone that is part of a facial skeleton [Automatically generated definition]. OBOL:automatic UMLS:C0015455 ncithesaurus:Facial_Bone bone of facial skeleton OBOL:automatic facial bone EMAPA:19019 facial skeleton bone OBOL:automatic bone of viscerocranium OBOL:automatic viscerocranium bone OBOL:automatic A bone that is part of a trunk [Automatically generated definition]. EMAPA:36583 MA:0000512 bone of torso bone of trunk bone organ of torso bone organ of trunk torso bone torso bone organ trunk bone organ uberon UBERON:0003463 trunk bone A bone that is part of a trunk [Automatically generated definition]. OBOL:automatic bone of torso OBOL:automatic bone of trunk OBOL:automatic bone organ of torso OBOL:automatic bone organ of trunk OBOL:automatic torso bone OBOL:automatic torso bone organ OBOL:automatic trunk bone organ OBOL:automatic A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle) the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc EFO:0003842 GAID:198 NCIT:C12982 UMLS:C0448188 bone of hind limb bone of hindlimb bone of inferior member bone of lower extremity bone organ of hind limb bone organ of hindlimb bone organ of lower extremity hind limb bone hind limb bone organ hindlimb bone organ uberon UBERON:0003464 hindlimb bone A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle) the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc MA UMLS:C0448188 ncithesaurus:Bone_of_the_Lower_Extremity bone of hind limb OBOL:automatic bone of hindlimb OBOL:automatic bone of inferior member OBOL:automatic bone of lower extremity OBOL:automatic bone organ of hind limb OBOL:automatic bone organ of hindlimb OBOL:automatic bone organ of lower extremity OBOL:automatic hind limb bone OBOL:automatic hind limb bone organ OBOL:automatic hindlimb bone organ OBOL:automatic A bone that is part of a lower arm [Automatically generated definition]. EMAPA:35347 MA:0000598 antebrachial region bone antebrachial region bone organ arm zeugopod bone arm zeugopod bone organ lower arm bone zeugopod bone, forelimb zeugopod bone, upper wing zeugopod bone uberon UBERON:0003466 forelimb zeugopod bone A bone that is part of a lower arm [Automatically generated definition]. OBOL:automatic antebrachial region bone OBOL:automatic antebrachial region bone organ OBOL:automatic arm zeugopod bone OBOL:automatic arm zeugopod bone organ OBOL:automatic lower arm bone MA:0000598 zeugopod bone, forelimb OBOL:automatic zeugopod bone, upper OBOL:automatic wing zeugopod bone NCBITaxon:8782 OBOL:automatic The ureteral branches of renal artery are small branches which supply the ureter. ureteric artery EMAPA:37676 FMA:70491 MA:0002074 uberon UBERON:0003468 ureteric segment of renal artery FMA FMA The ureteral branches of renal artery are small branches which supply the ureter. ureteric artery MA:0002074 EMAPA:37676 MA:th An artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37569 MA:0001804 uberon UBERON:0003469 respiratory system artery An artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37569 MA:th The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. EMAPA:37429 FMA:49567 MA:0001916 arteria labialis inferior inferior labial artery inferior labial branch of facial artery ramus labialis inferior (arteria facialis) ramus labialis inferior arteriae facialis uberon UBERON:0003471 artery of lower lip FMA The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. EMAPA:37429 MA:th arteria labialis inferior inferior labial artery FMA:49567 inferior labial branch of facial artery FMA:49567 ramus labialis inferior (arteria facialis) FMA:TA ramus labialis inferior arteriae facialis An artery that supplies blood to the cerebellum. EHDAA2:0000228 EHDAA:5290 EMAPA:37074 MA:0001933 NCIT:C52845 UMLS:C0226246 uberon UBERON:0003472 cerebellar artery http://upload.wikimedia.org/wikipedia/commons/e/e1/CerebellumArteries.jpg An artery that supplies blood to the cerebellum. EMAPA:37074 MA:th UMLS:C0226246 ncithesaurus:Cerebellar_Artery An artery that is part of a thoracic cavity[cjm]. in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity EMAPA:37241 MA:0001902 MESH:D013895 uberon thoracic artery UBERON:0003473 thoracic cavity artery An artery that is part of a thoracic cavity[cjm]. in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity MA EMAPA:37241 MA:th thoracic artery MESH:A07.231.114.891 One of the arteries supplying a meninix[Automatically generated definition]. EMAPA:37104 GAID:499 MA:0002001 MESH:D008576 uberon UBERON:0003474 meningeal artery One of the arteries supplying a meninix[Automatically generated definition]. EMAPA:37104 MA:th A vein that is part of a ureter [Automatically generated definition]. EMAPA:37679 MA:0002250 ureter vein vein of ureter uberon UBERON:0003475 ureteric vein A vein that is part of a ureter [Automatically generated definition]. OBOL:automatic EMAPA:37679 MA:th ureter vein OBOL:automatic vein of ureter OBOL:automatic A vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37584 MA:0001809 MA:0001810 apparatus respiratorius vein respiratory system vein vein of apparatus respiratorius vein of respiratory system uberon UBERON:0003476 respiratory system venous blood vessel A vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37584 MA:th apparatus respiratorius vein OBOL:automatic respiratory system vein OBOL:automatic vein of apparatus respiratorius OBOL:automatic vein of respiratory system OBOL:automatic The inferior labial vein is the vein receiving blood from the lower lip. EMAPA:37202 FMA:52541 MA:0002253 inferior labial vein lower lip vein vena labialis inferior uberon venae labiales inferiores UBERON:0003478 vein of lower lip http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png The inferior labial vein is the vein receiving blood from the lower lip. EMAPA:37202 MA:th inferior labial vein FMA:52541 lower lip vein OBOL:automatic vena labialis inferior venae labiales inferiores A vein that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37242 MA:0001903 cavity of chest vein cavity of thorax vein chest cavity vein pectoral cavity vein vein of cavity of chest vein of cavity of thorax vein of chest cavity vein of pectoral cavity vein of thoracic cavity uberon UBERON:0003479 thoracic cavity vein A vein that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37242 MA:th cavity of chest vein OBOL:automatic cavity of thorax vein OBOL:automatic chest cavity vein OBOL:automatic pectoral cavity vein OBOL:automatic vein of cavity of chest OBOL:automatic vein of cavity of thorax OBOL:automatic vein of chest cavity OBOL:automatic vein of pectoral cavity OBOL:automatic vein of thoracic cavity OBOL:automatic A vein that is part of a clitoris [Automatically generated definition]. EMAPA:37201 MA:0002252 clitoris vein uberon UBERON:0003480 vein of clitoris A vein that is part of a clitoris [Automatically generated definition]. OBOL:automatic EMAPA:37201 MA:th clitoris vein OBOL:automatic A vein that is part of a tail [Automatically generated definition]. see also caudal vein AAO:0011105 EMAPA:37761 MA:0002233 XAO:0000393 post-vent region vein vein of post-vent region vein of tail uberon caudal vein UBERON:0003481 tail vein A vein that is part of a tail [Automatically generated definition]. OBOL:automatic EMAPA:37761 MA:th post-vent region vein OBOL:automatic vein of post-vent region OBOL:automatic vein of tail OBOL:automatic caudal vein A portion of lymphoid tissue that is part of a thymus [Automatically generated definition]. EMAPA:37766 MA:0002673 MESH:A06.407.850 NCIT:C38515 UMLS:C1515429 lymphoid tissue of thymus lymphoid tissue of thymus gland thymus gland lymphoid tissue uberon UBERON:0003483 thymus lymphoid tissue A portion of lymphoid tissue that is part of a thymus [Automatically generated definition]. OBOL:automatic EMAPA:37766 MA:th UMLS:C1515429 ncithesaurus:Thymic_Lymphoid_Tissue lymphoid tissue of thymus OBOL:automatic lymphoid tissue of thymus gland OBOL:automatic thymus gland lymphoid tissue OBOL:automatic A sebaceous gland that is part of a camera-type eye. Example: a tarsal gland. EMAPA:37531 MA:0002452 camera-type eye sebaceous gland sebaceous gland of camera-type eye sebaceous gland of vertebrate eye vertebrate eye sebaceous gland uberon UBERON:0003484 eye sebaceous gland MA A sebaceous gland that is part of a camera-type eye. Example: a tarsal gland. EMAPA:37531 MA:th camera-type eye sebaceous gland OBOL:automatic sebaceous gland of camera-type eye OBOL:automatic sebaceous gland of vertebrate eye OBOL:automatic vertebrate eye sebaceous gland OBOL:automatic A sebaceous gland that is part of a vagina [Automatically generated definition]. EMAPA:37793 MA:0001732 sebaceous gland of vagina uberon UBERON:0003485 vagina sebaceous gland A sebaceous gland that is part of a vagina [Automatically generated definition]. OBOL:automatic EMAPA:37793 MA:th sebaceous gland of vagina OBOL:automatic A holocrine gland of the dermis that secretes sebum into hair follicles. MA:0000149 cutaneous sebaceous gland sebaceous gland of skin uberon UBERON:0003487 skin sebaceous gland A holocrine gland of the dermis that secretes sebum into hair follicles. MP:0009535 sebaceous gland of skin OBOL:automatic An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37575 MA:0001808 apparatus respiratorius blood capillary endothelium apparatus respiratorius capillary endothelium apparatus respiratorius capillary vessel endothelium apparatus respiratorius endothelium of blood capillary apparatus respiratorius endothelium of capillary apparatus respiratorius endothelium of capillary vessel blood capillary endothelium of apparatus respiratorius blood capillary endothelium of respiratory system capillary endothelium of apparatus respiratorius capillary endothelium of respiratory system capillary vessel endothelium of apparatus respiratorius capillary vessel endothelium of respiratory system endothelium of blood capillary of apparatus respiratorius endothelium of blood capillary of respiratory system endothelium of capillary of apparatus respiratorius endothelium of capillary of respiratory system endothelium of capillary vessel of apparatus respiratorius endothelium of capillary vessel of respiratory system respiratory system blood capillary endothelium respiratory system capillary vessel endothelium respiratory system endothelium of blood capillary respiratory system endothelium of capillary respiratory system endothelium of capillary vessel uberon UBERON:0003489 respiratory system capillary endothelium true An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37575 MA:th apparatus respiratorius blood capillary endothelium OBOL:automatic apparatus respiratorius capillary endothelium OBOL:automatic apparatus respiratorius capillary vessel endothelium OBOL:automatic apparatus respiratorius endothelium of blood capillary OBOL:automatic apparatus respiratorius endothelium of capillary OBOL:automatic apparatus respiratorius endothelium of capillary vessel OBOL:automatic blood capillary endothelium of apparatus respiratorius OBOL:automatic blood capillary endothelium of respiratory system OBOL:automatic capillary endothelium of apparatus respiratorius OBOL:automatic capillary endothelium of respiratory system OBOL:automatic capillary vessel endothelium of apparatus respiratorius OBOL:automatic capillary vessel endothelium of respiratory system OBOL:automatic endothelium of blood capillary of apparatus respiratorius OBOL:automatic endothelium of blood capillary of respiratory system OBOL:automatic endothelium of capillary of apparatus respiratorius OBOL:automatic endothelium of capillary of respiratory system OBOL:automatic endothelium of capillary vessel of apparatus respiratorius OBOL:automatic endothelium of capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary endothelium OBOL:automatic respiratory system capillary vessel endothelium OBOL:automatic respiratory system endothelium of blood capillary OBOL:automatic respiratory system endothelium of capillary OBOL:automatic respiratory system endothelium of capillary vessel OBOL:automatic A venule that is part of a respiratory system [Automatically generated definition]. EMAPA:37587 MA:0001813 apparatus respiratorius venule venule of apparatus respiratorius venule of respiratory system uberon UBERON:0003494 respiratory system venule A venule that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37587 MA:th apparatus respiratorius venule OBOL:automatic venule of apparatus respiratorius OBOL:automatic venule of respiratory system OBOL:automatic An arteriole that is part of a respiratory system [Automatically generated definition]. EMAPA:37568 MA:0001803 uberon UBERON:0003495 respiratory system arteriole true An arteriole that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37568 MA:th A blood vessel that is part of a head [Automatically generated definition]. EMAPA:36610 MA:0000575 adult head blood vessel blood vessel of adult head blood vessel of head uberon UBERON:0003496 head blood vessel true A blood vessel that is part of a head [Automatically generated definition]. OBOL:automatic adult head blood vessel OBOL:automatic blood vessel of adult head OBOL:automatic blood vessel of head OBOL:automatic A blood vessel that is part of an abdomen [Automatically generated definition]. MA:0000518 blood vessel of abdomen uberon UBERON:0003497 abdomen blood vessel UBERON:0012254 A blood vessel that is part of an abdomen [Automatically generated definition]. OBOL:automatic blood vessel of abdomen OBOL:automatic UBERON:0012254 abdominal aorta artery A blood vessel that is part of a heart [Automatically generated definition]. EMAPA:35397 MA:0002483 blood vessel of heart uberon cardiac blood vessel UBERON:0003498 heart blood vessel A blood vessel that is part of a heart [Automatically generated definition]. OBOL:automatic blood vessel of heart OBOL:automatic cardiac blood vessel EMAPA:35397 A blood vessel that is part of a brain [Automatically generated definition]. EMAPA:35182 MA:0002769 blood vessel of brain uberon UBERON:0003499 brain blood vessel A blood vessel that is part of a brain [Automatically generated definition]. OBOL:automatic blood vessel of brain OBOL:automatic A blood vessel that is part of a cornea [Automatically generated definition]. follow up on tracker item EMAPA:36611 MA:0001241 blood vessel of cornea cornea blood vessel uberon UBERON:0003500 corneal blood vessel A blood vessel that is part of a cornea [Automatically generated definition]. blood vessel of cornea OBOL:automatic cornea blood vessel OBOL:automatic A blood vessel that is part of a retina [Automatically generated definition]. EMAPA:36520 GAID:509 MA:0001317 MESH:D012171 XAO:0004153 blood vessel of inner layer of eyeball blood vessel of retina blood vessel of tunica interna of eyeball inner layer of eyeball blood vessel retinal blood vessel tunica interna of eyeball blood vessel uberon UBERON:0003501 retina blood vessel A blood vessel that is part of a retina [Automatically generated definition]. OBOL:automatic blood vessel of inner layer of eyeball OBOL:automatic blood vessel of retina OBOL:automatic blood vessel of tunica interna of eyeball OBOL:automatic inner layer of eyeball blood vessel OBOL:automatic retinal blood vessel OBOL:automatic tunica interna of eyeball blood vessel OBOL:automatic A blood vessel that is part of a neck [Automatically generated definition]. EMAPA:37236 MA:0000583 blood vessel of neck blood vessel of neck (volume) neck (volume) blood vessel uberon UBERON:0003502 neck blood vessel A blood vessel that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37236 MA:th blood vessel of neck OBOL:automatic blood vessel of neck (volume) OBOL:automatic neck (volume) blood vessel OBOL:automatic A blood vessel that is part of a leg [Automatically generated definition]. EMAPA:36500 MA:0000669 blood vessel of leg uberon UBERON:0003503 leg blood vessel A blood vessel that is part of a leg [Automatically generated definition]. OBOL:automatic blood vessel of leg OBOL:automatic A blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:35731 EMAPA:35995 MA:0001799 apparatus respiratorius blood vessel blood vessel of apparatus respiratorius blood vessel of respiratory system uberon UBERON:0003504 respiratory system blood vessel A blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius blood vessel OBOL:automatic blood vessel of apparatus respiratorius OBOL:automatic blood vessel of respiratory system OBOL:automatic A blood vessel that is part of a trachea. UBERON:0003525 EMAPA:35874 MA:0001852 blood vessel of trachea uberon UBERON:0003505 trachea blood vessel A blood vessel that is part of a trachea. OBOL:automatic blood vessel of trachea OBOL:automatic A blood vessel that is part of a chest [Automatically generated definition]. EMAPA:37239 MA:0000549 anterior thoracic region blood vessel anterolateral part of thorax blood vessel blood vessel of anterior thoracic region blood vessel of anterolateral part of thorax blood vessel of chest blood vessel of front of thorax front of thorax blood vessel uberon UBERON:0003506 chest blood vessel A blood vessel that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37239 MA:th anterior thoracic region blood vessel OBOL:automatic anterolateral part of thorax blood vessel OBOL:automatic blood vessel of anterior thoracic region OBOL:automatic blood vessel of anterolateral part of thorax OBOL:automatic blood vessel of chest OBOL:automatic blood vessel of front of thorax OBOL:automatic front of thorax blood vessel OBOL:automatic A blood vessel that is part of an arm [Automatically generated definition]. EMAPA:37293 MA:0000591 blood vessel of arm uberon UBERON:0003507 arm blood vessel A blood vessel that is part of an arm [Automatically generated definition]. OBOL:automatic EMAPA:37293 MA:th blood vessel of arm OBOL:automatic A blood vessel that is part of a toe [Automatically generated definition]. EMAPA:37302 MA:0000645 blood vessel of digit of foot blood vessel of digit of terminal segment of free lower limb blood vessel of digitus pedis blood vessel of foot digit blood vessel of terminal segment of free lower limb digit blood vessel of toe digit of foot blood vessel digit of terminal segment of free lower limb blood vessel digitus pedis blood vessel foot digit blood vessel hind limb digit blood vessel terminal segment of free lower limb digit blood vessel toe blood vessel foot digit blood vessel uberon UBERON:0003508 pedal digit blood vessel A blood vessel that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37302 MA:th blood vessel of digit of foot OBOL:automatic blood vessel of digit of terminal segment of free lower limb OBOL:automatic blood vessel of digitus pedis OBOL:automatic blood vessel of foot digit OBOL:automatic blood vessel of terminal segment of free lower limb digit OBOL:automatic blood vessel of toe OBOL:automatic digit of foot blood vessel OBOL:automatic digit of terminal segment of free lower limb blood vessel OBOL:automatic digitus pedis blood vessel OBOL:automatic foot digit blood vessel MA:0000645 hind limb digit blood vessel OBOL:accepted terminal segment of free lower limb digit blood vessel OBOL:automatic toe blood vessel OBOL:automatic foot digit blood vessel NCBITaxon:9606 OBOL:accepted A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. EMAPA:35144 MA:0000061 uberon UBERON:0003509 only in MA - supertype of artery, arteriole, aorta. arterial blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. A blood vessel that is part of a iris [Automatically generated definition]. EMAPA:37387 MA:0001290 ZFA:0005568 blood vessel of iris uberon UBERON:0003511 iris blood vessel A blood vessel that is part of a iris [Automatically generated definition]. OBOL:automatic EMAPA:37387 MA:th blood vessel of iris OBOL:automatic A blood vessel that is part of a lung [Automatically generated definition]. EMAPA:32867 MA:0002457 blood vessel of lung uberon pulmonary vascular element UBERON:0003512 lung blood vessel A blood vessel that is part of a lung [Automatically generated definition]. OBOL:automatic blood vessel of lung OBOL:automatic pulmonary vascular element EMAPA:32867 A blood vessel that is part of a trunk [Automatically generated definition]. EMAPA:37237 MA:0000511 blood vessel of torso blood vessel of trunk torso blood vessel uberon UBERON:0003513 trunk blood vessel A blood vessel that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37237 MA:th blood vessel of torso OBOL:automatic blood vessel of trunk OBOL:automatic torso blood vessel OBOL:automatic A blood vessel that is part of a limb [Automatically generated definition]. EMAPA:36598 MA:0000687 blood vessel of limb uberon UBERON:0003514 limb blood vessel A blood vessel that is part of a limb [Automatically generated definition]. OBOL:automatic blood vessel of limb OBOL:automatic A blood vessel that is part of a forelimb [Automatically generated definition]. EMAPA:37292 MA:0000611 anteriormost limb blood vessel blood vessel of anteriormost limb blood vessel of fore limb blood vessel of forelimb blood vessel of upper extremity fore limb blood vessel wing blood vessel uberon UBERON:0003515 forelimb blood vessel A blood vessel that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37292 MA:th anteriormost limb blood vessel OBOL:automatic blood vessel of anteriormost limb OBOL:automatic blood vessel of fore limb OBOL:automatic blood vessel of forelimb OBOL:automatic blood vessel of upper extremity OBOL:automatic fore limb blood vessel OBOL:automatic wing blood vessel NCBITaxon:8782 OBOL:automatic A blood vessel that is part of a hindlimb [Automatically generated definition]. EMAPA:37298 MA:0000659 blood vessel of hind limb blood vessel of hindlimb blood vessel of lower extremity hind limb blood vessel uberon UBERON:0003516 hindlimb blood vessel A blood vessel that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37298 MA:th blood vessel of hind limb OBOL:automatic blood vessel of hindlimb OBOL:automatic blood vessel of lower extremity OBOL:automatic hind limb blood vessel OBOL:automatic A blood vessel that is part of a kidney [Automatically generated definition]. EMAPA:28457 MA:0001682 TAO:0005306 ZFA:0005306 blood vessel of kidney renal blood vessel uberon UBERON:0003517 kidney blood vessel A blood vessel that is part of a kidney [Automatically generated definition]. OBOL:automatic blood vessel of kidney OBOL:automatic renal blood vessel OBOL:automatic A blood vessel that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37240 MA:0000554 blood vessel of cavity of chest blood vessel of cavity of thorax blood vessel of chest cavity blood vessel of pectoral cavity blood vessel of thoracic cavity cavity of chest blood vessel cavity of thorax blood vessel chest cavity blood vessel pectoral cavity blood vessel uberon UBERON:0003519 thoracic cavity blood vessel A blood vessel that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37240 MA:th blood vessel of cavity of chest OBOL:automatic blood vessel of cavity of thorax OBOL:automatic blood vessel of chest cavity OBOL:automatic blood vessel of pectoral cavity OBOL:automatic blood vessel of thoracic cavity OBOL:automatic cavity of chest blood vessel OBOL:automatic cavity of thorax blood vessel OBOL:automatic chest cavity blood vessel OBOL:automatic pectoral cavity blood vessel OBOL:automatic A blood vessel that is part of a pelvis [Automatically generated definition]. EMAPA:37244 MA:0000531 blood vessel of pelvis uberon UBERON:0003520 pelvis blood vessel A blood vessel that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37244 MA:th blood vessel of pelvis OBOL:automatic A blood vessel that is part of a foot [Automatically generated definition]. EMAPA:37301 MA:0000642 blood vessel of foot foot blood vessel uberon UBERON:0003521 pes blood vessel A blood vessel that is part of a foot [Automatically generated definition]. OBOL:automatic EMAPA:37301 MA:th blood vessel of foot OBOL:automatic foot blood vessel MA:0000642 A blood vessel that is part of a finger [Automatically generated definition]. EMAPA:37297 MA:0000621 blood vessel of digit of terminal segment of free upper limb blood vessel of terminal segment of free upper limb digit digit of terminal segment of free upper limb blood vessel finger blood vessel hand digit blood vessel terminal segment of free upper limb digit blood vessel hand digit blood vessel uberon UBERON:0003522 manual digit blood vessel A blood vessel that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37297 MA:th blood vessel of digit of terminal segment of free upper limb OBOL:automatic blood vessel of terminal segment of free upper limb digit OBOL:automatic digit of terminal segment of free upper limb blood vessel OBOL:automatic finger blood vessel OBOL:automatic hand digit blood vessel MA:0000621 terminal segment of free upper limb digit blood vessel OBOL:automatic hand digit blood vessel NCBITaxon:9606 OBOL:accepted A blood vessel that is part of a manus [Automatically generated definition]. EMAPA:37296 MA:0000618 blood vessel of hand blood vessel of manus hand blood vessel uberon UBERON:0003523 manus blood vessel A blood vessel that is part of a manus [Automatically generated definition]. OBOL:automatic EMAPA:37296 MA:th blood vessel of hand OBOL:automatic blood vessel of manus OBOL:automatic hand blood vessel MA:0000618 A blood vessel that is part of a tail [Automatically generated definition]. EMAPA:35848 MA:0000695 blood vessel of post-vent region blood vessel of tail post-vent region blood vessel uberon UBERON:0003524 tail blood vessel A blood vessel that is part of a tail [Automatically generated definition]. OBOL:automatic blood vessel of post-vent region OBOL:automatic blood vessel of tail OBOL:automatic post-vent region blood vessel OBOL:automatic A capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37574 MA:0001807 apparatus respiratorius blood capillary apparatus respiratorius capillary apparatus respiratorius capillary vessel blood capillary of apparatus respiratorius blood capillary of respiratory system capillary of apparatus respiratorius capillary of respiratory system capillary vessel of apparatus respiratorius capillary vessel of respiratory system respiratory system blood capillary respiratory system capillary vessel uberon UBERON:0003526 respiratory system capillary A capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37574 MA:th apparatus respiratorius blood capillary OBOL:automatic apparatus respiratorius capillary OBOL:automatic apparatus respiratorius capillary vessel OBOL:automatic blood capillary of apparatus respiratorius OBOL:automatic blood capillary of respiratory system OBOL:automatic capillary of apparatus respiratorius OBOL:automatic capillary of respiratory system OBOL:automatic capillary vessel of apparatus respiratorius OBOL:automatic capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary OBOL:automatic respiratory system capillary vessel OBOL:automatic A capillary that is part of a kidney [Automatically generated definition]. EMAPA:31443 MA:0002586 blood capillary of kidney capillary of kidney capillary vessel of kidney kidney blood capillary kidney capillary vessel renal capillary uberon UBERON:0003527 kidney capillary A capillary that is part of a kidney [Automatically generated definition]. OBOL:automatic blood capillary of kidney OBOL:automatic capillary of kidney OBOL:automatic capillary vessel of kidney OBOL:automatic kidney blood capillary OBOL:automatic kidney capillary vessel OBOL:automatic renal capillary OBOL:automatic A gray matter that is part of a brain [Automatically generated definition]. EMAPA:35184 MA:0000810 NCIT:C49333 UMLS:C1707348 brain grey matter brain grey substance gray matter of brain grey matter of brain grey substance of brain uberon UBERON:0003528 brain gray matter A gray matter that is part of a brain [Automatically generated definition]. OBOL:automatic UMLS:C1707348 ncithesaurus:Cerebral_Gray_Matter brain grey matter MA:0000810 brain grey substance OBOL:automatic gray matter of brain OBOL:automatic grey matter of brain OBOL:automatic grey substance of brain OBOL:automatic An lymphatic vessel endothelium that is part of a respiratory system [Automatically generated definition]. EMAPA:37581 MA:0001825 apparatus respiratorius endothelium of lymph vessel apparatus respiratorius lymph vessel endothelium apparatus respiratorius lymphatic vessel endothelium endothelium of lymph vessel of apparatus respiratorius endothelium of lymph vessel of respiratory system lymph vessel endothelium of apparatus respiratorius lymph vessel endothelium of respiratory system lymphatic vessel endothelium of apparatus respiratorius lymphatic vessel endothelium of respiratory system respiratory system endothelium of lymph vessel respiratory system lymph vessel endothelium respiratory system lymphatic vessel endothelium uberon UBERON:0003529 respiratory system lymphatic vessel endothelium An lymphatic vessel endothelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37581 MA:th apparatus respiratorius endothelium of lymph vessel OBOL:automatic apparatus respiratorius lymph vessel endothelium OBOL:automatic apparatus respiratorius lymphatic vessel endothelium OBOL:automatic endothelium of lymph vessel of apparatus respiratorius OBOL:automatic endothelium of lymph vessel of respiratory system OBOL:automatic lymph vessel endothelium of apparatus respiratorius OBOL:automatic lymph vessel endothelium of respiratory system OBOL:automatic lymphatic vessel endothelium of apparatus respiratorius OBOL:automatic lymphatic vessel endothelium of respiratory system OBOL:automatic respiratory system endothelium of lymph vessel OBOL:automatic respiratory system lymph vessel endothelium OBOL:automatic respiratory system lymphatic vessel endothelium OBOL:automatic A zone of skin that is part of a toe [Automatically generated definition]. EMAPA:32942 FMA:37852 MA:0000650 NCIT:C52719 UMLS:C1708089 digit of foot skin digit of terminal segment of free lower limb skin digitus pedis skin foot digit skin hind limb digit skin skin of digit of foot skin of digit of terminal segment of free lower limb skin of digitus pedis skin of foot digit skin of terminal segment of free lower limb digit skin of toe terminal segment of free lower limb digit skin toe skin foot digit skin uberon UBERON:0003530 pedal digit skin A zone of skin that is part of a toe [Automatically generated definition]. OBOL:automatic UMLS:C1708089 ncithesaurus:Foot_Digit_Skin digit of foot skin OBOL:automatic digit of terminal segment of free lower limb skin OBOL:automatic digitus pedis skin OBOL:automatic foot digit skin MA:0000650 hind limb digit skin OBOL:accepted skin of digit of foot OBOL:automatic skin of digit of terminal segment of free lower limb OBOL:automatic skin of digitus pedis OBOL:automatic skin of foot digit OBOL:automatic skin of terminal segment of free lower limb digit OBOL:automatic skin of toe OBOL:automatic terminal segment of free lower limb digit skin OBOL:automatic toe skin OBOL:automatic foot digit skin NCBITaxon:9606 OBOL:accepted A zone of skin that is part of a forelimb [Automatically generated definition]. TODO - check free limb vs pectoral complex EMAPA:32612 FMA:23101 MA:0000617 NCIT:C12296 UMLS:C0222212 anteriormost limb skin fore limb skin skin of fore limb skin of forelimb skin of upper limb upper limb skin wing skin uberon UBERON:0003531 forelimb skin A zone of skin that is part of a forelimb [Automatically generated definition]. OBOL:automatic UMLS:C0222212 ncithesaurus:Skin_of_the_Upper_Limb_and_Shoulder anteriormost limb skin OBOL:automatic fore limb skin OBOL:automatic skin of fore limb OBOL:automatic skin of forelimb OBOL:automatic skin of upper limb FMA:23101 upper limb skin FMA:23101 wing skin NCBITaxon:8782 OBOL:automatic A zone of skin that is part of a hindlimb [Automatically generated definition]. TODO - check free limb vs pelvic complex EMAPA:32620 FMA:23102 MA:0000665 NCIT:C12297 UMLS:C0222268 hind limb skin lower limb skin skin of hind limb skin of hindlimb skin of lower extremity skin of lower limb uberon UBERON:0003532 hindlimb skin A zone of skin that is part of a hindlimb [Automatically generated definition]. OBOL:automatic UMLS:C0222268 ncithesaurus:Skin_of_the_Lower_Limb_and_Hip hind limb skin OBOL:automatic lower limb skin FMA:23102 skin of hind limb OBOL:automatic skin of hindlimb OBOL:automatic skin of lower extremity OBOL:automatic skin of lower limb FMA:23102 A zone of skin that is part of a finger [Automatically generated definition]. EMAPA:32648 FMA:38304 MA:0000626 NCIT:C52720 UMLS:C1708318 digit of hand skin digit of terminal segment of free upper limb skin digitus manus skin finger skin fore limb digit skin hand digit skin skin of digit of hand skin of digit of terminal segment of free upper limb skin of digitus manus skin of finger skin of hand digit skin of terminal segment of free upper limb digit terminal segment of free upper limb digit skin hand digit skin uberon UBERON:0003533 manual digit skin A zone of skin that is part of a finger [Automatically generated definition]. OBOL:automatic UMLS:C1708318 ncithesaurus:Hand_Digit_Skin digit of hand skin OBOL:automatic digit of terminal segment of free upper limb skin OBOL:automatic digitus manus skin OBOL:automatic finger skin OBOL:automatic fore limb digit skin OBOL:accepted hand digit skin MA:0000626 skin of digit of hand OBOL:automatic skin of digit of terminal segment of free upper limb OBOL:automatic skin of digitus manus OBOL:automatic skin of finger OBOL:automatic skin of hand digit OBOL:automatic skin of terminal segment of free upper limb digit OBOL:automatic terminal segment of free upper limb digit skin OBOL:automatic hand digit skin NCBITaxon:9606 OBOL:accepted A zone of skin that is part of a tail [Automatically generated definition]. EMAPA:36502 MA:0000700 post-vent region skin skin of post-vent region skin of tail uberon UBERON:0003534 tail skin A zone of skin that is part of a tail [Automatically generated definition]. OBOL:automatic post-vent region skin OBOL:automatic skin of post-vent region OBOL:automatic skin of tail OBOL:automatic A nerve trunk that is part of a vagus nerve. UBERON:0006308 EHDAA2:0002160 EHDAA:4659 EMAPA:17272 FMA:6221 MA:0001150 VHOG:0000736 trunk of vagal nerve trunk of vagus nerve vagal X nerve trunk vagal nerve trunk vagus nerve trunk vagus neural trunk uberon UBERON:0003535 vagus X nerve trunk A nerve trunk that is part of a vagus nerve. OBOL:automatic trunk of vagus nerve FMA:6221 vagal X nerve trunk EMAPA:17272 vagal nerve trunk EMAPA:17272 vagus neural trunk FMA:6221 A bronchiole that is part of a right lung [Automatically generated definition]. EMAPA:35425 MA:0001787 NCIT:C49279 UMLS:C0225670 bronchiole of right lung lobular bronchiole of right lung right lung lobular bronchiole uberon UBERON:0003538 right lung bronchiole A bronchiole that is part of a right lung [Automatically generated definition]. OBOL:automatic UMLS:C0225670 ncithesaurus:Right_Lung_Bronchiole bronchiole of right lung OBOL:automatic lobular bronchiole of right lung OBOL:automatic right lung lobular bronchiole OBOL:automatic A bronchiole that is part of a left lung [Automatically generated definition]. EMAPA:19000 MA:0001778 NCIT:C49252 UMLS:C0225674 bronchiole of left lung left lung lobular bronchiole lobular bronchiole of left lung uberon UBERON:0003539 left lung bronchiole A bronchiole that is part of a left lung [Automatically generated definition]. OBOL:automatic UMLS:C0225674 ncithesaurus:Left_Lung_Bronchiole bronchiole of left lung OBOL:automatic left lung lobular bronchiole OBOL:automatic lobular bronchiole of left lung OBOL:automatic A terminal bronchiole that is part of a right lung [Automatically generated definition]. EMAPA:36638 MA:0001789 NCIT:C49294 UMLS:C1709961 bronchiolus terminalis of right lung right lung bronchiolus terminalis terminal bronchiole of right lung uberon UBERON:0003540 right lung terminal bronchiole A terminal bronchiole that is part of a right lung [Automatically generated definition]. OBOL:automatic UMLS:C1709961 ncithesaurus:Right_Lung_Terminal_Bronchiole bronchiolus terminalis of right lung OBOL:automatic right lung bronchiolus terminalis OBOL:automatic terminal bronchiole of right lung OBOL:automatic A terminal bronchiole that is part of a left lung [Automatically generated definition]. EMAPA:36636 MA:0001780 NCIT:C49255 UMLS:C1708675 bronchiolus terminalis of left lung left lung bronchiolus terminalis terminal bronchiole of left lung uberon UBERON:0003541 left lung terminal bronchiole A terminal bronchiole that is part of a left lung [Automatically generated definition]. OBOL:automatic UMLS:C1708675 ncithesaurus:Left_Lung_Terminal_Bronchiole bronchiolus terminalis of left lung OBOL:automatic left lung bronchiolus terminalis OBOL:automatic terminal bronchiole of left lung OBOL:automatic A meninx that is part of a brain [Automatically generated definition]. Meninges that are part of the brain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] CALOHA:TS-2147 EMAPA:32662 EV:0100312 MA:0000813 VHOG:0000013 brain meninges meninges of brain meninx of brain uberon UBERON:0003547 brain meninx A meninx that is part of a brain [Automatically generated definition]. OBOL:automatic Meninges that are part of the brain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000013 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000013 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 brain meninges OBOL:automatic meninges of brain OBOL:automatic meninx of brain OBOL:automatic A meninx that is part of a forebrain [Automatically generated definition]. EMAPA:17764 EMAPA:17774 EMAPA:37543 MA:0000883 forebrain meninx meninges of forebrain meninx of forebrain uberon UBERON:0003548 forebrain meninges A meninx that is part of a forebrain [Automatically generated definition]. OBOL:automatic EMAPA:37543 MA:th forebrain meninx OBOL:automatic meninges of forebrain OBOL:automatic meninx of forebrain OBOL:automatic The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule. The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:32667 EV:0100315 MA:0000816 NCIT:C49335 UMLS:C1706994 VHOG:0000470 brain pia mater of neuraxis pia mater of brain pia mater of neuraxis of brain uberon UBERON:0003549 brain pia mater The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule. MP:0009026 The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000470 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000470 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C1706994 ncithesaurus:Brain_Pia_Mater brain pia mater of neuraxis OBOL:automatic pia mater of brain OBOL:automatic pia mater of neuraxis of brain OBOL:automatic A pia mater that is part of a forebrain [Automatically generated definition]. EMAPA:17767 EMAPA:17777 EMAPA:37546 MA:0000886 forebrain pia mater of neuraxis pia mater of forebrain pia mater of neuraxis of forebrain uberon UBERON:0003550 forebrain pia mater A pia mater that is part of a forebrain [Automatically generated definition]. OBOL:automatic EMAPA:37546 MA:th forebrain pia mater of neuraxis OBOL:automatic pia mater of forebrain OBOL:automatic pia mater of neuraxis of forebrain OBOL:automatic A pia mater that is part of a midbrain [Automatically generated definition]. Pia mater that is part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001175 EMAPA:17794 MA:0001061 RETIRED_EHDAA2:0001110 VHOG:0000467 midbrain pia mater of neuraxis pia mater of midbrain pia mater of neuraxis of midbrain uberon mesencephalon pia mater UBERON:0003551 midbrain pia mater A pia mater that is part of a midbrain [Automatically generated definition]. OBOL:automatic Pia mater that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000467 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000467 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 midbrain pia mater of neuraxis OBOL:automatic pia mater of midbrain OBOL:automatic pia mater of neuraxis of midbrain OBOL:automatic mesencephalon pia mater VHOG:0000467 A pia mater that is part of a telencephalon [Automatically generated definition]. Pia mater that is part of the telencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001992 EMAPA:17777 MA:0000982 VHOG:0000476 pia mater of neuraxis of telencephalon pia mater of telencephalon telencephalon pia mater of neuraxis uberon UBERON:0003552 telencephalon pia mater A pia mater that is part of a telencephalon [Automatically generated definition]. OBOL:automatic Pia mater that is part of the telencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000476 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000476 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 pia mater of neuraxis of telencephalon OBOL:automatic pia mater of telencephalon OBOL:automatic telencephalon pia mater of neuraxis OBOL:automatic A pia mater that is part of a diencephalon [Automatically generated definition]. Pia mater that is part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000400 EMAPA:17767 MA:0000829 VHOG:0000475 between brain pia mater between brain pia mater of neuraxis diencephalon pia mater of neuraxis interbrain pia mater interbrain pia mater of neuraxis mature diencephalon pia mater mature diencephalon pia mater of neuraxis pia mater of between brain pia mater of diencephalon pia mater of interbrain pia mater of mature diencephalon pia mater of neuraxis of between brain pia mater of neuraxis of diencephalon pia mater of neuraxis of interbrain pia mater of neuraxis of mature diencephalon uberon UBERON:0003553 diencephalon pia mater A pia mater that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Pia mater that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000475 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000475 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 between brain pia mater OBOL:automatic between brain pia mater of neuraxis OBOL:automatic diencephalon pia mater of neuraxis OBOL:automatic interbrain pia mater OBOL:automatic interbrain pia mater of neuraxis OBOL:automatic mature diencephalon pia mater OBOL:automatic mature diencephalon pia mater of neuraxis OBOL:automatic pia mater of between brain OBOL:automatic pia mater of diencephalon OBOL:automatic pia mater of interbrain OBOL:automatic pia mater of mature diencephalon OBOL:automatic pia mater of neuraxis of between brain OBOL:automatic pia mater of neuraxis of diencephalon OBOL:automatic pia mater of neuraxis of interbrain OBOL:automatic pia mater of neuraxis of mature diencephalon OBOL:automatic A pia mater that is part of a hindbrain [Automatically generated definition]. Pia mater that is part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0000772 EMAPA:17786 MA:0000990 VHOG:0000466 hindbrain pia mater of neuraxis pia mater of hindbrain pia mater of neuraxis of hindbrain uberon rhombencephalon pia mater UBERON:0003554 hindbrain pia mater A pia mater that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Pia mater that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000466 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000466 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 hindbrain pia mater of neuraxis OBOL:automatic pia mater of hindbrain OBOL:automatic pia mater of neuraxis of hindbrain OBOL:automatic rhombencephalon pia mater VHOG:0000466 A pia mater that is part of a spinal cord [Automatically generated definition]. The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EHDAA2:0001896 EMAPA:17807 MA:0001133 NCIT:C49800 UMLS:C1710148 VHOG:0000468 pia mater of neuraxis of spinal cord pia mater of spinal cord spinal cord pia mater of neuraxis uberon UBERON:0003555 spinal cord pia mater A pia mater that is part of a spinal cord [Automatically generated definition]. OBOL:automatic The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000468 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000468 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 UMLS:C1710148 ncithesaurus:Spinal_Cord_Pia_Mater pia mater of neuraxis of spinal cord OBOL:automatic pia mater of spinal cord OBOL:automatic spinal cord pia mater of neuraxis OBOL:automatic An arachnoid mater that is part of a forebrain [Automatically generated definition]. EMAPA:17765 EMAPA:17775 EMAPA:37544 MA:0000884 arachnoid mater of forebrain arachnoid mater of neuraxis of forebrain arachnoid of forebrain forebrain arachnoid forebrain arachnoid mater of neuraxis uberon UBERON:0003556 forebrain arachnoid mater An arachnoid mater that is part of a forebrain [Automatically generated definition]. OBOL:automatic EMAPA:37544 MA:th arachnoid mater of forebrain OBOL:automatic arachnoid mater of neuraxis of forebrain OBOL:automatic arachnoid of forebrain OBOL:automatic forebrain arachnoid OBOL:automatic forebrain arachnoid mater of neuraxis OBOL:automatic An arachnoid mater that is part of a midbrain [Automatically generated definition]. Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17792 MA:0001059 VHOG:0000233 arachnoid mater of midbrain arachnoid mater of neuraxis of midbrain arachnoid of midbrain midbrain arachnoid midbrain arachnoid mater of neuraxis uberon mesencephalon arachnoid mater UBERON:0003557 midbrain arachnoid mater An arachnoid mater that is part of a midbrain [Automatically generated definition]. OBOL:automatic Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000233 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000233 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoid mater of midbrain OBOL:automatic arachnoid mater of neuraxis of midbrain OBOL:automatic arachnoid of midbrain OBOL:automatic midbrain arachnoid OBOL:automatic midbrain arachnoid mater of neuraxis OBOL:automatic mesencephalon arachnoid mater VHOG:0000233 An arachnoid mater that is part of a diencephalon [Automatically generated definition]. Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17765 MA:0000827 VHOG:0000231 arachnoid mater of between brain arachnoid mater of diencephalon arachnoid mater of interbrain arachnoid mater of mature diencephalon arachnoid mater of neuraxis of between brain arachnoid mater of neuraxis of diencephalon arachnoid mater of neuraxis of interbrain arachnoid mater of neuraxis of mature diencephalon arachnoid of between brain arachnoid of diencephalon arachnoid of interbrain arachnoid of mature diencephalon between brain arachnoid between brain arachnoid mater between brain arachnoid mater of neuraxis diencephalon arachnoid diencephalon arachnoid mater of neuraxis interbrain arachnoid interbrain arachnoid mater interbrain arachnoid mater of neuraxis mature diencephalon arachnoid mature diencephalon arachnoid mater mature diencephalon arachnoid mater of neuraxis uberon UBERON:0003558 diencephalon arachnoid mater An arachnoid mater that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000231 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000231 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoid mater of between brain OBOL:automatic arachnoid mater of diencephalon OBOL:automatic arachnoid mater of interbrain OBOL:automatic arachnoid mater of mature diencephalon OBOL:automatic arachnoid mater of neuraxis of between brain OBOL:automatic arachnoid mater of neuraxis of diencephalon OBOL:automatic arachnoid mater of neuraxis of interbrain OBOL:automatic arachnoid mater of neuraxis of mature diencephalon OBOL:automatic arachnoid of between brain OBOL:automatic arachnoid of diencephalon OBOL:automatic arachnoid of interbrain OBOL:automatic arachnoid of mature diencephalon OBOL:automatic between brain arachnoid OBOL:automatic between brain arachnoid mater OBOL:automatic between brain arachnoid mater of neuraxis OBOL:automatic diencephalon arachnoid OBOL:automatic diencephalon arachnoid mater of neuraxis OBOL:automatic interbrain arachnoid OBOL:automatic interbrain arachnoid mater OBOL:automatic interbrain arachnoid mater of neuraxis OBOL:automatic mature diencephalon arachnoid OBOL:automatic mature diencephalon arachnoid mater OBOL:automatic mature diencephalon arachnoid mater of neuraxis OBOL:automatic An arachnoid mater that is part of a hindbrain [Automatically generated definition]. Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17784 MA:0000988 VHOG:0000236 arachnoid mater of hindbrain arachnoid mater of neuraxis of hindbrain arachnoid of hindbrain hindbrain arachnoid hindbrain arachnoid mater of neuraxis uberon rhombencephalon arachnoid mater UBERON:0003559 hindbrain arachnoid mater An arachnoid mater that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000236 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000236 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoid mater of hindbrain OBOL:automatic arachnoid mater of neuraxis of hindbrain OBOL:automatic arachnoid of hindbrain OBOL:automatic hindbrain arachnoid OBOL:automatic hindbrain arachnoid mater of neuraxis OBOL:automatic rhombencephalon arachnoid mater VHOG:0000236 An arachnoid mater that is part of a spinal cord [Automatically generated definition]. The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17805 MA:0001131 VHOG:0000234 arachnoid mater of neuraxis of spinal cord arachnoid mater of spinal cord arachnoid of spinal cord spinal cord arachnoid spinal cord arachnoid mater of neuraxis uberon UBERON:0003560 spinal cord arachnoid mater An arachnoid mater that is part of a spinal cord [Automatically generated definition]. OBOL:automatic The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000234 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000234 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoid mater of neuraxis of spinal cord OBOL:automatic arachnoid mater of spinal cord OBOL:automatic arachnoid of spinal cord OBOL:automatic spinal cord arachnoid OBOL:automatic spinal cord arachnoid mater of neuraxis OBOL:automatic A dura mater that is part of a forebrain. EMAPA:17766 EMAPA:37545 MA:0000885 dura mater of forebrain dura mater of neuraxis of forebrain forebrain dura mater of neuraxis uberon UBERON:0003561 forebrain dura mater A dura mater that is part of a forebrain. OBOL:automatic EMAPA:37545 MA:th dura mater of forebrain OBOL:automatic dura mater of neuraxis of forebrain OBOL:automatic forebrain dura mater of neuraxis OBOL:automatic A dura mater that is part of a midbrain [Automatically generated definition]. Dura mater that is part of the midbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17793 MA:0001060 VHOG:0000410 dura mater of midbrain dura mater of neuraxis of midbrain midbrain dura mater of neuraxis uberon mesencephalon dura mater UBERON:0003562 midbrain dura mater A dura mater that is part of a midbrain [Automatically generated definition]. OBOL:automatic Dura mater that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000410 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000410 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 dura mater of midbrain OBOL:automatic dura mater of neuraxis of midbrain OBOL:automatic midbrain dura mater of neuraxis OBOL:automatic mesencephalon dura mater VHOG:0000410 A dura mater that is part of a telencephalon [Automatically generated definition]. EMAPA:17776 MA:0000981 dura mater of neuraxis of telencephalon dura mater of telencephalon telencephalon dura mater of neuraxis uberon UBERON:0003563 telencephalon dura mater A dura mater that is part of a telencephalon [Automatically generated definition]. OBOL:automatic dura mater of neuraxis of telencephalon OBOL:automatic dura mater of telencephalon OBOL:automatic telencephalon dura mater of neuraxis OBOL:automatic A dura mater that is part of a diencephalon [Automatically generated definition]. Dura mater that is part of the diencephalon. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17766 MA:0000828 VHOG:0000258 between brain dura mater between brain dura mater of neuraxis diencephalon dura mater of neuraxis dura mater of between brain dura mater of diencephalon dura mater of interbrain dura mater of mature diencephalon dura mater of neuraxis of between brain dura mater of neuraxis of diencephalon dura mater of neuraxis of interbrain dura mater of neuraxis of mature diencephalon interbrain dura mater interbrain dura mater of neuraxis mature diencephalon dura mater mature diencephalon dura mater of neuraxis uberon UBERON:0003564 diencephalon dura mater A dura mater that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Dura mater that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000258 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000258 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 between brain dura mater OBOL:automatic between brain dura mater of neuraxis OBOL:automatic diencephalon dura mater of neuraxis OBOL:automatic dura mater of between brain OBOL:automatic dura mater of diencephalon OBOL:automatic dura mater of interbrain OBOL:automatic dura mater of mature diencephalon OBOL:automatic dura mater of neuraxis of between brain OBOL:automatic dura mater of neuraxis of diencephalon OBOL:automatic dura mater of neuraxis of interbrain OBOL:automatic dura mater of neuraxis of mature diencephalon OBOL:automatic interbrain dura mater OBOL:automatic interbrain dura mater of neuraxis OBOL:automatic mature diencephalon dura mater OBOL:automatic mature diencephalon dura mater of neuraxis OBOL:automatic A dura mater that is part of a hindbrain [Automatically generated definition]. Dura mater that is part of the hindbrain. [Bgee_curator][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:17785 MA:0000989 VHOG:0000409 dura mater of hindbrain dura mater of neuraxis of hindbrain hindbrain dura mater of neuraxis uberon rhombencephalon dura mater UBERON:0003565 hindbrain dura mater A dura mater that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Dura mater that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000409 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000409 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 dura mater of hindbrain OBOL:automatic dura mater of neuraxis of hindbrain OBOL:automatic hindbrain dura mater of neuraxis OBOL:automatic rhombencephalon dura mater VHOG:0000409 A portion of connective tissue that is part of a head [Automatically generated definition]. EMAPA:16098 MA:0000577 adult head connective tissue adult head portion of connective tissue adult head textus connectivus connective tissue of adult head connective tissue of head head portion of connective tissue head textus connectivus portion of connective tissue of adult head portion of connective tissue of head textus connectivus of adult head textus connectivus of head uberon UBERON:0003566 head connective tissue A portion of connective tissue that is part of a head [Automatically generated definition]. OBOL:automatic adult head connective tissue OBOL:automatic adult head portion of connective tissue OBOL:automatic adult head textus connectivus OBOL:automatic connective tissue of adult head OBOL:automatic connective tissue of head OBOL:automatic head portion of connective tissue OBOL:automatic head textus connectivus OBOL:automatic portion of connective tissue of adult head OBOL:automatic portion of connective tissue of head OBOL:automatic textus connectivus of adult head OBOL:automatic textus connectivus of head OBOL:automatic A portion of connective tissue that is part of an abdomen [Automatically generated definition]. MA:0000519 abdomen portion of connective tissue abdomen textus connectivus connective tissue of abdomen portion of connective tissue of abdomen textus connectivus of abdomen uberon UBERON:0003567 abdomen connective tissue A portion of connective tissue that is part of an abdomen [Automatically generated definition]. OBOL:automatic abdomen portion of connective tissue OBOL:automatic abdomen textus connectivus OBOL:automatic connective tissue of abdomen OBOL:automatic portion of connective tissue of abdomen OBOL:automatic textus connectivus of abdomen OBOL:automatic A portion of connective tissue that is part of a neck [Automatically generated definition]. EMAPA:37250 MA:0000585 connective tissue of neck connective tissue of neck (volume) neck (volume) connective tissue neck (volume) portion of connective tissue neck (volume) textus connectivus neck portion of connective tissue neck textus connectivus portion of connective tissue of neck portion of connective tissue of neck (volume) textus connectivus of neck textus connectivus of neck (volume) uberon UBERON:0003568 neck connective tissue A portion of connective tissue that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37250 MA:th connective tissue of neck OBOL:automatic connective tissue of neck (volume) OBOL:automatic neck (volume) connective tissue OBOL:automatic neck (volume) portion of connective tissue OBOL:automatic neck (volume) textus connectivus OBOL:automatic neck portion of connective tissue OBOL:automatic neck textus connectivus OBOL:automatic portion of connective tissue of neck OBOL:automatic portion of connective tissue of neck (volume) OBOL:automatic textus connectivus of neck OBOL:automatic textus connectivus of neck (volume) OBOL:automatic A portion of connective tissue that is part of a leg [Automatically generated definition]. EMAPA:37324 MA:0000671 connective tissue of leg leg portion of connective tissue leg textus connectivus portion of connective tissue of leg textus connectivus of leg uberon UBERON:0003569 leg connective tissue A portion of connective tissue that is part of a leg [Automatically generated definition]. OBOL:automatic EMAPA:37324 MA:th connective tissue of leg OBOL:automatic leg portion of connective tissue OBOL:automatic leg textus connectivus OBOL:automatic portion of connective tissue of leg OBOL:automatic textus connectivus of leg OBOL:automatic A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:35968 EMAPA:35977 MA:0001814 apparatus respiratorius connective tissue apparatus respiratorius portion of connective tissue apparatus respiratorius textus connectivus connective tissue of apparatus respiratorius connective tissue of respiratory system portion of connective tissue of apparatus respiratorius portion of connective tissue of respiratory system respiratory system portion of connective tissue respiratory system textus connectivus textus connectivus of apparatus respiratorius textus connectivus of respiratory system uberon UBERON:0003570 respiratory system connective tissue A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius connective tissue OBOL:automatic apparatus respiratorius portion of connective tissue OBOL:automatic apparatus respiratorius textus connectivus OBOL:automatic connective tissue of apparatus respiratorius OBOL:automatic connective tissue of respiratory system OBOL:automatic portion of connective tissue of apparatus respiratorius OBOL:automatic portion of connective tissue of respiratory system OBOL:automatic respiratory system portion of connective tissue OBOL:automatic respiratory system textus connectivus OBOL:automatic textus connectivus of apparatus respiratorius OBOL:automatic textus connectivus of respiratory system OBOL:automatic A portion of connective tissue that is part of a trachea. EMAPA:35876 MA:0001853 connective tissue of trachea connective tissue of windpipe uberon UBERON:0003571 trachea connective tissue A portion of connective tissue that is part of a trachea. OBOL:automatic connective tissue of trachea OBOL:automatic connective tissue of windpipe OBOL:automatic A portion of connective tissue that is part of a chest [Automatically generated definition]. EMAPA:37254 MA:0000550 anterior thoracic region connective tissue anterior thoracic region portion of connective tissue anterior thoracic region textus connectivus anterolateral part of thorax connective tissue anterolateral part of thorax portion of connective tissue anterolateral part of thorax textus connectivus chest portion of connective tissue chest textus connectivus connective tissue of anterior thoracic region connective tissue of anterolateral part of thorax connective tissue of chest connective tissue of front of thorax front of thorax connective tissue front of thorax portion of connective tissue front of thorax textus connectivus portion of connective tissue of anterior thoracic region portion of connective tissue of anterolateral part of thorax portion of connective tissue of chest portion of connective tissue of front of thorax textus connectivus of anterior thoracic region textus connectivus of anterolateral part of thorax textus connectivus of chest textus connectivus of front of thorax uberon UBERON:0003572 chest connective tissue A portion of connective tissue that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37254 MA:th anterior thoracic region connective tissue OBOL:automatic anterior thoracic region portion of connective tissue OBOL:automatic anterior thoracic region textus connectivus OBOL:automatic anterolateral part of thorax connective tissue OBOL:automatic anterolateral part of thorax portion of connective tissue OBOL:automatic anterolateral part of thorax textus connectivus OBOL:automatic chest portion of connective tissue OBOL:automatic chest textus connectivus OBOL:automatic connective tissue of anterior thoracic region OBOL:automatic connective tissue of anterolateral part of thorax OBOL:automatic connective tissue of chest OBOL:automatic connective tissue of front of thorax OBOL:automatic front of thorax connective tissue OBOL:automatic front of thorax portion of connective tissue OBOL:automatic front of thorax textus connectivus OBOL:automatic portion of connective tissue of anterior thoracic region OBOL:automatic portion of connective tissue of anterolateral part of thorax OBOL:automatic portion of connective tissue of chest OBOL:automatic portion of connective tissue of front of thorax OBOL:automatic textus connectivus of anterior thoracic region OBOL:automatic textus connectivus of anterolateral part of thorax OBOL:automatic textus connectivus of chest OBOL:automatic textus connectivus of front of thorax OBOL:automatic A portion of connective tissue that is part of an arm [Automatically generated definition]. EMAPA:37316 MA:0000593 uberon UBERON:0003573 arm connective tissue A portion of connective tissue that is part of an arm [Automatically generated definition]. OBOL:automatic EMAPA:37316 MA:th A portion of connective tissue that is part of a elbow [Automatically generated definition]. EMAPA:37318 MA:0000609 connective tissue of cubital region connective tissue of elbow textus connectivus of cubital region uberon UBERON:0003574 elbow connective tissue A portion of connective tissue that is part of a elbow [Automatically generated definition]. OBOL:automatic EMAPA:37318 MA:th connective tissue of cubital region OBOL:automatic connective tissue of elbow OBOL:automatic textus connectivus of cubital region OBOL:automatic A portion of connective tissue that is part of a wrist [Automatically generated definition]. EMAPA:37320 MA:0000636 carpal region connective tissue connective tissue of carpal region connective tissue of wrist uberon UBERON:0003575 wrist connective tissue A portion of connective tissue that is part of a wrist [Automatically generated definition]. OBOL:automatic EMAPA:37320 MA:th carpal region connective tissue OBOL:automatic connective tissue of carpal region OBOL:automatic connective tissue of wrist OBOL:automatic A portion of connective tissue that is part of a hip [Automatically generated definition]. EMAPA:37323 MA:0000656 connective tissue of hip connective tissue of hip region connective tissue of regio coxae uberon UBERON:0003576 hip connective tissue A portion of connective tissue that is part of a hip [Automatically generated definition]. OBOL:automatic EMAPA:37323 MA:th connective tissue of hip OBOL:automatic connective tissue of hip region OBOL:automatic connective tissue of regio coxae OBOL:automatic A portion of connective tissue that is part of a toe [Automatically generated definition]. EMAPA:37330 MA:0000647 connective tissue of digit of foot connective tissue of digitus pedis connective tissue of foot digit connective tissue of toe digitus pedis textus connectivus foot digit connective tissue hind limb digit connective tissue foot digit connective tissue uberon UBERON:0003578 pedal digit connective tissue A portion of connective tissue that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37330 MA:th connective tissue of digit of foot OBOL:automatic connective tissue of digitus pedis OBOL:automatic connective tissue of foot digit OBOL:automatic connective tissue of toe OBOL:automatic digitus pedis textus connectivus OBOL:automatic foot digit connective tissue MA:0000647 hind limb digit connective tissue OBOL:accepted foot digit connective tissue NCBITaxon:9606 OBOL:accepted A portion of connective tissue that is part of a shoulder [Automatically generated definition]. EMAPA:37315 MA:0000632 connective tissue of shoulder portion of connective tissue of shoulder shoulder portion of connective tissue shoulder textus connectivus textus connectivus of shoulder uberon UBERON:0003579 shoulder connective tissue A portion of connective tissue that is part of a shoulder [Automatically generated definition]. OBOL:automatic EMAPA:37315 MA:th connective tissue of shoulder OBOL:automatic portion of connective tissue of shoulder OBOL:automatic shoulder portion of connective tissue OBOL:automatic shoulder textus connectivus OBOL:automatic textus connectivus of shoulder OBOL:automatic A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37548 MA:0002409 connective tissue of lower respiratory tract lower respiratory tract portion of connective tissue lower respiratory tract textus connectivus portion of connective tissue of lower respiratory tract textus connectivus of lower respiratory tract uberon UBERON:0003580 lower respiratory tract connective tissue A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37548 MA:th connective tissue of lower respiratory tract OBOL:automatic lower respiratory tract portion of connective tissue OBOL:automatic lower respiratory tract textus connectivus OBOL:automatic portion of connective tissue of lower respiratory tract OBOL:automatic textus connectivus of lower respiratory tract OBOL:automatic A portion of connective tissue that is part of a nasopharynx [Automatically generated definition]. EMAPA:37682 MA:0001864 connective tissue of nasal part of pharynx connective tissue of nasopharynx connective tissue of rhinopharynx nasal part of pharynx connective tissue nasal part of pharynx portion of connective tissue nasal part of pharynx textus connectivus nasopharynx portion of connective tissue nasopharynx textus connectivus portion of connective tissue of nasal part of pharynx portion of connective tissue of nasopharynx portion of connective tissue of rhinopharynx rhinopharynx connective tissue rhinopharynx portion of connective tissue rhinopharynx textus connectivus textus connectivus of nasal part of pharynx textus connectivus of nasopharynx textus connectivus of rhinopharynx uberon UBERON:0003582 nasopharynx connective tissue A portion of connective tissue that is part of a nasopharynx [Automatically generated definition]. OBOL:automatic EMAPA:37682 MA:th connective tissue of nasal part of pharynx OBOL:automatic connective tissue of nasopharynx OBOL:automatic connective tissue of rhinopharynx OBOL:automatic nasal part of pharynx connective tissue OBOL:automatic nasal part of pharynx portion of connective tissue OBOL:automatic nasal part of pharynx textus connectivus OBOL:automatic nasopharynx portion of connective tissue OBOL:automatic nasopharynx textus connectivus OBOL:automatic portion of connective tissue of nasal part of pharynx OBOL:automatic portion of connective tissue of nasopharynx OBOL:automatic portion of connective tissue of rhinopharynx OBOL:automatic rhinopharynx connective tissue OBOL:automatic rhinopharynx portion of connective tissue OBOL:automatic rhinopharynx textus connectivus OBOL:automatic textus connectivus of nasal part of pharynx OBOL:automatic textus connectivus of nasopharynx OBOL:automatic textus connectivus of rhinopharynx OBOL:automatic A portion of connective tissue that is part of a larynx [Automatically generated definition]. EMAPA:35471 MA:0001754 NCIT:C49245 UMLS:C1708651 connective tissue of larynx larynx portion of connective tissue larynx textus connectivus portion of connective tissue of larynx textus connectivus of larynx uberon laryngeal connective tissue UBERON:0003583 larynx connective tissue A portion of connective tissue that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C1708651 ncithesaurus:Laryngeal_Connective_Tissue connective tissue of larynx OBOL:automatic larynx portion of connective tissue OBOL:automatic larynx textus connectivus OBOL:automatic portion of connective tissue of larynx OBOL:automatic textus connectivus of larynx OBOL:automatic laryngeal connective tissue EMAPA:35471 A portion of connective tissue that is part of a dermis [Automatically generated definition]. EMAPA:36509 MA:0000799 connective tissue of dermis dermis portion of connective tissue dermis textus connectivus portion of connective tissue of dermis textus connectivus of dermis uberon UBERON:0003585 dermis connective tissue A portion of connective tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic connective tissue of dermis OBOL:automatic dermis portion of connective tissue OBOL:automatic dermis textus connectivus OBOL:automatic portion of connective tissue of dermis OBOL:automatic textus connectivus of dermis OBOL:automatic A portion of connective tissue that is part of a trunk [Automatically generated definition]. EMAPA:37252 MA:0000513 connective tissue of torso connective tissue of trunk portion of connective tissue of torso portion of connective tissue of trunk textus connectivus of torso textus connectivus of trunk torso connective tissue torso portion of connective tissue torso textus connectivus trunk portion of connective tissue trunk textus connectivus uberon UBERON:0003586 trunk connective tissue A portion of connective tissue that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37252 MA:th connective tissue of torso OBOL:automatic connective tissue of trunk OBOL:automatic portion of connective tissue of torso OBOL:automatic portion of connective tissue of trunk OBOL:automatic textus connectivus of torso OBOL:automatic textus connectivus of trunk OBOL:automatic torso connective tissue OBOL:automatic torso portion of connective tissue OBOL:automatic torso textus connectivus OBOL:automatic trunk portion of connective tissue OBOL:automatic trunk textus connectivus OBOL:automatic A portion of connective tissue that is part of a limb [Automatically generated definition]. EMAPA:37313 MA:0000689 connective tissue of limb limb portion of connective tissue limb textus connectivus portion of connective tissue of limb textus connectivus of limb uberon UBERON:0003587 limb connective tissue A portion of connective tissue that is part of a limb [Automatically generated definition]. OBOL:automatic EMAPA:37313 MA:th connective tissue of limb OBOL:automatic limb portion of connective tissue OBOL:automatic limb textus connectivus OBOL:automatic portion of connective tissue of limb OBOL:automatic textus connectivus of limb OBOL:automatic A portion of connective tissue that is part of a forelimb [Automatically generated definition]. EMAPA:37314 MA:0000613 connective tissue of anteriormost limb connective tissue of fore limb connective tissue of forelimb connective tissue of superior member connective tissue of upper extremity wing connective tissue uberon UBERON:0003588 forelimb connective tissue A portion of connective tissue that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37314 MA:th connective tissue of anteriormost limb OBOL:automatic connective tissue of fore limb OBOL:automatic connective tissue of forelimb OBOL:automatic connective tissue of superior member OBOL:automatic connective tissue of upper extremity OBOL:automatic wing connective tissue NCBITaxon:8782 OBOL:automatic A portion of connective tissue that is part of a hindlimb [Automatically generated definition]. EMAPA:37322 MA:0000661 connective tissue of hind limb connective tissue of hindlimb connective tissue of inferior member connective tissue of lower extremity hind limb connective tissue uberon UBERON:0003589 hindlimb connective tissue A portion of connective tissue that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37322 MA:th connective tissue of hind limb OBOL:automatic connective tissue of hindlimb OBOL:automatic connective tissue of inferior member OBOL:automatic connective tissue of lower extremity OBOL:automatic hind limb connective tissue OBOL:automatic A portion of connective tissue that is part of a bronchus [Automatically generated definition]. EMAPA:32690 EMAPA:35193 MA:0001831 NCIT:C49210 UMLS:C1707052 bronchi connective tissue bronchi portion of connective tissue bronchi textus connectivus bronchial trunk connective tissue bronchial trunk portion of connective tissue bronchial trunk textus connectivus bronchus portion of connective tissue bronchus textus connectivus connective tissue of bronchi connective tissue of bronchial trunk connective tissue of bronchus portion of connective tissue of bronchi portion of connective tissue of bronchial trunk portion of connective tissue of bronchus textus connectivus of bronchi textus connectivus of bronchial trunk textus connectivus of bronchus uberon bronchial connective tissue bronchial mesenchyme UBERON:0003592 bronchus connective tissue A portion of connective tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707052 ncithesaurus:Bronchus_Connective_Tissue bronchi connective tissue OBOL:automatic bronchi portion of connective tissue OBOL:automatic bronchi textus connectivus OBOL:automatic bronchial trunk connective tissue OBOL:automatic bronchial trunk portion of connective tissue OBOL:automatic bronchial trunk textus connectivus OBOL:automatic bronchus portion of connective tissue OBOL:automatic bronchus textus connectivus OBOL:automatic connective tissue of bronchi OBOL:automatic connective tissue of bronchial trunk OBOL:automatic connective tissue of bronchus OBOL:automatic portion of connective tissue of bronchi OBOL:automatic portion of connective tissue of bronchial trunk OBOL:automatic portion of connective tissue of bronchus OBOL:automatic textus connectivus of bronchi OBOL:automatic textus connectivus of bronchial trunk OBOL:automatic textus connectivus of bronchus OBOL:automatic bronchial connective tissue EMAPA:35193 bronchial mesenchyme EMAPA:32690 A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37255 MA:0000555 cavity of chest connective tissue cavity of chest portion of connective tissue cavity of chest textus connectivus cavity of thorax connective tissue cavity of thorax portion of connective tissue cavity of thorax textus connectivus chest cavity connective tissue chest cavity portion of connective tissue chest cavity textus connectivus connective tissue of cavity of chest connective tissue of cavity of thorax connective tissue of chest cavity connective tissue of pectoral cavity connective tissue of thoracic cavity pectoral cavity connective tissue pectoral cavity portion of connective tissue pectoral cavity textus connectivus portion of connective tissue of cavity of chest portion of connective tissue of cavity of thorax portion of connective tissue of chest cavity portion of connective tissue of pectoral cavity portion of connective tissue of thoracic cavity textus connectivus of cavity of chest textus connectivus of cavity of thorax textus connectivus of chest cavity textus connectivus of pectoral cavity textus connectivus of thoracic cavity thoracic cavity portion of connective tissue thoracic cavity textus connectivus uberon UBERON:0003593 thoracic cavity connective tissue A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37255 MA:th cavity of chest connective tissue OBOL:automatic cavity of chest portion of connective tissue OBOL:automatic cavity of chest textus connectivus OBOL:automatic cavity of thorax connective tissue OBOL:automatic cavity of thorax portion of connective tissue OBOL:automatic cavity of thorax textus connectivus OBOL:automatic chest cavity connective tissue OBOL:automatic chest cavity portion of connective tissue OBOL:automatic chest cavity textus connectivus OBOL:automatic connective tissue of cavity of chest OBOL:automatic connective tissue of cavity of thorax OBOL:automatic connective tissue of chest cavity OBOL:automatic connective tissue of pectoral cavity OBOL:automatic connective tissue of thoracic cavity OBOL:automatic pectoral cavity connective tissue OBOL:automatic pectoral cavity portion of connective tissue OBOL:automatic pectoral cavity textus connectivus OBOL:automatic portion of connective tissue of cavity of chest OBOL:automatic portion of connective tissue of cavity of thorax OBOL:automatic portion of connective tissue of chest cavity OBOL:automatic portion of connective tissue of pectoral cavity OBOL:automatic portion of connective tissue of thoracic cavity OBOL:automatic textus connectivus of cavity of chest OBOL:automatic textus connectivus of cavity of thorax OBOL:automatic textus connectivus of chest cavity OBOL:automatic textus connectivus of pectoral cavity OBOL:automatic textus connectivus of thoracic cavity OBOL:automatic thoracic cavity portion of connective tissue OBOL:automatic thoracic cavity textus connectivus OBOL:automatic A portion of connective tissue that is part of a pelvis [Automatically generated definition]. EMAPA:37257 MA:0000533 connective tissue of pelvis pelvis portion of connective tissue pelvis textus connectivus portion of connective tissue of pelvis textus connectivus of pelvis uberon UBERON:0003594 pelvis connective tissue A portion of connective tissue that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37257 MA:th connective tissue of pelvis OBOL:automatic pelvis portion of connective tissue OBOL:automatic pelvis textus connectivus OBOL:automatic portion of connective tissue of pelvis OBOL:automatic textus connectivus of pelvis OBOL:automatic A portion of connective tissue that is part of a foot [Automatically generated definition]. EMAPA:37329 MA:0000644 connective tissue of foot connective tissue of terminal segment of free lower limb foot connective tissue textus connectivus of pes uberon UBERON:0003595 pes connective tissue A portion of connective tissue that is part of a foot [Automatically generated definition]. OBOL:automatic EMAPA:37329 MA:th connective tissue of foot OBOL:automatic connective tissue of terminal segment of free lower limb OBOL:automatic foot connective tissue MA:0000644 textus connectivus of pes OBOL:automatic A portion of connective tissue that is part of an ankle [Automatically generated definition]. EMAPA:37328 MA:0000639 connective tissue of ankle tarsal region connective tissue uberon UBERON:0003596 ankle connective tissue A portion of connective tissue that is part of an ankle [Automatically generated definition]. OBOL:automatic EMAPA:37328 MA:th connective tissue of ankle OBOL:automatic tarsal region connective tissue A portion of connective tissue that is part of a finger [Automatically generated definition]. EMAPA:37321 MA:0000623 connective tissue of digit of hand connective tissue of digitus manus connective tissue of finger connective tissue of hand digit fore limb digit connective tissue hand digit connective tissue hand digit connective tissue uberon UBERON:0003597 manual digit connective tissue A portion of connective tissue that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37321 MA:th connective tissue of digit of hand OBOL:automatic connective tissue of digitus manus OBOL:automatic connective tissue of finger OBOL:automatic connective tissue of hand digit OBOL:automatic fore limb digit connective tissue OBOL:accepted hand digit connective tissue MA:0000623 hand digit connective tissue NCBITaxon:9606 OBOL:accepted A portion of connective tissue that is part of a hand [Automatically generated definition]. EMAPA:35392 MA:0000620 connective tissue of hand connective tissue of terminal segment of free upper limb hand connective tissue uberon UBERON:0003598 manus connective tissue A portion of connective tissue that is part of a hand [Automatically generated definition]. OBOL:automatic connective tissue of hand OBOL:automatic connective tissue of terminal segment of free upper limb OBOL:automatic hand connective tissue MA:0000620 A portion of connective tissue that is part of a tail [Automatically generated definition]. EMAPA:16749 MA:0000697 connective tissue of post-vent region connective tissue of tail portion of connective tissue of post-vent region portion of connective tissue of tail post-vent region connective tissue post-vent region portion of connective tissue post-vent region textus connectivus tail portion of connective tissue tail textus connectivus textus connectivus of post-vent region textus connectivus of tail uberon UBERON:0003599 tail connective tissue A portion of connective tissue that is part of a tail [Automatically generated definition]. OBOL:automatic connective tissue of post-vent region OBOL:automatic connective tissue of tail OBOL:automatic portion of connective tissue of post-vent region OBOL:automatic portion of connective tissue of tail OBOL:automatic post-vent region connective tissue OBOL:automatic post-vent region portion of connective tissue OBOL:automatic post-vent region textus connectivus OBOL:automatic tail portion of connective tissue OBOL:automatic tail textus connectivus OBOL:automatic textus connectivus of post-vent region OBOL:automatic textus connectivus of tail OBOL:automatic A cartilage that is part of a neck [Automatically generated definition]. EMAPA:37251 MA:0000586 cartilage of neck cartilage of neck (volume) neck (volume) cartilage uberon UBERON:0003601 neck cartilage A cartilage that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37251 MA:th cartilage of neck OBOL:automatic cartilage of neck (volume) OBOL:automatic neck (volume) cartilage OBOL:automatic A cartilage that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37547 MA:0001819 NCIT:C49256 UMLS:C1708759 cartilage of lower respiratory tract uberon UBERON:0003603 lower respiratory tract cartilage A cartilage that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37547 MA:th UMLS:C1708759 ncithesaurus:Lower_Respiratory_Tract_Cartilage cartilage of lower respiratory tract OBOL:automatic the ring-shaped cartilaginous structures that support the trachea check whether to classify as part of splanchoncranium in mammals the rings are incomplete, in avians the rings are complete. EMAPA:18699 EMAPA:35875 FMA:7434 MA:0001857 NCIT:C49304 UMLS:C1710456 cartilage of trachea cartilage of windpipe cartilaginous ring of trachea cartilaginous trachea cartilage cartilago trachealis tracheal cartilage windpipe cartilage uberon cartilage of the trachea cartilagines tracheales ring of the trachea trachea ring tracheal ring UBERON:0003604 trachea cartilage http://upload.wikimedia.org/wikipedia/commons/5/56/Gray952.png the ring-shaped cartilaginous structures that support the trachea J:97123 MGI:smb MP:0003120 UMLS:C1710456 ncithesaurus:Trachea_Cartilage cartilage of trachea OBOL:automatic cartilage of windpipe OBOL:automatic cartilaginous ring of trachea EMAPA:18699 cartilaginous trachea cartilage OBOL:automatic cartilago trachealis FMA:7434 tracheal cartilage FMA:7434 windpipe cartilage OBOL:automatic cartilage of the trachea cartilagines tracheales ring of the trachea tracheal ring A skin gland that is part of a camera-type eye [Automatically generated definition]. EMAPA:37530 MA:0002451 camera-type eye skin gland camera-type eye skin glands camera-type eye skin glands set skin gland of camera-type eye skin gland of vertebrate eye skin glands of camera-type eye skin glands of vertebrate eye skin glands set of camera-type eye skin glands set of vertebrate eye vertebrate eye skin gland vertebrate eye skin glands vertebrate eye skin glands set uberon UBERON:0003605 eye skin gland A skin gland that is part of a camera-type eye [Automatically generated definition]. OBOL:automatic EMAPA:37530 MA:th camera-type eye skin gland OBOL:automatic camera-type eye skin glands OBOL:automatic camera-type eye skin glands set OBOL:automatic skin gland of camera-type eye OBOL:automatic skin gland of vertebrate eye OBOL:automatic skin glands of camera-type eye OBOL:automatic skin glands of vertebrate eye OBOL:automatic skin glands set of camera-type eye OBOL:automatic skin glands set of vertebrate eye OBOL:automatic vertebrate eye skin gland OBOL:automatic vertebrate eye skin glands OBOL:automatic vertebrate eye skin glands set OBOL:automatic A long bone that is part of a limb [Automatically generated definition]. EMAPA:35495 MA:0000298 long bone of limb uberon UBERON:0003606 limb long bone A long bone that is part of a limb [Automatically generated definition]. OBOL:automatic long bone of limb OBOL:automatic A long bone that is part of a forelimb [Automatically generated definition]. EMAPA:35350 MA:0000299 anteriormost limb long bone fore limb long bone long bone of anteriormost limb long bone of fore limb long bone of forelimb long bone of superior member long bone of upper extremity superior member long bone upper extremity long bone wing long bone uberon UBERON:0003607 forelimb long bone A long bone that is part of a forelimb [Automatically generated definition]. OBOL:automatic anteriormost limb long bone OBOL:automatic fore limb long bone OBOL:automatic long bone of anteriormost limb OBOL:automatic long bone of fore limb OBOL:automatic long bone of forelimb OBOL:automatic long bone of superior member OBOL:automatic long bone of upper extremity OBOL:automatic superior member long bone OBOL:automatic upper extremity long bone OBOL:automatic wing long bone NCBITaxon:8782 OBOL:automatic A long bone that is part of a hindlimb [Automatically generated definition]. EMAPA:35403 MA:0000300 hind limb long bone inferior member long bone long bone of hind limb long bone of hindlimb long bone of inferior member long bone of lower extremity lower extremity long bone uberon UBERON:0003608 hindlimb long bone A long bone that is part of a hindlimb [Automatically generated definition]. OBOL:automatic hind limb long bone OBOL:automatic inferior member long bone OBOL:automatic long bone of hind limb OBOL:automatic long bone of hindlimb OBOL:automatic long bone of inferior member OBOL:automatic long bone of lower extremity OBOL:automatic lower extremity long bone OBOL:automatic The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MA:0002859 adult aorta elastic connective tissue adult aorta elastic tissue adult aorta textus connectivus elasticus aorta elastic connective tissue aorta elastic lamina aorta elastic laminae aorta textus connectivus elasticus dorsal aorta elastic connective tissue dorsal aorta elastic tissue dorsal aorta textus connectivus elasticus elastic connective tissue of adult aorta elastic connective tissue of aorta elastic connective tissue of dorsal aorta elastic connective tissue of trunk of aortic tree elastic tissue of adult aorta elastic tissue of aorta elastic tissue of dorsal aorta elastic tissue of trunk of aortic tree textus connectivus elasticus of adult aorta textus connectivus elasticus of aorta textus connectivus elasticus of dorsal aorta textus connectivus elasticus of trunk of aortic tree trunk of aortic tree elastic connective tissue trunk of aortic tree elastic tissue trunk of aortic tree textus connectivus elasticus uberon UBERON:0003609 aorta elastic tissue The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MP:0009862 adult aorta elastic connective tissue OBOL:automatic adult aorta elastic tissue OBOL:automatic adult aorta textus connectivus elasticus OBOL:automatic aorta elastic connective tissue OBOL:automatic aorta elastic lamina MP:0009862 aorta elastic laminae MP:0009862 aorta textus connectivus elasticus OBOL:automatic dorsal aorta elastic connective tissue OBOL:automatic dorsal aorta elastic tissue OBOL:automatic dorsal aorta textus connectivus elasticus OBOL:automatic elastic connective tissue of adult aorta OBOL:automatic elastic connective tissue of aorta OBOL:automatic elastic connective tissue of dorsal aorta OBOL:automatic elastic connective tissue of trunk of aortic tree OBOL:automatic elastic tissue of adult aorta OBOL:automatic elastic tissue of aorta OBOL:automatic elastic tissue of dorsal aorta OBOL:automatic elastic tissue of trunk of aortic tree OBOL:automatic textus connectivus elasticus of adult aorta OBOL:automatic textus connectivus elasticus of aorta OBOL:automatic textus connectivus elasticus of dorsal aorta OBOL:automatic textus connectivus elasticus of trunk of aortic tree OBOL:automatic trunk of aortic tree elastic connective tissue OBOL:automatic trunk of aortic tree elastic tissue OBOL:automatic trunk of aortic tree textus connectivus elasticus OBOL:automatic The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MA:0002858 cardiac elastic tissue elastic connective tissue of heart elastic tissue of heart heart elastic connective tissue heart textus connectivus elasticus textus connectivus elasticus of heart uberon UBERON:0003610 heart elastic tissue The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MP:0009863 cardiac elastic tissue MP:0009863 elastic connective tissue of heart OBOL:automatic elastic tissue of heart OBOL:automatic heart elastic connective tissue OBOL:automatic heart textus connectivus elasticus OBOL:automatic textus connectivus elasticus of heart OBOL:automatic An elastic tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37579 MA:0001820 apparatus respiratorius elastic connective tissue apparatus respiratorius elastic tissue apparatus respiratorius textus connectivus elasticus elastic connective tissue of apparatus respiratorius elastic connective tissue of respiratory system elastic tissue of apparatus respiratorius elastic tissue of respiratory system respiratory system elastic connective tissue respiratory system textus connectivus elasticus textus connectivus elasticus of apparatus respiratorius textus connectivus elasticus of respiratory system uberon UBERON:0003611 respiratory system elastic tissue An elastic tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37579 MA:th apparatus respiratorius elastic connective tissue OBOL:automatic apparatus respiratorius elastic tissue OBOL:automatic apparatus respiratorius textus connectivus elasticus OBOL:automatic elastic connective tissue of apparatus respiratorius OBOL:automatic elastic connective tissue of respiratory system OBOL:automatic elastic tissue of apparatus respiratorius OBOL:automatic elastic tissue of respiratory system OBOL:automatic respiratory system elastic connective tissue OBOL:automatic respiratory system textus connectivus elasticus OBOL:automatic textus connectivus elasticus of apparatus respiratorius OBOL:automatic textus connectivus elasticus of respiratory system OBOL:automatic An elastic tissue that is part of a circulatory system [Automatically generated definition]. MA:0002857 cardiovascular system elastic connective tissue cardiovascular system textus connectivus elasticus circulatory system elastic connective tissue circulatory system elastic tissue circulatory system textus connectivus elasticus elastic connective tissue of cardiovascular system elastic connective tissue of circulatory system elastic tissue of cardiovascular system elastic tissue of circulatory system textus connectivus elasticus of cardiovascular system textus connectivus elasticus of circulatory system uberon UBERON:0003613 cardiovascular system elastic tissue An elastic tissue that is part of a circulatory system [Automatically generated definition]. OBOL:automatic cardiovascular system elastic connective tissue OBOL:automatic cardiovascular system textus connectivus elasticus OBOL:automatic circulatory system elastic connective tissue OBOL:automatic circulatory system elastic tissue OBOL:automatic circulatory system textus connectivus elasticus OBOL:automatic elastic connective tissue of cardiovascular system OBOL:automatic elastic connective tissue of circulatory system OBOL:automatic elastic tissue of cardiovascular system OBOL:automatic elastic tissue of circulatory system OBOL:automatic textus connectivus elasticus of cardiovascular system OBOL:automatic textus connectivus elasticus of circulatory system OBOL:automatic Elastic tissue layer that lines a blood vessel layer. elastic lamina elastic laminae EMAPA:36300 MA:0002856 blood vessel elastic connective tissue blood vessel textus connectivus elasticus elastic connective tissue of blood vessel elastic tissue of blood vessel textus connectivus elasticus of blood vessel vascular elastic lamina vascular elastic laminae vascular elastic tissue uberon UBERON:0003614 blood vessel elastic tissue Elastic tissue layer that lines a blood vessel layer. elastic lamina MP:0006083 elastic laminae MP:0006083 blood vessel elastic connective tissue OBOL:automatic blood vessel textus connectivus elasticus OBOL:automatic elastic connective tissue of blood vessel OBOL:automatic elastic tissue of blood vessel OBOL:automatic textus connectivus elasticus of blood vessel OBOL:automatic vascular elastic lamina vascular elastic laminae vascular elastic tissue MP:0006083 Elastic tissue that is part of a lung [Automatically generated definition]. MA:0002860 elastic connective tissue of lung elastic tissue of lung lung elastic connective tissue lung textus connectivus elasticus textus connectivus elasticus of lung pulmonary elastic fiber uberon UBERON:0003615 lung elastic tissue Elastic tissue that is part of a lung [Automatically generated definition]. OBOL:automatic elastic connective tissue of lung OBOL:automatic elastic tissue of lung OBOL:automatic lung elastic connective tissue OBOL:automatic lung textus connectivus elasticus OBOL:automatic textus connectivus elasticus of lung OBOL:automatic pulmonary elastic fiber An elastic tissue that is part of a bronchus [Automatically generated definition]. MA:0001838 NCIT:C49211 UMLS:C1707053 bronchi elastic connective tissue bronchi elastic tissue bronchi textus connectivus elasticus bronchial trunk elastic connective tissue bronchial trunk elastic tissue bronchial trunk textus connectivus elasticus bronchus elastic connective tissue bronchus textus connectivus elasticus elastic connective tissue of bronchi elastic connective tissue of bronchial trunk elastic connective tissue of bronchus elastic tissue of bronchi elastic tissue of bronchial trunk elastic tissue of bronchus textus connectivus elasticus of bronchi textus connectivus elasticus of bronchial trunk textus connectivus elasticus of bronchus uberon UBERON:0003616 bronchus elastic tissue An elastic tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707053 ncithesaurus:Bronchus_Elastic_Tissue bronchi elastic connective tissue OBOL:automatic bronchi elastic tissue OBOL:automatic bronchi textus connectivus elasticus OBOL:automatic bronchial trunk elastic connective tissue OBOL:automatic bronchial trunk elastic tissue OBOL:automatic bronchial trunk textus connectivus elasticus OBOL:automatic bronchus elastic connective tissue OBOL:automatic bronchus textus connectivus elasticus OBOL:automatic elastic connective tissue of bronchi OBOL:automatic elastic connective tissue of bronchial trunk OBOL:automatic elastic connective tissue of bronchus OBOL:automatic elastic tissue of bronchi OBOL:automatic elastic tissue of bronchial trunk OBOL:automatic elastic tissue of bronchus OBOL:automatic textus connectivus elasticus of bronchi OBOL:automatic textus connectivus elasticus of bronchial trunk OBOL:automatic textus connectivus elasticus of bronchus OBOL:automatic An elastic tissue that is part of a trachea [Automatically generated definition]. MA:0001861 cartilaginous trachea elastic connective tissue cartilaginous trachea elastic tissue cartilaginous trachea textus connectivus elasticus elastic connective tissue of cartilaginous trachea elastic connective tissue of vertebrate trachea elastic connective tissue of windpipe elastic tissue of cartilaginous trachea elastic tissue of vertebrate trachea elastic tissue of windpipe textus connectivus elasticus of cartilaginous trachea textus connectivus elasticus of vertebrate trachea textus connectivus elasticus of windpipe vertebrate trachea elastic connective tissue vertebrate trachea elastic tissue vertebrate trachea textus connectivus elasticus windpipe elastic connective tissue windpipe elastic tissue windpipe textus connectivus elasticus uberon UBERON:0003617 trachea elastic tissue An elastic tissue that is part of a trachea [Automatically generated definition]. OBOL:automatic cartilaginous trachea elastic connective tissue OBOL:automatic cartilaginous trachea elastic tissue OBOL:automatic cartilaginous trachea textus connectivus elasticus OBOL:automatic elastic connective tissue of cartilaginous trachea OBOL:automatic elastic connective tissue of vertebrate trachea OBOL:automatic elastic connective tissue of windpipe OBOL:automatic elastic tissue of cartilaginous trachea OBOL:automatic elastic tissue of vertebrate trachea OBOL:automatic elastic tissue of windpipe OBOL:automatic textus connectivus elasticus of cartilaginous trachea OBOL:automatic textus connectivus elasticus of vertebrate trachea OBOL:automatic textus connectivus elasticus of windpipe OBOL:automatic vertebrate trachea elastic connective tissue OBOL:automatic vertebrate trachea elastic tissue OBOL:automatic vertebrate trachea textus connectivus elasticus OBOL:automatic windpipe elastic connective tissue OBOL:automatic windpipe elastic tissue OBOL:automatic windpipe textus connectivus elasticus OBOL:automatic The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. EMAPA:35138 FMA:74433 MA:0002903 adult aorta tunica media dorsal aorta tunica media trunk of aortic tree tunica media tunica media of adult aorta tunica media of aorta tunica media of dorsal aorta tunica media of trunk of aortic tree uberon UBERON:0003618 aorta tunica media The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. MP:0009873 adult aorta tunica media OBOL:automatic dorsal aorta tunica media OBOL:automatic trunk of aortic tree tunica media OBOL:automatic tunica media of adult aorta OBOL:automatic tunica media of aorta OBOL:automatic tunica media of dorsal aorta OBOL:automatic tunica media of trunk of aortic tree OBOL:automatic The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. BTO:0005553 EMAPA:35137 FMA:74419 MA:0002904 adult aorta tunica intima dorsal aorta tunica intima trunk of aortic tree tunica intima tunica intima of adult aorta tunica intima of aorta tunica intima of dorsal aorta tunica intima of trunk of aortic tree uberon UBERON:0003619 aorta tunica intima The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. MP:0009872 adult aorta tunica intima OBOL:automatic dorsal aorta tunica intima OBOL:automatic trunk of aortic tree tunica intima OBOL:automatic tunica intima of adult aorta OBOL:automatic tunica intima of aorta OBOL:automatic tunica intima of dorsal aorta OBOL:automatic tunica intima of trunk of aortic tree OBOL:automatic A phalanx that is part of a hand digit 1 [Automatically generated definition]. EMAPA:19113 FMA:35477 MA:0001389 NCIT:C52777 UMLS:C1711344 fore limb digit 1 phalanx hand digit 1 phalanx manual digit I phalanx phalanx of hand digit 1 phalanx of thumb thumb phalanx hand digit 1 phalanx uberon UBERON:0003620 manual digit 1 phalanx A phalanx that is part of a hand digit 1 [Automatically generated definition]. OBOL:automatic UMLS:C1711344 ncithesaurus:Hand_Digit_1_Phalanx fore limb digit 1 phalanx OBOL:accepted hand digit 1 phalanx MA:0001389 manual digit I phalanx phalanx of hand digit 1 OBOL:automatic phalanx of thumb OBOL:automatic thumb phalanx OBOL:automatic hand digit 1 phalanx NCBITaxon:9606 OBOL:accepted 5th digit of the manus. AAO:0010643 EHDAA2:0000535 EMAPA:17441 FMA:24949 MA:0000458 NCIT:C52838 UMLS:C0230403 5th digit of hand 5th finger digit 5 of fore-paw fifth digit of hand fifth finger finger 5 fore digit V fore limb digit 5 hand digit 5 manual digit V hand digit 5 little finger uberon manual digitus V manual digitus minimus manus digiti minimi manus quintus UBERON:0003625 manual digit 5 http://upload.wikimedia.org/wikipedia/commons/e/ed/Pink.jpg 5th digit of the manus. UMLS:C0230403 ncithesaurus:Hand_Digit_5 digit 5 of fore-paw EMAPA:17441 fifth digit of hand FMA:24949 finger 5 EHDAA2:0000535 fore digit V AAO:0010643 fore limb digit 5 OBOL:accepted hand digit 5 MA:0000458 manual digit V hand digit 5 NCBITaxon:9606 OBOL:accepted manual digitus V manual digitus minimus manus quintus 1st digit of the hind autopod. AAO:0010644 BTO:0002349 EHDAA2:0002037 EMAPA:17460 FMA:25047 GAID:45 MA:0000465 MESH:D006214 NCIT:C52839 UMLS:C1708079 VSAO:0000201 digit 1 of hind-paw digit 1 of pes digitus primus pedis foot digit 1 great toe hallex hallux hallux; digitus primus [I] hind digit 1 hind digit I hind limb digit 1 pedal digit 1 pedal digit I pes digit I preaxial digit of hindlimb toe 1 big toe foot digit 1 hindlimb dewclaw uberon digitus primus (I) pedis first toe large toe UBERON:0003631 pedal digit 1 http://upload.wikimedia.org/wikipedia/commons/a/ab/RightFootToes.jpg 1st digit of the hind autopod. UMLS:C1708079 ncithesaurus:Foot_Digit_1 digit 1 of hind-paw EMAPA:17460 digitus primus pedis foot digit 1 MA:0000465 great toe FMA:25047 hallux FMA:TA hallux; digitus primus [I] FMA:25047 hind digit I AAO:0010644 hind limb digit 1 OBOL:accepted pedal digit I toe 1 EHDAA2:0002037 foot digit 1 NCBITaxon:9606 OBOL:accepted hindlimb dewclaw digitus primus (I) pedis BTO:0002349 first toe EMAPA:17460 large toe EMAPA:17460 5th digit of the hind autopod. AAO:0010658 BTO:0002353 EHDAA2:0002057 EMAPA:17472 FMA:25053 MA:0000469 NCIT:C52843 UMLS:C1708087 5th toe digit 5 of hind-paw digitus V of pes digitus minimus pedis digitus minimus; digitus quintus [v] digitus quintus [V] digitus quintus [V] pedis digitus quintus of pes digitus quintus pedis fifth digit of foot fifth toe foot digit 5 hind digit 5 hind digit V hind limb digit 5 pedal digit V pedal digitus minimus pes digit V toe 5 foot digit 5 little toe uberon digitus quintus (V) pedis UBERON:0003635 pedal digit 5 http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png 5th digit of the hind autopod. UMLS:C1708087 ncithesaurus:Foot_Digit_5 digit 5 of hind-paw EMAPA:17472 digitus minimus pedis digitus minimus; digitus quintus [v] FMA:25053 digitus quintus [V] FMA:25053 digitus quintus [V] pedis FMA:25053 FMA:TA digitus quintus pedis fifth digit of foot FMA:25053 fifth toe FMA:25053 foot digit 5 MA:0000469 hind digit V AAO:0010658 hind limb digit 5 OBOL:accepted pedal digit V toe 5 EHDAA2:0002057 foot digit 5 NCBITaxon:9606 OBOL:accepted digitus quintus (V) pedis BTO:0002353 A phalanx that is part of a hand digit 5 [Automatically generated definition]. EMAPA:19121 FMA:35489 MA:0001393 NCIT:C52773 UMLS:C1708317 5 th digit of hand digit long bone 5 th digit of hand long bone of digit 5 th digit of hand phalanx 5 th finger digit long bone 5 th finger long bone of digit 5 th finger phalanx digit long bone of 5 th digit of hand digit long bone of 5 th finger digit long bone of fifth finger digit long bone of hand digit 5 fifth finger digit long bone fifth finger long bone of digit fifth finger phalanx fore limb digit 5 phalanx hand digit 5 digit long bone hand digit 5 long bone of digit hand digit 5 phalanx little finger phalanx long bone of digit of 5 th digit of hand long bone of digit of 5 th finger long bone of digit of fifth finger long bone of digit of hand digit 5 manual digit V phalanx phalanx of 5 th digit of hand phalanx of 5 th finger phalanx of 5th finger phalanx of fifth digit of hand phalanx of fifth finger phalanx of hand digit 5 phalanx of little finger phalanx of manual digitus minimus hand digit 5 phalanx uberon UBERON:0003639 manual digit 5 phalanx A phalanx that is part of a hand digit 5 [Automatically generated definition]. OBOL:automatic UMLS:C1708317 ncithesaurus:Hand_Digit_5_Phalanx 5 th digit of hand digit long bone OBOL:automatic 5 th digit of hand long bone of digit OBOL:automatic 5 th digit of hand phalanx OBOL:automatic 5 th finger digit long bone OBOL:automatic 5 th finger long bone of digit OBOL:automatic 5 th finger phalanx OBOL:automatic digit long bone of 5 th digit of hand OBOL:automatic digit long bone of 5 th finger OBOL:automatic digit long bone of fifth finger OBOL:automatic digit long bone of hand digit 5 OBOL:automatic fifth finger digit long bone OBOL:automatic fifth finger long bone of digit OBOL:automatic fifth finger phalanx OBOL:automatic fore limb digit 5 phalanx OBOL:accepted hand digit 5 digit long bone OBOL:automatic hand digit 5 long bone of digit OBOL:automatic hand digit 5 phalanx MA:0001393 little finger phalanx FMA:35489 long bone of digit of 5 th digit of hand OBOL:automatic long bone of digit of 5 th finger OBOL:automatic long bone of digit of fifth finger OBOL:automatic long bone of digit of hand digit 5 OBOL:automatic manual digit V phalanx phalanx of 5 th digit of hand OBOL:automatic phalanx of 5 th finger OBOL:automatic phalanx of fifth digit of hand FMA:35489 phalanx of fifth finger OBOL:automatic phalanx of hand digit 5 OBOL:automatic phalanx of little finger FMA:35489 phalanx of manual digitus minimus OBOL:automatic hand digit 5 phalanx NCBITaxon:9606 OBOL:accepted A phalanx that is part of a foot digit 1 [Automatically generated definition]. EMAPA:19124 FMA:32884 MA:0001381 NCIT:C52778 UMLS:C1708080 big toe phalanx digit long bone of foot digit 1 digit long bone of hallux foot digit 1 digit long bone foot digit 1 long bone of digit foot digit 1 phalanx hallux digit long bone hallux long bone of digit hallux phalanx hind limb digit 1 phalanx long bone of digit of foot digit 1 long bone of digit of hallux pedal digit I phalanx phalanx of big toe phalanx of first digit of foot phalanx of foot digit 1 phalanx of great toe phalanx of hallux foot digit 1 phalanx uberon phalanx of first toe UBERON:0003640 pedal digit 1 phalanx A phalanx that is part of a foot digit 1 [Automatically generated definition]. OBOL:automatic UMLS:C1708080 ncithesaurus:Foot_Digit_1_Phalanx big toe phalanx FMA:32884 digit long bone of foot digit 1 OBOL:automatic digit long bone of hallux OBOL:automatic foot digit 1 digit long bone OBOL:automatic foot digit 1 long bone of digit OBOL:automatic foot digit 1 phalanx MA:0001381 hallux digit long bone OBOL:automatic hallux long bone of digit OBOL:automatic hallux phalanx OBOL:automatic hind limb digit 1 phalanx OBOL:accepted long bone of digit of foot digit 1 OBOL:automatic long bone of digit of hallux OBOL:automatic pedal digit I phalanx phalanx of big toe FMA:32884 phalanx of first digit of foot FMA:32884 phalanx of foot digit 1 OBOL:automatic phalanx of great toe FMA:32884 phalanx of hallux OBOL:automatic foot digit 1 phalanx NCBITaxon:9606 OBOL:accepted phalanx of first toe FMA:32884 An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:37565 MA:0001800 uberon UBERON:0003643 respiratory system arterial blood vessel An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37565 MA:th An arterial blood vessel that is part of a kidney [Automatically generated definition]. EMAPA:31436 MA:0002578 uberon kidney arterial system UBERON:0003644 kidney arterial blood vessel An arterial blood vessel that is part of a kidney [Automatically generated definition]. OBOL:automatic kidney arterial system EMAPA:31436 A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 1. The first metacarpal bone or the metacarpal bone of the thumb is the first bone of the thumb. It is connected to the trapezium of the carpus at the first carpometacarpal joint and to the proximal thumb phalanx at the first metacarpophalangeal joint[Wikipedia:First_metacarpal_bone]. 1 AAO:0010616 EMAPA:19112 FMA:23899 MA:0001364 NCIT:C52796 UMLS:C1708987 finger 1 metacarpus first digit of hand metacarpal first digit of hand metacarpal bone first metacarpal bone hand digit 1 metacarpal hand digit 1 metacarpal bone manual digit 1 metacarpus metacarpal 1 metacarpal I metacarpal bone digit 1 metacarpal bone of digit I metacarpal bone of first digit of hand metacarpal bone of hand digit 1 metacarpal bone of thumb metacarpal of first digit of hand metacarpal of hand digit 1 metacarpal of thumb thumb metacarpal thumb metacarpal bone uberon forelimb digit 1 metacarpus UBERON:0003645 metacarpal bone of digit 1 A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 1. OBOL:automatic The first metacarpal bone or the metacarpal bone of the thumb is the first bone of the thumb. It is connected to the trapezium of the carpus at the first carpometacarpal joint and to the proximal thumb phalanx at the first metacarpophalangeal joint[Wikipedia:First_metacarpal_bone]. UMLS:C1708987 ncithesaurus:Metacarpal_Bone_Digit_1 first digit of hand metacarpal OBOL:automatic first digit of hand metacarpal bone OBOL:automatic first metacarpal bone FMA:23899 hand digit 1 metacarpal OBOL:automatic hand digit 1 metacarpal bone OBOL:automatic metacarpal I FMA:23899 metacarpal bone digit 1 MA:0001364 metacarpal bone of digit I metacarpal bone of first digit of hand OBOL:automatic metacarpal bone of hand digit 1 OBOL:automatic metacarpal bone of thumb OBOL:automatic metacarpal of first digit of hand OBOL:automatic metacarpal of hand digit 1 OBOL:automatic metacarpal of thumb OBOL:automatic thumb metacarpal OBOL:automatic thumb metacarpal bone OBOL:automatic forelimb digit 1 metacarpus EMAPA:19112 A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 5. Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that articulates with carpal 5(4) proximally and with the proximal phalanx of digit V(IV) distally.[AAO] The fifth metacarpal bone (metacarpal bone of the little finger or pinky finger) is the most lateral metacarpal[Wikipedia:Fifth_metacarpal_bone]. FMA also has FMA:36782 ! Bone of fifth metacarpal bone 5 AAO:0000855 EMAPA:19120 FMA:23903 MA:0001368 NCIT:C52792 UMLS:C1711224 5 th digit of hand metacarpal 5 th digit of hand metacarpal bone 5 th finger metacarpal 5 th finger metacarpal bone fifth finger metacarpal fifth finger metacarpal bone fifth metacarpal bone finger 5 metacarpus hand digit 5 metacarpal hand digit 5 metacarpal bone manual digit 5 metacarpus metacarpal 5 metacarpal V metacarpal bone digit 5 metacarpal bone of 5 th digit of hand metacarpal bone of 5 th finger metacarpal bone of digit V metacarpal bone of fifth finger metacarpal bone of hand digit 5 metacarpal of 5 th digit of hand metacarpal of 5 th finger metacarpal of fifth finger metacarpal of hand digit 5 uberon forelimb digit 5 metacarpus UBERON:0003649 metacarpal bone of digit 5 A metacarpal bone that distally_connected_to a proximal phalanx of manual digit 5. OBOL:automatic Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that articulates with carpal 5(4) proximally and with the proximal phalanx of digit V(IV) distally.[AAO] 2012-06-20 AAO:0000855 AAO AAO:LAP The fifth metacarpal bone (metacarpal bone of the little finger or pinky finger) is the most lateral metacarpal[Wikipedia:Fifth_metacarpal_bone]. FMA also has FMA:36782 ! Bone of fifth metacarpal bone FMA UMLS:C1711224 ncithesaurus:Metacarpal_Bone_Digit_5 5 th digit of hand metacarpal OBOL:automatic 5 th digit of hand metacarpal bone OBOL:automatic 5 th finger metacarpal OBOL:automatic 5 th finger metacarpal bone OBOL:automatic fifth finger metacarpal OBOL:automatic fifth finger metacarpal bone OBOL:automatic fifth metacarpal bone FMA:23903 hand digit 5 metacarpal OBOL:automatic hand digit 5 metacarpal bone OBOL:automatic metacarpal bone digit 5 MA:0001368 metacarpal bone of 5 th digit of hand OBOL:automatic metacarpal bone of 5 th finger OBOL:automatic metacarpal bone of digit V metacarpal bone of fifth finger OBOL:automatic metacarpal bone of hand digit 5 OBOL:automatic metacarpal of 5 th digit of hand OBOL:automatic metacarpal of 5 th finger OBOL:automatic metacarpal of fifth finger OBOL:automatic metacarpal of hand digit 5 OBOL:automatic forelimb digit 5 metacarpus EMAPA:19120 A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 1. Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with the prepollex and tarsal 1 proximally and with the proximal phalanx of digit I distally.[AAO] The first metatarsal bone is the bone in the body of the foot just behind the big toe. It is remarkable for its great thickness, and is the shortest of the metatarsal bones. The body is strong, and of well-marked prismoid form. The base presents, as a rule, no articular facets on its sides, but occasionally on the lateral side there is an oval facet, by which it articulates with the second metatarsal. Its proximal articular surface is of large size and kidney-shaped; its circumference is grooved, for the tarsometatarsal ligaments, and medially gives insertion to part of the tendon of the Tibialis anterior; its plantar angle presents a rough oval prominence for the insertion of the tendon of the Peronæus longus. The head is large; on its plantar surface are two grooved facets, on which glide sesamoid bones; the facets are separated by a smooth elevation[Wikipedia:First_metatarsal_bone]. 1 AAO:0000925 EMAPA:19123 FMA:24502 MA:0001369 NCIT:C52791 UMLS:C1708999 first metatarsal bone foot digit 1 metatarsal bone hallux metatarsal bone metatarsal 1 metatarsal I metatarsal bone digit 1 metatarsal bone of digit I metatarsal bone of foot digit 1 metatarsal bone of hallux toe 1 metatarsal toe 1 metatarsus uberon hindlimb digit 1 metatarsus UBERON:0003650 metatarsal bone of digit 1 A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 1. OBOL:automatic Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with the prepollex and tarsal 1 proximally and with the proximal phalanx of digit I distally.[AAO] 2012-06-20 AAO:0000925 AAO AAO:LAP The first metatarsal bone is the bone in the body of the foot just behind the big toe. It is remarkable for its great thickness, and is the shortest of the metatarsal bones. The body is strong, and of well-marked prismoid form. The base presents, as a rule, no articular facets on its sides, but occasionally on the lateral side there is an oval facet, by which it articulates with the second metatarsal. Its proximal articular surface is of large size and kidney-shaped; its circumference is grooved, for the tarsometatarsal ligaments, and medially gives insertion to part of the tendon of the Tibialis anterior; its plantar angle presents a rough oval prominence for the insertion of the tendon of the Peronæus longus. The head is large; on its plantar surface are two grooved facets, on which glide sesamoid bones; the facets are separated by a smooth elevation[Wikipedia:First_metatarsal_bone]. UMLS:C1708999 ncithesaurus:Metatarsal_Bone_Digit_1 first metatarsal bone FMA:24502 foot digit 1 metatarsal bone OBOL:automatic hallux metatarsal bone OBOL:automatic metatarsal I AAO:0000925 metatarsal bone digit 1 MA:0001369 metatarsal bone of digit I metatarsal bone of foot digit 1 OBOL:automatic metatarsal bone of hallux OBOL:automatic hindlimb digit 1 metatarsus EMAPA:19123 A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 5. Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with tarsal 5 or the distal head of the tibiale-fibulare proximally and with the proximal phalanx of digit V distally.[AAO] The fifth metatarsal bone is recognized by a rough eminence, the tuberosity, on the lateral side of its base. The base articulates behind, by a triangular surface cut obliquely in a transverse direction, with the cuboid; and medially, with the fourth metatarsal. On the medial part of its dorsal surface is inserted the tendon of the Peronæus tertius and on the dorsal surface of the tuberosity that of the Peronæus brevis. A strong band of the plantar aponeurosis connects the projecting part of the tuberosity with the lateral process of the tuberosity of the calcaneus. The plantar surface of the base is grooved for the tendon of the Abductor digiti quinti, and gives origin to the Flexor digiti quinti brevis. The base of the metatarsal is often injured and a particularly notorious fracture is the Jones fracture. When the tuberosity is broken, it is called a pseudo-Jones fracture or a dancer's fracture. This is a common fracture of the fifth metatarsal. Stress fractures are common in the fifth metatarsal among athletes[Wikipedia:Fifth_metatarsal_bone]. 5 AAO:0000929 EMAPA:19131 FMA:24506 MA:0001373 NCIT:C52787 UMLS:C1709003 fifth metatarsal bone foot digit 5 metatarsal bone metatarsal 5 metatarsal V metatarsal bone digit 5 metatarsal bone of digit V metatarsal bone of foot digit 5 toe 5 metatarsal toe 5 metatarsus uberon hindlimb digit 5 metatarsus UBERON:0003654 metatarsal bone of digit 5 A metatarsal bone that distally_connected_to a proximal phalanx of pedal digit 5. OBOL:automatic Dumb-bell-shaped bone of endochondral origin with cartilaginous epiphyses that articulates with tarsal 5 or the distal head of the tibiale-fibulare proximally and with the proximal phalanx of digit V distally.[AAO] 2012-06-20 AAO:0000929 AAO AAO:LAP The fifth metatarsal bone is recognized by a rough eminence, the tuberosity, on the lateral side of its base. The base articulates behind, by a triangular surface cut obliquely in a transverse direction, with the cuboid; and medially, with the fourth metatarsal. On the medial part of its dorsal surface is inserted the tendon of the Peronæus tertius and on the dorsal surface of the tuberosity that of the Peronæus brevis. A strong band of the plantar aponeurosis connects the projecting part of the tuberosity with the lateral process of the tuberosity of the calcaneus. The plantar surface of the base is grooved for the tendon of the Abductor digiti quinti, and gives origin to the Flexor digiti quinti brevis. The base of the metatarsal is often injured and a particularly notorious fracture is the Jones fracture. When the tuberosity is broken, it is called a pseudo-Jones fracture or a dancer's fracture. This is a common fracture of the fifth metatarsal. Stress fractures are common in the fifth metatarsal among athletes[Wikipedia:Fifth_metatarsal_bone]. UMLS:C1709003 ncithesaurus:Metatarsal_Bone_Digit_5 fifth metatarsal bone FMA:24506 foot digit 5 metatarsal bone OBOL:automatic metatarsal V AAO:0000929 metatarsal bone digit 5 MA:0001373 metatarsal bone of digit V metatarsal bone of foot digit 5 OBOL:automatic hindlimb digit 5 metatarsus EMAPA:19131 A bone that is part of a mesopodial skeleton. The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost EMAPA:36579 MA:0000295 basipodium bone carpal/tarsal bone mesopod bone mesopodial bone uberon UBERON:0003656 mesopodium bone UBERON:cjm https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern A bone that is part of a mesopodial skeleton. The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost basipodium bone MA:th carpal/tarsal bone MA:0000295 Any joint that is part of a (free) limb. EMAPA:36501 FMA:321558 MA:0000691 galen:LimbJoint joint of limb joint of limb skeletal system skeletal limb joint uberon UBERON:0003657 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses limb joint Any joint that is part of a (free) limb. joint of limb skeletal system OBOL:automatic skeletal limb joint GO:0036023 Any muscle organ that is part of a hip [Automatically generated definition]. MA:0000657 hip muscle organ hip region muscle organ muscle organ of hip muscle organ of hip region muscle organ of regio coxae regio coxae muscle organ uberon UBERON:0003658 hip muscle prolog Any muscle organ that is part of a hip [Automatically generated definition]. OBOL:automatic hip muscle organ OBOL:automatic hip region muscle organ OBOL:automatic muscle organ of hip OBOL:automatic muscle organ of hip region OBOL:automatic muscle organ of regio coxae OBOL:automatic regio coxae muscle organ OBOL:automatic Any muscle organ that is part of a toe [Automatically generated definition]. EMAPA:37333 MA:0000648 digit of foot muscle organ digit of terminal segment of free lower limb muscle organ digitus pedis muscle organ foot digit muscle foot digit muscle organ hind limb digit muscle muscle organ of digit of foot muscle organ of digit of terminal segment of free lower limb muscle organ of digitus pedis muscle organ of foot digit muscle organ of terminal segment of free lower limb digit muscle organ of toe terminal segment of free lower limb digit muscle organ toe muscle organ foot digit muscle uberon UBERON:0003659 pedal digit muscle Any muscle organ that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37333 MA:th digit of foot muscle organ OBOL:automatic digit of terminal segment of free lower limb muscle organ OBOL:automatic digitus pedis muscle organ OBOL:automatic foot digit muscle MA:0000648 foot digit muscle organ OBOL:automatic hind limb digit muscle OBOL:accepted muscle organ of digit of foot OBOL:automatic muscle organ of digit of terminal segment of free lower limb OBOL:automatic muscle organ of digitus pedis OBOL:automatic muscle organ of foot digit OBOL:automatic muscle organ of terminal segment of free lower limb digit OBOL:automatic muscle organ of toe OBOL:automatic terminal segment of free lower limb digit muscle organ OBOL:automatic toe muscle organ OBOL:automatic foot digit muscle NCBITaxon:9606 OBOL:accepted Any muscle organ that is part of a limb [Automatically generated definition]. EMAPA:32700 MA:0000692 limb muscle organ limb skeletal muscle muscle organ of limb uberon UBERON:0003661 limb muscle prolog Any muscle organ that is part of a limb [Automatically generated definition]. OBOL:automatic limb muscle organ OBOL:accepted limb skeletal muscle OBOL:exploratory muscle organ of limb OBOL:accepted Any muscle organ that is part of a forelimb. FMA and MA class actually refer to muscles of entire pectoral complex UBERON:0005634 AAO:0000204 BTO:0000479 EMAPA:36049 FMA:37348 fore limb muscle organ forelimb muscle organ free upper limb muscle muscle of free upper limb muscle of upper limb upper limb skeletal muscle wing muscle uberon arm muscle system musculature of arm musculature of the arm UBERON:0003662 forelimb muscle prolog Any muscle organ that is part of a forelimb. OBOL:automatic FMA and MA class actually refer to muscles of entire pectoral complex FMA fore limb muscle organ OBOL:automatic forelimb muscle organ OBOL:automatic free upper limb muscle FMA:37348 muscle of free upper limb FMA:37348 muscle of upper limb FMA:9621 upper limb skeletal muscle wing muscle Geisha:syn NCBITaxon:8782 wing muscle NCBITaxon:8782 OBOL:automatic arm muscle system EHDAA2:0000141 musculature of arm musculature of the arm Any muscle organ that is part of a hindlimb [Automatically generated definition]. AAO:0000222 EFO:0001928 FMA:37368 free lower limb muscle hind limb muscle organ hindlimb muscle organ inferior member muscle organ lower extremity muscle organ lower limb skeletal muscle muscle of free lower limb muscle of posterior limb muscle organ of hind limb muscle organ of hindlimb muscle organ of inferior member muscle organ of lower extremity uberon UBERON:0003663 hindlimb muscle prolog Any muscle organ that is part of a hindlimb [Automatically generated definition]. OBOL:automatic free lower limb muscle FMA:37368 hind limb muscle organ OBOL:automatic hindlimb muscle organ OBOL:automatic inferior member muscle organ OBOL:automatic lower extremity muscle organ OBOL:automatic lower limb skeletal muscle muscle of free lower limb FMA:37368 muscle of posterior limb muscle organ of hind limb OBOL:automatic muscle organ of hindlimb OBOL:automatic muscle organ of inferior member OBOL:automatic muscle organ of lower extremity OBOL:automatic Any muscle organ that is part of a finger [Automatically generated definition]. EMAPA:37331 MA:0000624 digit of hand muscle organ digit of terminal segment of free upper limb muscle organ digitus manus muscle organ finger muscle organ fore limb digit muscle hand digit muscle hand digit muscle organ muscle organ of digit of hand muscle organ of digit of terminal segment of free upper limb muscle organ of digitus manus muscle organ of finger muscle organ of hand digit muscle organ of terminal segment of free upper limb digit terminal segment of free upper limb digit muscle organ hand digit muscle uberon UBERON:0003664 manual digit muscle Any muscle organ that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37331 MA:th digit of hand muscle organ OBOL:automatic digit of terminal segment of free upper limb muscle organ OBOL:automatic digitus manus muscle organ OBOL:automatic finger muscle organ OBOL:automatic fore limb digit muscle OBOL:accepted hand digit muscle MA:0000624 hand digit muscle organ OBOL:automatic muscle organ of digit of hand OBOL:automatic muscle organ of digit of terminal segment of free upper limb OBOL:automatic muscle organ of digitus manus OBOL:automatic muscle organ of finger OBOL:automatic muscle organ of hand digit OBOL:automatic muscle organ of terminal segment of free upper limb digit OBOL:automatic terminal segment of free upper limb digit muscle organ OBOL:automatic hand digit muscle NCBITaxon:9606 OBOL:accepted A muscle organ that attaches to a tail vertebra [Automatically generated definition]. the BTO class may possibly refer to an invertebrate structure AAO:0000081 BTO:0001905 EMAPA:37759 MA:0000699 caudal muscle muscle organ of post-vent region muscle organ of tail post-vent region muscle organ tail muscle tail muscle organ uberon UBERON:0003665 post-anal tail muscle A muscle organ that attaches to a tail vertebra [Automatically generated definition]. OBOL:automatic the BTO class may possibly refer to an invertebrate structure BTO EMAPA:37759 MA:th muscle organ of post-vent region OBOL:automatic muscle organ of tail OBOL:automatic post-vent region muscle organ OBOL:automatic tail muscle MA:0000699 tail muscle organ OBOL:automatic A small fluid-filled sac lined by synovial membrane with an inner capillary layer of slimy fluid. It provides a cushion between bones and tendons and/or muscles around a joint. This helps to reduce friction between the bones and allows free movement. Bursae are filled with synovial fluid and are found around most major joints of the body. bursa FMA:9692 GAID:252 MESH:D002061 NCIT:C33717 UMLS:C0006441 galen:Bursa uberon bursa synovialis UBERON:0003668 synovial bursa http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png A small fluid-filled sac lined by synovial membrane with an inner capillary layer of slimy fluid. It provides a cushion between bones and tendons and/or muscles around a joint. This helps to reduce friction between the bones and allows free movement. Bursae are filled with synovial fluid and are found around most major joints of the body. bursa FMA:9692 UMLS:C0006441 ncithesaurus:Synovial_Bursa bursa synovialis A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl. Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO] The teeth collectively in the dental arch. Dentition ordinarily refers to the natural teeth in position in their alveoli. (MeSH[ncithesaurus:Dentition]) In FMA this is an anatomical set AAO:0000126 FMA:75150 GAID:1249 MESH:A14.254 NCIT:C13072 OpenCyc:Mx4rvVi65JwpEbGdrcN5Y29ycA UMLS:C0011443 dentes set of teeth teeth teeth set uberon collection of teeth teeth UBERON:0003672 dentition A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl. Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO] 2012-06-20 AAO:0000126 AAO AAO:LAP The teeth collectively in the dental arch. Dentition ordinarily refers to the natural teeth in position in their alveoli. (MeSH[ncithesaurus:Dentition]) ncithesaurus:Dentition In FMA this is an anatomical set FMA UMLS:C0011443 ncithesaurus:Dentition dentes FMA:75150 FMA:TA set of teeth FMA:75150 teeth FMA:75150 teeth set FMA:75150 The part of a tooth that is implanted in the gum; the root is normally located below the neck of the tooth, covered by cementum rather than enamel, and attached by the periodontal ligament to the alveolar bone EMAPA:37975 FMA:55624 GAID:1280 MESH:A14.254.900.750 radix corona root of tooth tooth root uberon UBERON:0003677 tooth root The part of a tooth that is implanted in the gum; the root is normally located below the neck of the tooth, covered by cementum rather than enamel, and attached by the periodontal ligament to the alveolar bone MP:0011165 EMAPA:37975 MA:th radix corona FMA:55624 root of tooth FMA:55624 tooth root FMA:55624 The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity EFO:0000213 EMAPA:36505 FMA:12266 GAID:17 MA:0003057 MESH:A01.047.025 NCIT:C12664 OpenCyc:Mx4rvZR1TJwpEbGdrcN5Y29ycA UMLS:C0230168 galen:AbdominalCavity cavity of abdominal compartment cavity of compartment of abdomen space of abdominal compartment uberon cavitas abdominis UBERON:0003684 abdominal cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). UBERON:cjm in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity FMA UMLS:C0230168 ncithesaurus:Abdominal_Cavity cavity of abdominal compartment FMA:12266 cavity of compartment of abdomen FMA:12266 space of abdominal compartment FMA:12266 cavitas abdominis cavitas abdominis GAID:17 Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture. sutura suture EMAPA:35263 FMA:7493 GAID:211 MA:0001475 MESH:D003393 cranium suture suture joint of skull suture of cranium uberon UBERON:0003685 cranial suture GO Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture. FMA:71385 ISBN:3110148986 suture FMA:71385 cranium suture OBOL:automatic suture of cranium OBOL:automatic In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] AAO:0010826 EMAPA:37868 FMA:75306 GAID:228 MESH:D005539 NCIT:C12495 OpenCyc:Mx4rwOm-FpwpEbGdrcN5Y29ycA TAO:0002045 UMLS:C0016519 ZFA:0005387 uberon UBERON:0003687 Design pattern notes: check whether this fits the foramen design pattern foramen magnum http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] 2012-08-14 TAO:0002045 TAO TAO:wd EMAPA:37868 MA:th UMLS:C0016519 ncithesaurus:Foramen_Magnum The outermost part of the spinal canal. It is the space within the canal (formed by the surrounding vertebrae) lying outside the dura mater. epidural extradural In humans the epidural space contains lymphatics, spinal nerve roots, loose fatty tissue, small arteries, and a network of large, thin-walled blood vessels called the epidural venous plexus in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail FMA:71228 GAID:243 MESH:D004824 cavum epidurale cavum extradurale extradural space spatium epidurale spatium extradurale uberon epidural cavity UBERON:0003691 epidural space The outermost part of the spinal canal. It is the space within the canal (formed by the surrounding vertebrae) lying outside the dura mater. in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail FMA cavum epidurale cavum extradurale extradural space FMA:71228 spatium epidurale spatium extradurale FMA:71228 FMA:TA epidural cavity The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted]. we follow FMA in making these joints part of digits. We include carpometacarpophalangeal joint as a synonym - these joints connect to the carpometacarpus - this is not necessarily inconsistent with the relationship for this class to metacarpal bone, as the carpometacarpus could be considered to have a metacarpal as part metacarpal joint EMAPA:19302 FMA:35246 GAID:255 MA:0000453 MESH:A02.835.583.345.512 NCIT:C33106 OpenCyc:Mx4rwNt8wJwpEbGdrcN5Y29ycA UMLS:C0025525 galen:MetacarpoPhalangealJoint MP joint metacarpo-phalangeal joint carpometacarpophalangeal joint uberon articulationes metacarpophalangeae metacarpal phalangeal joint UBERON:0003695 metacarpophalangeal joint http://upload.wikimedia.org/wikipedia/commons/5/53/Gray337.png The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted]. metacarpal joint FMA:35246 UMLS:C0025525 ncithesaurus:Metacarpophalangeal_Joint MP joint FMA:35246 metacarpo-phalangeal joint MA:0000453 carpometacarpophalangeal joint NCBITaxon:8782 articulationes metacarpophalangeae metacarpal phalangeal joint HP:0004294 The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral. we follow FMA in making these joints part of digits http://purl.bioontology.org/ontology/provisional/1ddd2e2d-2ace-4c87-8ec6-d3b5730b3e7c http://purl.bioontology.org/ontology/provisional/8378426c-67ca-4bab-a9cf-531093b9b95e FMA:35222 GAID:258 MESH:D008683 NCIT:C33108 OpenCyc:Mx4rwCtS0pwpEbGdrcN5Y29ycA UMLS:C0025589 galen:MetatarsoPhalangealJoint metatarsal-phalangeal joint uberon articulationes metatarsophalangeae metatarsal joint metatarsalphalangeal joint metatarsophalangeal metatarsophalangeal articulation UBERON:0003696 metatarsophalangeal joint http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray268.png The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral. UMLS:C0025589 ncithesaurus:Metatarsophalangeal_Joint metatarsal-phalangeal joint PHENOSCAPE:ad articulationes metatarsophalangeae metatarsal joint FMA:35222 metatarsalphalangeal joint metatarsophalangeal metatarsophalangeal articulation The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. EMAPA:37064 FMA:10429 FMA:259054 GAID:26 MESH:A01.047.050 NCIT:C77608 UMLS:C0836916 paries abdominalis wall of abdomen wall of abdomen proper uberon abdominal wall proper layers of the abdominal wall paries abdominalis UBERON:0003697 abdominal wall http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. ncithesaurus:Abdominal_Wall EMAPA:37064 MA:th UMLS:C0836916 ncithesaurus:Abdominal_Wall paries abdominalis wall of abdomen FMA:259054 wall of abdomen proper FMA:10429 abdominal wall proper FMA:10429 layers of the abdominal wall paries abdominalis Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct. includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct FMA:14678 GAID:281 MA:0002659 MESH:D017734 NCIT:C32573 UMLS:C0206187 uberon bile duct extrahepatic part extrahepatic biliary system UBERON:0003703 extrahepatic bile duct Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct. MESH:A03.159.183.079 UMLS:C0206187 ncithesaurus:Extrahepatic_Bile_Duct bile duct extrahepatic part MA:0002659 extrahepatic biliary system GAID:281 Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct. includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO] FMA:15766 GAID:287 MA:0001630 MESH:D001653 NCIT:C12677 TAO:0005169 UMLS:C0005401 ZFA:0005169 bile duct intrahepatic part uberon intrahepatic biliary system UBERON:0003704 intrahepatic bile duct FMA MA Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct. MESH:A03.159.183.158 Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO] 2012-08-14 TAO:0005169 TAO ZFIN:curator UMLS:C0005401 ncithesaurus:Intrahepatic_Bile_Duct bile duct intrahepatic part MA:0001630 A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis arterial circle EHDAA2:0000252 EHDAA:9758 EMAPA:37829 FMA:50454 GAID:486 MESH:D002941 OpenCyc:Mx4rwSrCwJwpEbGdrcN5Y29ycA arterial circle of Willis cerebral arterial circle uberon Willis circle circulus arteriosus cerebri UBERON:0003709 circle of Willis http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg FMA-modified FMA-modified A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis arterial circle EMAPA:37829 MA:th cerebral arterial circle GAID:486 Willis circle GAID:486 circulus arteriosus cerebri The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava. EHDAA2:0000182 EHDAA:9868 FMA:4723 GAID:529 MESH:D016121 NCIT:C32816 OpenCyc:Mx4rvz3aUJwpEbGdrcN5Y29ycA UMLS:C0006095 galen:BrachiocephalicVein brachiocephalic venous tree innominate vein uberon innomiate vein innominate trunk innominate vein innominate veins vena brachiocephalica venae anonyma UBERON:0003711 brachiocephalic vein http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava. UMLS:C0006095 ncithesaurus:Innominate_Vein brachiocephalic venous tree FMA:4723 innominate vein FMA:4723 innomiate vein innominate trunk innominate vein innominate vein GAID:529 innominate veins vena brachiocephalica vena brachiocephalica venae anonyma A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. EMAPA:37226 FMA:14331 GAID:541 MA:0002164 MESH:D013162 NCIT:C33608 OpenCyc:Mx4rwCt0eZwpEbGdrcN5Y29ycA UMLS:C0038001 galen:SplenicVein vena splenica uberon lienal vein vena lienalis UBERON:0003713 splenic vein http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. ncithesaurus:Splenic_Vein EMAPA:37226 MA:th UMLS:C0038001 ncithesaurus:Splenic_Vein vena splenica FMA:14331 FMA:TA lienal vein MA:0002164 vena lienalis Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] FMA definition includes vasculature AAO:0000325 AEO:0000123 EHDAA2:0003123 FMA:9642 GAID:609 MESH:D009417 NCIT:C13052 OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ UMLS:C0027757 nerve tissue nervous tissue portion of neural tissue uberon UBERON:0003714 neural tissue Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. FMA:9642 One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] 2012-06-20 AAO:0000325 AAO AAO:LAP FMA definition includes vasculature FMA UMLS:C0027757 ncithesaurus:Nervous_Tissue nerve tissue FMA:9642 nervous tissue FMA:9642 portion of neural tissue FMA:9642 The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers BAMS:spn EMAPA:37959 FMA:5883 GAID:800 MESH:D013153 uberon splanchnic nerves visceral nerve UBERON:0003715 splanchnic nerve The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. MP:0008318 EMAPA:37959 MA:th splanchnic nerves BAMS:spn visceral nerve A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. recurrent nerve AAO:0010754 FMA:6246 GAID:804 MESH:D012009 VHOG:0001347 nervus laryngeus recurrens recurrent laryngeal nerve from vagus nerve vagus X nerve recurrent laryngeal branch uberon inferior laryngeal nerve ramus recurrens UBERON:0003716 recurrent laryngeal nerve Wikipedia A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. AAO:0010754 recurrent nerve nervus laryngeus recurrens vagus X nerve recurrent laryngeal branch VHOG:0001347 inferior laryngeal nerve GAID:804 ramus recurrens AAO:0010754 The lingual nerve is a branch of the mandibular nerve (CN V3), itself a branch of the trigeminal nerve, which supplies sensory innervation to the tongue. It also carries fibers from the facial nerve, which return taste information from the anterior two thirds of the tongue. BAMS:5lg EMAPA:19168 FMA:53218 GAID:835 MA:0001102 MESH:D008036 lingual branch of trigeminal nerve trigeminal V nerve lingual branch trigeminal nerve lingual branch uberon UBERON:0003721 lingual nerve The lingual nerve is a branch of the mandibular nerve (CN V3), itself a branch of the trigeminal nerve, which supplies sensory innervation to the tongue. It also carries fibers from the facial nerve, which return taste information from the anterior two thirds of the tongue. trigeminal V nerve lingual branch MA:0001102 The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls. FMA:5860 GAID:857 MESH:D013900 OpenCyc:Mx4rwSJp_ZwpEbGdrcN5Y29ycA nervus thoracis thoracic spinal nerve uberon nervi thoracici pectoral nerve UBERON:0003726 thoracic nerve The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls. MESH:A08.800.800.720.800 nervus thoracis FMA:5860 FMA:TA thoracic spinal nerve FMA:5860 nervi thoracici pectoral nerve GAID:857 The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]. EMAPA:18227 FMA:6028 GAID:858 MESH:D007367 NCIT:C32825 UMLS:C1285089 anterior ramus of thoracic nerve anterior ramus of thoracic spinal nerve ramus anterior, nervus thoracicus thoracic anterior ramus ventral ramus of thoracic spinal nerve uberon nervi intercostales UBERON:0003727 intercostal nerve http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray819.png The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]. UMLS:C1285089 ncithesaurus:Intercostal_Nerve anterior ramus of thoracic nerve FMA:6028 anterior ramus of thoracic spinal nerve FMA:6028 ramus anterior, nervus thoracicus FMA:6028 thoracic anterior ramus FMA:6028 ventral ramus of thoracic spinal nerve FMA:6028 nervi intercostales The central part of the thoracic cavity enclosed by the left and right pleurae. mediastinal CALOHA:TS-2338 EFO:0003057 EMAPA:36001 FMA:9826 GAID:94 MA:0003075 MESH:A01.911.800.500 NCIT:C12748 OpenCyc:Mx4rv2OKJ5wpEbGdrcN5Y29ycA UMLS:C0025066 mediastinal part of chest uberon UBERON:0003728 mediastinum http://upload.wikimedia.org/wikipedia/commons/a/ab/Mediastinum.png FMA The central part of the thoracic cavity enclosed by the left and right pleurae. UBERON:cjm UMLS:C0025066 ncithesaurus:Mediastinum mediastinal part of chest FMA:9826 A mucous membrane that lines the mouth. this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa) the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. BTO:0002860 CALOHA:TS-0716 EMAPA:26937 FMA:59660 GAID:951 MA:0002794 MESH:D009061 NCIT:C77637 UMLS:C0026639 mouth mucosa mouth mucous membrane mouth organ mucosa mucosa of mouth mucous membrane of mouth oral mucous membrane oral part of viscerocranial mucosa tunica mucosa oris uberon buccal mucosa mucosal lining of mouth oral mucosa tunica mucosa oris UBERON:0003729 mouth mucosa A mucous membrane that lines the mouth. the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. UMLS:C0026639 ncithesaurus:Oral_Mucosa mouth mucosa FMA:59660 mouth mucous membrane OBOL:accepted mouth organ mucosa OBOL:accepted mucosa of mouth OBOL:accepted mucous membrane of mouth FMA:59660 oral part of viscerocranial mucosa FMA:59660 tunica mucosa oris FMA:59660 FMA:TA buccal mucosa GAID:951 mucosal lining of mouth MA:0002794 oral mucosa GAID:951 tunica mucosa oris A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]. AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204] EMAPA:36141 prostate ductal progenitor prostatic bud uberon prostate gland bud prostate primordium UBERON:0003820 prostate bud A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]. GO:0060513 prostate ductal progenitor prostate gland bud EMAPA:36141 A bone of the metapodial skeleton EMAPA:37284 MA:0000301 metacarpal or metatarsal bone metacarpal/metatarsal metacarpal/metatarsal bone metapodi bone metapodial bone metapodium bone uberon UBERON:0003821 metapodium bone https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern A bone of the metapodial skeleton EMAPA:37284 MA:th metacarpal/metatarsal bone MA:0000301 metapodi bone metapodial bone metapodium bone The part of the forelimb between pectoral region and the elbow, corresponding to the humerus. Segment of the hindleg corresponding to the humerus.[AAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] anatomical usage, the term arm refers specifically to the segment between the shoulder and the elbow, while the segment between the elbow and wrist is the forearm. However, in common, literary, and historical usage, arm refers to the entire upper limb from shoulder to wrist. FMA uses the term Arm for this class, so we place it here. Naming conventions for pod terms under discussion within phenoscape group. AAO:0000199 EHDAA2:0002112 EHDAA:4186 EHDAA:6234 EMAPA:17424 FMA:24890 MA:0000035 MESH:D001132 NCIT:C32141 OpenCyc:Mx4rvVj0Z5wpEbGdrcN5Y29ycA UMLS:C0446516 VHOG:0000343 VSAO:0005057 galen:Arm brachial region brachium fore propodium forelimb propodium forelimb stylopodial element forelimb stylopodium proximal segment of free upper limb regio brachialis stylopod of arm stylopod of forelimb upper arm wing stylopod uberon arm UBERON:0003822 forelimb stylopod MA The part of the forelimb between pectoral region and the elbow, corresponding to the humerus. Segment of the hindleg corresponding to the humerus.[AAO] 2012-06-20 AAO:0000887 AAO AAO:LAP Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000343 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 UMLS:C0446516 ncithesaurus:Arm brachium VSAO:0005057 fore propodium AAO:0000199 forelimb stylopodial element MA:th forelimb stylopodium OBOL:automatic regio brachialis FMA:24890 FMA:TA upper arm MA:0000035 wing stylopod NCBITaxon:8782 OBOL:automatic arm FMA:24890 The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants. Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] sural FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here EFO:0003051 EHDAA2:0001030 EHDAA:5165 EHDAA:6190 EMAPA:17496 FMA:24979 FMA:24984 MA:0000051 MESH:D007866 NCIT:C32974 OpenCyc:Mx4rvczZBpwpEbGdrcN5Y29ycA UMLS:C1140621 VHOG:0000348 VSAO:0005060 galen:Leg calf of leg crus crus of hindlimb hind limb middle limb segment hind limb zeudopodium hind limb zeugopod hindlimb epipodium hindlimb middle limb segment hindlimb zeudopodium hindlimb zeugopod hindlimb zeugopodium intermediate segment of free lower limb lower extremity middle limb segment lower extremity zeugopod lower leg middle limb segment of hind limb middle limb segment of hindlimb posterior curral region posterior leg region posterior part of leg posterior region of leg regio cruris posterior regio surae shank sura sural region zeugopod of hind limb zeugopod of hindlimb calf uberon hind epipodium leg UBERON:0003823 hindlimb zeugopod MA The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants. PHENOSCAPE:curators Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0000348 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion FMA UMLS:C1140621 ncithesaurus:Leg calf of leg FMA:24984 crus VSAO:0005060 hind limb middle limb segment OBOL:automatic hind limb zeudopodium VHOG:0000348 hind limb zeugopod OBOL:automatic hindlimb middle limb segment OBOL:automatic hindlimb zeudopodium VHOG:0000348 hindlimb zeugopod OBOL:automatic hindlimb zeugopodium OBOL:automatic intermediate segment of free lower limb FMA:24979 lower extremity middle limb segment OBOL:automatic lower extremity zeugopod OBOL:automatic lower leg MA:0000051 middle limb segment of hind limb OBOL:automatic middle limb segment of hindlimb posterior curral region FMA:24984 posterior leg region FMA:24984 posterior part of leg FMA:24984 posterior region of leg FMA:24984 regio cruris posterior FMA:24984 FMA:TA regio surae FMA:24984 FMA:TA shank VSAO:0005060 sura FMA:24984 FMA:TA sural region FMA:24984 zeugopod of hind limb OBOL:automatic zeugopod of hindlimb OBOL:automatic hind epipodium leg FMA:24979 MESH:A01.378.610.500 A nerve that is part of a thorax [Automatically generated definition]. EMAPA:37265 MA:0000562 MESH:D013900 nerve of thorax thoracic segment nerve thorax nerve uberon upper body nerve UBERON:0003824 nerve of thoracic segment A nerve that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37265 MA:th nerve of thorax OBOL:automatic thoracic segment nerve MA:0000562 thorax nerve OBOL:automatic upper body nerve MA:0000562 A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37061 MA:0000528 abdominal segment nerve uberon UBERON:0003825 nerve of abdominal segment A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37061 MA:th abdominal segment nerve MA:0000528 A bone that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:35893 MA:0000682 uberon femur UBERON:0003826 May be merged into femur. See https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376 upper leg bone A bone that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic femur A bone that is part of a thorax [Automatically generated definition]. EMAPA:37247 MA:0000559 bone of thorax bone organ of thorax thorax bone thorax bone organ uberon upper body bone UBERON:0003827 thoracic segment bone A bone that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37247 MA:th bone of thorax OBOL:automatic bone organ of thorax OBOL:automatic thorax bone OBOL:automatic thorax bone organ OBOL:automatic upper body bone MA:0000559 A bone that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37058 MA:0000525 abdominal segment of trunk bone abdominal segment of trunk bone organ bone of abdominal segment of trunk bone organ of abdominal segment of trunk uberon UBERON:0003828 abdominal segment bone A bone that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37058 MA:th abdominal segment of trunk bone OBOL:automatic abdominal segment of trunk bone organ OBOL:automatic bone of abdominal segment of trunk OBOL:automatic bone organ of abdominal segment of trunk OBOL:automatic Any muscle tissue that is part of the urethra. EMAPA:37787 MA:0002649 uberon urethral muscle layer UBERON:0003829 urethra muscle tissue Any muscle tissue that is part of the urethra. UBERON:cjm EMAPA:37787 MA:th urethral muscle layer MA:0002649 Any muscle organ that is part of a thorax [Automatically generated definition]. MA:0000561 muscle organ of thorax thorax muscle organ uberon upper body muscle UBERON:0003830 thoracic segment muscle prolog Any muscle organ that is part of a thorax [Automatically generated definition]. OBOL:automatic muscle organ of thorax OBOL:automatic thorax muscle organ OBOL:automatic upper body muscle MA:0000561 Any muscle organ that is part of a respiratory system [Automatically generated definition]. EMAPA:35733 MA:0001828 apparatus respiratorius muscle organ muscle organ of apparatus respiratorius muscle organ of respiratory system respiratory system muscle organ uberon UBERON:0003831 respiratory system muscle Any muscle organ that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius muscle organ OBOL:automatic muscle organ of apparatus respiratorius OBOL:automatic muscle organ of respiratory system OBOL:automatic respiratory system muscle organ OBOL:automatic Any muscle organ that is part of a esophagus [Automatically generated definition]. merge muscle and muscle layer? EMAPA:26983 MA:0002682 esophageal muscle esophagus muscle organ gullet muscle organ muscle organ of esophagus muscle organ of gullet muscle organ of oesophagus oesophagus muscle organ uberon UBERON:0003832 esophagus muscle MA Any muscle organ that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus muscle organ OBOL:automatic gullet muscle organ OBOL:automatic muscle organ of esophagus OBOL:automatic muscle organ of gullet OBOL:automatic muscle organ of oesophagus OBOL:automatic oesophagus muscle organ OBOL:automatic A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37060 MA:0000527 abdominal segment of trunk muscle organ muscle organ of abdominal segment of trunk uberon UBERON:0003833 abdominal segment muscle A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37060 MA:th abdominal segment of trunk muscle organ OBOL:automatic muscle organ of abdominal segment of trunk OBOL:automatic A blood vessel that is part of a thorax [Automatically generated definition]. EMAPA:37238 MA:0000558 blood vessel of thorax thorax blood vessel uberon upper body blood vessel UBERON:0003834 thoracic segment blood vessel A blood vessel that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37238 MA:th blood vessel of thorax OBOL:automatic thorax blood vessel OBOL:automatic upper body blood vessel MA:0000558 A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37057 MA:0000524 abdominal segment of trunk blood vessel blood vessel of abdominal segment of trunk uberon UBERON:0003835 abdominal segment blood vessel A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37057 MA:th abdominal segment of trunk blood vessel OBOL:automatic blood vessel of abdominal segment of trunk OBOL:automatic A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37063 FMA:264898 MA:0000530 abdominal segment of trunk skin skin of abdominal segment of trunk uberon UBERON:0003836 abdominal segment skin A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37063 MA:th abdominal segment of trunk skin OBOL:automatic skin of abdominal segment of trunk OBOL:automatic A portion of connective tissue that is part of a thorax [Automatically generated definition]. EMAPA:37253 MA:0000560 connective tissue of thorax portion of connective tissue of thorax textus connectivus of thorax thorax connective tissue thorax portion of connective tissue thorax textus connectivus uberon upper body connective tissue UBERON:0003837 thoracic segment connective tissue A portion of connective tissue that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37253 MA:th connective tissue of thorax OBOL:automatic portion of connective tissue of thorax OBOL:automatic textus connectivus of thorax OBOL:automatic thorax connective tissue OBOL:automatic thorax portion of connective tissue OBOL:automatic thorax textus connectivus OBOL:automatic upper body connective tissue MA:0000560 A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37059 MA:0000526 abdominal segment of trunk connective tissue abdominal segment of trunk portion of connective tissue abdominal segment of trunk textus connectivus connective tissue of abdominal segment of trunk portion of connective tissue of abdominal segment of trunk textus connectivus of abdominal segment of trunk uberon UBERON:0003838 abdominal segment connective tissue A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37059 MA:th abdominal segment of trunk connective tissue OBOL:automatic abdominal segment of trunk portion of connective tissue OBOL:automatic abdominal segment of trunk textus connectivus OBOL:automatic connective tissue of abdominal segment of trunk OBOL:automatic portion of connective tissue of abdominal segment of trunk OBOL:automatic textus connectivus of abdominal segment of trunk OBOL:automatic A limb joint that is part of a forelimb [Automatically generated definition]. EMAPA:19204 MA:0000614 anteriormost limb joint of limb anteriormost limb limb joint fore limb joint of limb fore limb limb joint forelimb joint of limb forelimb limb joint joint of free upper limb joint of limb of anteriormost limb joint of limb of fore limb joint of limb of forelimb joint of limb of superior member joint of limb of upper extremity limb joint of anteriormost limb limb joint of fore limb limb joint of forelimb limb joint of superior member limb joint of upper extremity superior member joint of limb superior member limb joint upper extremity joint of limb upper extremity limb joint wing joint uberon UBERON:0003839 forelimb joint A limb joint that is part of a forelimb [Automatically generated definition]. OBOL:automatic anteriormost limb joint of limb OBOL:automatic anteriormost limb limb joint OBOL:automatic fore limb joint of limb OBOL:automatic fore limb limb joint OBOL:automatic forelimb joint of limb OBOL:automatic forelimb limb joint OBOL:automatic joint of free upper limb joint of limb of anteriormost limb OBOL:automatic joint of limb of fore limb OBOL:automatic joint of limb of forelimb OBOL:automatic joint of limb of superior member OBOL:automatic joint of limb of upper extremity OBOL:automatic limb joint of anteriormost limb OBOL:automatic limb joint of fore limb OBOL:automatic limb joint of forelimb OBOL:automatic limb joint of superior member OBOL:automatic limb joint of upper extremity OBOL:automatic superior member joint of limb OBOL:automatic superior member limb joint OBOL:automatic upper extremity joint of limb OBOL:automatic upper extremity limb joint OBOL:automatic wing joint NCBITaxon:8782 OBOL:automatic A limb joint that is part of a hindlimb [Automatically generated definition]. EMAPA:32635 MA:0000662 hind limb joint of limb hind limb limb joint hindlimb joint of limb hindlimb limb joint inferior member joint of limb inferior member limb joint joint of free lower limb joint of limb of hind limb joint of limb of hindlimb joint of limb of inferior member joint of limb of lower extremity joint of lower limb limb joint of hind limb limb joint of hindlimb limb joint of inferior member limb joint of lower extremity lower extremity joint of limb lower extremity limb joint uberon UBERON:0003840 hindlimb joint A limb joint that is part of a hindlimb [Automatically generated definition]. OBOL:automatic hind limb joint of limb OBOL:automatic hind limb limb joint OBOL:automatic hindlimb joint of limb OBOL:automatic hindlimb limb joint OBOL:automatic inferior member joint of limb OBOL:automatic inferior member limb joint OBOL:automatic joint of free lower limb joint of limb of hind limb OBOL:automatic joint of limb of hindlimb OBOL:automatic joint of limb of inferior member OBOL:automatic joint of limb of lower extremity OBOL:automatic joint of lower limb limb joint of hind limb OBOL:automatic limb joint of hindlimb OBOL:automatic limb joint of inferior member OBOL:automatic limb joint of lower extremity OBOL:automatic lower extremity joint of limb OBOL:automatic lower extremity limb joint OBOL:automatic A limb joint that is part of an autopod [Automatically generated definition]. EMAPA:35160 MA:0002715 autopod joint of limb autopod limb joint distal free limb segment joint of limb distal free limb segment limb joint joint of limb of autopod joint of limb of distal free limb segment limb joint of autopod limb joint of distal free limb segment uberon paw joint UBERON:0003841 autopod joint A limb joint that is part of an autopod [Automatically generated definition]. OBOL:automatic autopod joint of limb OBOL:automatic autopod limb joint OBOL:automatic distal free limb segment joint of limb OBOL:automatic distal free limb segment limb joint OBOL:automatic joint of limb of autopod OBOL:automatic joint of limb of distal free limb segment OBOL:automatic limb joint of autopod OBOL:automatic limb joint of distal free limb segment OBOL:automatic paw joint MA:0002715 An anatomical space that surrounded_by a neural tube. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] UBERON:0005713 AAO:0011073 EHDAA2:0001269 EHDAA:2889 EHDAA:914 EMAPA:16167 VHOG:0001119 XAO:0000252 cavity of neural tube lumen of neural tube neural tube neural lumen prosencoel uberon central lumen neural lumen neurocoel UBERON:0003842 neural tube lumen An anatomical space that surrounded_by a neural tube. OBOL:automatic (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001119 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 cavity of neural tube lumen of neural tube neural tube neural lumen EHDAA2:0001269 neural lumen EHDAA:2889 neurocoel VHOG:0001119 Epithelium that is part of a developing tooth or dental organ. see comments for dental organ. todo - full developmental relationships In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4) AAO:0011027 BTO:0001723 EMAPA:32903 MA:0003151 NCIT:C54296 TAO:0005134 UMLS:C1709309 VHOG:0001443 XAO:0003203 ZFA:0005134 dental epithelia dental epithelium odontogenic epithelium tooth epithelium uberon reduced enamel epithelium UBERON:0003843 dental epithelium epithelium JB Epithelium that is part of a developing tooth or dental organ. ZFA:0005134 In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4) UMLS:C1709309 ncithesaurus:Odontogenic_Epithelial_Remnants dental epithelia ZFA:0005134 dental epithelium ZFA:0005134 reduced enamel epithelium BTO:0001723 An epithelium that is part of a thymus, forming a supporting framework[MP,modified]. BTO:0001836 CALOHA:TS-1040 EHDAA2:0002019 EMAPA:35864 MA:0000768 NCIT:C45713 UMLS:C1711423 VHOG:0001426 ZFA:0005779 epithelial tissue of thymus epithelial tissue of thymus gland epithelium of thymus epithelium of thymus gland thymic epithelial tissue thymic epithelium thymus epithelial tissue thymus gland epithelial tissue thymus gland epithelium uberon UBERON:0003846 thymus epithelium An epithelium that is part of a thymus, forming a supporting framework[MP,modified]. MP:0009544 UMLS:C1711423 ncithesaurus:Thymic_Epithelial_Tissue epithelial tissue of thymus OBOL:automatic epithelial tissue of thymus gland OBOL:automatic epithelium of thymus OBOL:automatic epithelium of thymus gland OBOL:automatic thymic epithelium BTO:0001836 thymus epithelial tissue OBOL:automatic thymus gland epithelial tissue OBOL:automatic thymus gland epithelium OBOL:automatic A artery that supplies a thyroid gland. Part of the external carotid which supplies blood to the thyroid gland.[AAO] relationship loss: part_of external carotid (AAO:0010218)[AAO] AAO:0010490 EHDAA2:0002029 EHDAA:7372 EMAPA:18622 MA:0002066 NCIT:C53020 UMLS:C1711424 VHOG:0001366 uberon UBERON:0003847 thyroid artery A artery that supplies a thyroid gland. OBOL:automatic Part of the external carotid which supplies blood to the thyroid gland.[AAO] 2012-06-20 AAO:0010490 AAO AAO:BJB relationship loss: part_of external carotid (AAO:0010218)[AAO] 2012-06-20 AAO:0010490 AAO UMLS:C1711424 ncithesaurus:Thyroid_Artery In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. EHDAA2:0000719 EHDAA:8703 OpenCyc:Mx4rvlWYh5wpEbGdrcN5Y29ycA VHOG:0001340 gonad vein gonada vein vein of gonad vein of gonada uberon UBERON:0003848 gonadal vein http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. gonad vein OBOL:automatic gonada vein OBOL:automatic vein of gonad OBOL:automatic vein of gonada OBOL:automatic A neural crest that has_potential_to_developmentally_contribute_to a midbrain. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003591 EHDAA2:0001101 EHDAA:360 TAO:0000935 VHOG:0000796 ZFA:0000935 mesencephalic neural crest neural crest midbrain uberon UBERON:0003849 mesencephalic neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a midbrain. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000796 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 mesencephalic neural crest ZFA:0000935 neural crest midbrain ZFA:0000935 A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. Cranial neural crest that is part of the telencephalon.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003574 RETIRED_EHDAA2:0001991 TAO:0000812 VHOG:0000799 ZFA:0000812 neural crest telencephalon uberon UBERON:0003850 telencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. OBOL:automatic Cranial neural crest that is part of the telencephalon.[TAO] 2012-08-14 TAO:0000812 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000799 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 neural crest telencephalon ZFA:0000812 A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003573 EHDAA2:0000603 EMAPA:16518 TAO:0000811 VHOG:0000798 ZFA:0000811 diencephalic neural crest future diencephalon neural crest neural crest diencephalon neural crest of future diencephalon uberon UBERON:0003851 diencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000798 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 diencephalic neural crest ZFA:0000811 future diencephalon neural crest EHDAA2:0000603 neural crest diencephalon ZFA:0000811 neural crest of future diencephalon EMAPA:16518 A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. Cranial neural crest that is part of the hindbrain.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0001628 EHDAA:362 EMAPA:35747 TAO:0007063 VHOG:0001210 ZFA:0007063 neural crest hindbrain rhombencephalic neural crest uberon rhombomere neural crest UBERON:0003852 rhombencephalon neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. OBOL:automatic Cranial neural crest that is part of the hindbrain.[TAO] 2012-08-14 TAO:0007063 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001210 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 neural crest hindbrain ZFA:0007063 rhombencephalic neural crest ZFA:0007063 rhombomere neural crest EMAPA:35747 A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] EHDAA:696 EMAPA:16163 EMAPA:16881 VHOG:0001006 neural crest spinal cord uberon spinal neural crest UBERON:0003853 spinal cord neural crest A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] 2012-09-17 VHOG:0001006 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 neural crest spinal cord VHOG:0001006 spinal neural crest VHOG:0001006 A neural plate that develops_from a future spinal cord. Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] FMA:312957 TAO:0007021 VHOG:0000439 ZFA:0007021 neural plate of spinal cord uberon UBERON:0003854 spinal cord neural plate ZFA A neural plate that develops_from a future spinal cord. OBOL:automatic Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000439 VHOG (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] 2012-09-17 VHOG:0000439 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 neural plate of spinal cord OBOL:automatic Mesenchyme that is part of a developing gonad [Automatically generated definition]. EHDAA:5012 EMAPA:16858 EMAPA:17385 VHOG:0001090 gonada mesenchyme mesenchyme of gonad mesenchyme of gonada uberon UBERON:0003855 gonad mesenchyme Mesenchyme that is part of a developing gonad [Automatically generated definition]. OBOL:automatic gonada mesenchyme OBOL:automatic mesenchyme of gonad OBOL:automatic mesenchyme of gonada OBOL:automatic Mesenchyme enclosed by a dental organ that gives rise to an odontogenic papilla. we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme Mesenchyme enclosed by dental organ.[MP] Mesenchyme enclosed by dental organ.[TAO] EMAPA:32891 MA:0003152 TAO:0005139 VHOG_RETIRED:0001444 ZFA:0005139 dental mesenchyme dental organ mesenchyme enamel organ mesenchyme tooth enamel organ mesenchyme tooth mesenchyme uberon UBERON:0003856 uncondensed odontogenic mesenchyme Mesenchyme enclosed by a dental organ that gives rise to an odontogenic papilla. Mesenchyme enclosed by dental organ.[MP] MP J:153554 Mesenchyme enclosed by dental organ.[TAO] 2012-08-14 TAO:0005139 TAO ZFIN:curator dental mesenchyme ZFA:0005139 dental organ mesenchyme OBOL:automatic enamel organ mesenchyme OBOL:automatic tooth enamel organ mesenchyme OBOL:automatic tooth mesenchyme OBOL:automatic Mesenchyme that is part of a developing forelimb [Automatically generated definition]. EMAPA:32628 VHOG:0001109 anteriormost limb mesenchyme fore limb mesenchyme mesenchyme of anteriormost limb mesenchyme of fore limb mesenchyme of forelimb mesenchyme of superior member mesenchyme of upper extremity superior member mesenchyme upper extremity mesenchyme wing mesenchyme uberon UBERON:0003859 forelimb mesenchyme Mesenchyme that is part of a developing forelimb [Automatically generated definition]. OBOL:automatic anteriormost limb mesenchyme OBOL:automatic fore limb mesenchyme OBOL:automatic mesenchyme of anteriormost limb OBOL:automatic mesenchyme of fore limb OBOL:automatic mesenchyme of forelimb OBOL:automatic mesenchyme of superior member OBOL:automatic mesenchyme of upper extremity OBOL:automatic superior member mesenchyme OBOL:automatic upper extremity mesenchyme OBOL:automatic wing mesenchyme Geisha:syn NCBITaxon:8782 wing mesenchyme NCBITaxon:8782 OBOL:automatic Mesenchyme that is part of a developing hindlimb [Automatically generated definition]. EMAPA:32637 VHOG:0001074 hind limb mesenchyme inferior member mesenchyme lower extremity mesenchyme mesenchyme of hind limb mesenchyme of hindlimb mesenchyme of inferior member mesenchyme of lower extremity uberon UBERON:0003860 hindlimb mesenchyme Mesenchyme that is part of a developing hindlimb [Automatically generated definition]. OBOL:automatic hind limb mesenchyme OBOL:automatic inferior member mesenchyme OBOL:automatic lower extremity mesenchyme OBOL:automatic mesenchyme of hind limb OBOL:automatic mesenchyme of hindlimb OBOL:automatic mesenchyme of inferior member OBOL:automatic mesenchyme of lower extremity OBOL:automatic A phalanx that is part of a foot digit 5 [Automatically generated definition]. EMAPA:19132 FMA:32902 MA:0001385 NCIT:C52782 UMLS:C1708088 digit long bone of foot digit 5 foot digit 5 digit long bone foot digit 5 long bone of digit foot digit 5 phalanx hind limb digit 5 phalanx little toe phalanx long bone of digit of foot digit 5 pedal digit V phalanx phalanx of fifth digit of foot phalanx of fifth toe phalanx of foot digit 5 phalanx of little toe foot digit 5 phalanx uberon UBERON:0003863 pedal digit 5 phalanx A phalanx that is part of a foot digit 5 [Automatically generated definition]. OBOL:automatic UMLS:C1708088 ncithesaurus:Foot_Digit_5_Phalanx digit long bone of foot digit 5 OBOL:automatic foot digit 5 digit long bone OBOL:automatic foot digit 5 long bone of digit OBOL:automatic foot digit 5 phalanx MA:0001385 hind limb digit 5 phalanx OBOL:accepted little toe phalanx FMA:32902 long bone of digit of foot digit 5 OBOL:automatic pedal digit V phalanx phalanx of fifth digit of foot FMA:32902 phalanx of fifth toe FMA:32902 phalanx of foot digit 5 OBOL:automatic phalanx of little toe FMA:32902 foot digit 5 phalanx NCBITaxon:9606 OBOL:accepted A middle phalanx that is part of a finger [Automatically generated definition]. EMAPA:37306 FMA:75817 MA:0001394 NCIT:C12863 UMLS:C0223828 hand middle phalanx middle manual phalanx middle phalanx of finger middle phalanx of hand middle phalanx of manual digit phalanx media manus uberon UBERON:0003864 middle phalanx of manus A middle phalanx that is part of a finger [Automatically generated definition]. OBOL:automatic EMAPA:37306 MA:th UMLS:C0223828 ncithesaurus:Middle_Phalanx_of_the_Hand hand middle phalanx MA:0001394 middle phalanx of finger FMA:75817 middle phalanx of hand MA:0001394 phalanx media manus FMA:75817 FMA:TA A distal phalanx that is part of a finger [Automatically generated definition]. EMAPA:35393 FMA:75818 MA:0001388 NCIT:C52784 UMLS:C1269782 distal manual phalanx distal phalanx of finger distal phalanx of hand distal phalanx of manual digit hand distal phalanx phalanx distalis manus terminal phalanx of hand ungual phalanx of hand uberon UBERON:0003865 This is typically proximally connected to the middle phalanx of manus, except in some cases such as the manual digit 1 (thumb) of many mammals such as humans, where it connects to the proximal phalanx. It always connects to some phalanx, by definition distal phalanx of manus A distal phalanx that is part of a finger [Automatically generated definition]. OBOL:automatic UMLS:C1269782 ncithesaurus:Distal_Phalanx_of_Hand distal phalanx of finger FMA:75818 hand distal phalanx MA:0001388 phalanx distalis manus FMA:75818 FMA:TA terminal phalanx of hand ungual phalanx of hand A middle phalanx that is part of a toe [Automatically generated definition]. EMAPA:37311 FMA:75829 MA:0001386 foot middle phalanx middle pedal phalanx middle phalanx of foot middle phalanx of toe phalanx media pedis uberon UBERON:0003866 middle phalanx of pes A middle phalanx that is part of a toe [Automatically generated definition]. OBOL:automatic EMAPA:37311 MA:th foot middle phalanx MA:0001386 middle phalanx of toe FMA:75829 phalanx media pedis FMA:75829 FMA:TA A distal phalanx that is part of a pedal digit [Automatically generated definition]. EMAPA:37310 FMA:75830 MA:0001380 NCIT:C52783 UMLS:C0224026 distal pedal phalanx distal phalanx of foot distal phalanx of toe foot distal phalanx phalanx distalis pedis terminal phalanx of foot terminal phalanx of hindlimb ungual phalanx of foot ungual phalanx of hindlimb uberon UBERON:0003867 This is typically proximally connected to the middle phalanx of pes, except in some cases such as the pedal digit 1 (big toe) in many mammals such as humans, where it connects to the proximal phalanx. It always connects to some phalanx, by definition distal phalanx of pes A distal phalanx that is part of a pedal digit [Automatically generated definition]. OBOL:automatic EMAPA:37310 MA:th UMLS:C0224026 ncithesaurus:Distal_Phalanx_of_Foot distal phalanx of toe FMA:75830 foot distal phalanx MA:0001380 phalanx distalis pedis FMA:75830 FMA:TA terminal phalanx of foot terminal phalanx of hindlimb ungual phalanx of foot ungual phalanx of hindlimb A proximal phalanx that is part of a pedal digit [Automatically generated definition]. EMAPA:37312 FMA:75828 MA:0001387 NCIT:C52785 UMLS:C0224020 foot proximal phalanx phalanx proximalis pedis proximal pedal phalanx proximal phalanx of foot proximal phalanx of foot digit proximal phalanx of hind digit proximal phalanx of pes proximal phalanx of toe uberon UBERON:0003868 proximal phalanx of pes A proximal phalanx that is part of a pedal digit [Automatically generated definition]. OBOL:automatic EMAPA:37312 MA:th UMLS:C0224020 ncithesaurus:Proximal_Phalanx_of_Foot foot proximal phalanx MA:0001387 phalanx proximalis pedis FMA:75828 FMA:TA proximal phalanx of toe FMA:75828 A presumptive structure that has the potential to develop into a ganglion. uberon UBERON:0003869 presumptive ganglion A presumptive structure that has the potential to develop into a ganglion. OBOL:automatic A mesentery that is part of a uterus [Automatically generated definition]. EMAPA:35562 FMA:19816 MA:0002931 uberon mesentery of uterus UBERON:0003885 mesometrium A mesentery that is part of a uterus [Automatically generated definition]. OBOL:automatic mesentery of uterus FMA:19816 MA:0002931 An anatomical cavity that has the potential to develop into a coelemic cavity lumen. uberon body cavity precursor UBERON:0003886 future coelemic cavity lumen An anatomical cavity that has the potential to develop into a coelemic cavity lumen. OBOL:automatic The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 UMLS:C1512940 VHOG:0000316 somatic coelom uberon UBERON:0003887 intraembryonic coelom Wikipedia The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom MGI:anna MP:0012187 (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] 2012-09-17 VHOG:0000316 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 UMLS:C1512940 ncithesaurus:Intraembryonic_Coelom somatic coelom Initial section of the oviduct through which the ova pass from the ovary to the uterus Homologous to appendix testis salpinges salpinx CALOHA:TS-0732 EHDAA2:0000504 EMAPA:18984 EMAPA:35660 EV:0100112 FMA:18245 GAID:365 MA:0000385 MESH:D005187 NCIT:C12403 OpenCyc:Mx4rvViVeZwpEbGdrcN5Y29ycA UMLS:C0015560 galen:FallopianTube mammalian oviduct uterine tube (sensu Mammalia) uberon fallopian tubes female paramesonephric duct paramesonephric duct of female tuba uterina UBERON:0003889 fallopian tube http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg FMA-abduced-lr Initial section of the oviduct through which the ova pass from the ovary to the uterus MGI:smb MP:0003574 Homologous to appendix testis salpinges UMLS:C0015560 ncithesaurus:Fallopian_Tube mammalian oviduct female paramesonephric duct EHDAA2:0000504 paramesonephric duct of female EMAPA:35660 tuba uterina paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]. Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG] Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO] In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG] Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct UBERON:0005318 AAO:0010141 EHDAA2:0004048 EMAPA:27665 GAID:1309 MESH:A16.254.570 NCIT:C13260 RETIRED_EHDAA2:0001399 UMLS:C0026732 VHOG:0001199 XAO:0000330 Muellerian duct Müllerian duct ductus paramesonephricus paramesonephric duct early paramesonephric duct uberon UBERON:0003890 Mullerian duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png Wikipedia paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]. GO:0061205 Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG] 2012-09-17 VHOG:0001199 VHOG Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO] 2012-06-20 AAO:0010141 AAO AAO:RED In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG] 2012-09-17 VHOG:0001199 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559 UMLS:C0026732 ncithesaurus:Mullerian_Duct paramesonephric duct EMAPA:27665 early paramesonephric duct EHDAA2:0004048 Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. stromal FMA:81494 NCIT:C67387 UMLS:C0927195 uberon stromal connective tissue UBERON:0003891 stroma Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. UMLS:C0927195 ncithesaurus:Stroma_Connective_Tissue A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]. capsular EHDAA:4739 EHDAA:9061 FMA:85272 galen:Capsule uberon UBERON:0003893 see also: protective structure surrounding some species of bacteria and fungi. Note that FMA has classes such as Articular capsule that are not subtypes of Capsule (which is undefined in FMA). GO has 'capsule' which is a fungal structure, and 'external encapsulating structure' which is restricted to cells capsule A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]. A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum. consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ AAO:0011058 BTO:0003391 EFO:0002577 EFO:0003428 EHDAA2:0000744 EHDAA:973 EMAPA:16847 NCIT:C34277 TAO:0000124 UMLS:C0734013 UMLS:C1514451 XAO:0003266 ZFA:0000124 embryological hepatic plate primordium of the liver uberon hepatic plate liver bud liver endoderm UBERON:0003894 liver primordium EHDAA2 XAO EHDAA2 ventral foregut endoderm Zaret 1996 A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum. ISBN:3211492755 UMLS:C0734013 ncithesaurus:Hepatic_Cord UMLS:C1514451 ncithesaurus:Primordium_of_the_Liver embryological hepatic plate primordium of the liver ncithesaurus:Primordium_of_the_Liver hepatic plate EHDAA2:0000744 liver bud XAO:0003266 ZFA:0000124 liver endoderm EFO:0002577 One of the skeletal muscles of the head and neck, spine, and ribs. EHDAA:5982 EMAPA:18167 MA:0003153 RETIRED_EHDAA2:0000160 TAO:0001954 uberon UBERON:0003897 axial muscle One of the skeletal muscles of the head and neck, spine, and ribs. HP:0003327 A portion of skeletal muscle tissue in the trunk. skeletal muscle of torso skeletal muscle tissue of torso skeletal muscle tissue of trunk torso skeletal muscle torso skeletal muscle tissue trunk skeletal muscle trunk skeletal muscle tissue uberon UBERON:0003898 skeletal muscle tissue of trunk A portion of skeletal muscle tissue in the trunk. skeletal muscle of torso OBOL:automatic skeletal muscle tissue of torso OBOL:automatic skeletal muscle tissue of trunk OBOL:automatic torso skeletal muscle OBOL:automatic torso skeletal muscle tissue OBOL:automatic trunk skeletal muscle OBOL:automatic trunk skeletal muscle tissue OBOL:automatic The part of the retina that contains neurons and photoreceptor cells[GO]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011095 BTO:0000929 CALOHA:TS-0685 EHDAA2:0001253 EHDAA:4763 EMAPA:17171 EMAPA:18590 FMA:58628 MA:0000277 NCIT:C33166 TAO:0000046 UMLS:C1518263 VHOG:0000535 XAO:0003216 ZFA:0000046 neural layer of retina neural retina neuroretina stratum nervosum (retina) stratum nervosum retinae uberon neural retinal epithelium UBERON:0003902 retinal neural layer Bgee:AN The part of the retina that contains neurons and photoreceptor cells[GO]. GO:0003407 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000535 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C1518263 ncithesaurus:Neural_Retina neural layer of retina FMA:58628 neural retina XAO:0003216 ZFA:0000046 neuroretina ZFA:0000046 stratum nervosum (retina) FMA:58628 stratum nervosum retinae FMA:58628 FMA:TA neural retinal epithelium MA:000027 small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]. Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO] sinusoidal some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). FMA:63131 TAO:0005261 ZFA:0005261 sinusoidal blood vessel sinusoidal blood vessel endothelium uberon endothelium of irregular blood filled space sinusoidal capillary sinusoidal endothelium UBERON:0003909 sinusoid Wikipedia ZFA small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]. Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO] 2012-08-14 TAO:0005261 TAO ZFIN:curator some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). FMA sinusoidal blood vessel endothelium ZFA:0005261 sinusoidal capillary The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue. The CP epithelial layer is continuous with the ependymal cell layer that lines the ventricles, but unlike the ependyma, the epithelial layer has tight gap junctions between the cells on the side facing the ventricle (apical surface). These gap junctions prevent the majority of substances from crossing the cell layer into the CSF; thus the CP acts as a blood-CSF barrier EMAPA:36608 FMA:242811 MA:0000824 NCIT:C42079 UMLS:C1516506 choroid plexus epithelial tissue epithelial tissue of chorioid plexus of cerebral hemisphere epithelial tissue of choroid plexus epithelium of choroid plexus uberon UBERON:0003911 choroid plexus epithelium The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue. UBERON:cjm UMLS:C1516506 ncithesaurus:Choroid_Plexus_Epithelium choroid plexus epithelial tissue OBOL:automatic epithelial tissue of chorioid plexus of cerebral hemisphere OBOL:automatic epithelial tissue of choroid plexus OBOL:automatic epithelium of choroid plexus FMA:242811 hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. HAO:0001019 tooth-like organ uberon UBERON:0003913 see dermal denticle tooth-like structure hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food. tooth-like organ Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 epithelial tube Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GO:0060562 Any endothelium that has the quality of being cylindrical [Automatically generated definition]. uberon UBERON:0003915 endothelial tube Any endothelium that has the quality of being cylindrical [Automatically generated definition]. OBOL:automatic Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. check this mesenchyme of kidney uberon UBERON:0003918 kidney mesenchyme Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. GO:0072074 A blood vessel that carries blood from the capillaries toward the heart EMAPA:35932 FMA:86188 MA:0000066 segment of venous tree organ venous tree organ segment uberon UBERON:0003920 Compare to: vein venous blood vessel A blood vessel that carries blood from the capillaries toward the heart segment of venous tree organ FMA:86188 venous tree organ segment FMA:86188 embryonic structure that develops into pancreatic bud. in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds revisit after standardizing terms 'primordium', 'anlagen', 'bud' EFO:0002579 EFO:0003434 EHDAA2:0001382 EHDAA:2163 EMAPA:17066 FMA:79792 TAO:0000254 XAO:0001101 ZFA:0000254 pancreatic primordium uberon pancreatic anlage pancreatic endoderm primordial pancreas UBERON:0003921 pancreas primordium http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png Wikipedia embryonic structure that develops into pancreatic bud. in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds EHDAA2 pancreatic anlage ZFA:0000254 pancreatic endoderm EFO:0002579 primordial pancreas FMA:79792 The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. EFO:0003470 EMAPA:35645 NCIT:C34242 TAO:0001390 UMLS:C1283285 ZFA:0001390 pancreatic bud pancreatic buds uberon pancreas epithelium pancreatic anlage UBERON:0003922 pancreatic epithelial bud http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png EHDAA2 EHDAA2 zebrafish EHDAA2-inferred The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. UMLS:C1283285 ncithesaurus:Pancreatic_Bud pancreatic bud ZFA:0001390 pancreatic buds TAO:0001390 pancreas epithelium EMAPA:35645 pancreatic bud that gives rise to the accessory pancreatic duct. The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] AAO:0011031 EFO:0003465 EHDAA2:0001385 EMAPA:17067 TAO:0001370 VHOG:0001428 XAO:0000467 ZFA:0001370 pancreas dorsal primordium duct bud pancreas primordium dorsal bud primary pancreatic bud uberon dorsal pancreas anlage dorsal pancreatic anlage posterior pancreatic anlage posterior pancreatic bud UBERON:0003923 dorsal pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png EHDAA2 XAO pancreatic bud that gives rise to the accessory pancreatic duct. The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] 2012-06-20 AAO:0011031 AAO XAO:curator In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001428 VHOG DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000) pancreas dorsal primordium duct bud EHDAA2:0001385 primary pancreatic bud XAO:0000467 pancreatic bud that gives rise to the major pancreatic duct. In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP] the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship. AAO:0011111 EFO:0003464 EHDAA2:0001389 EMAPA:17256 TAO:0001369 VHOG:0001429 XAO:0001103 ZFA:0001369 pancreas primordium ventral bud pancreas ventral primordium duct bud uberon anterior pancreatic anlage anterior pancreatic bud ventral pancreas anlage ventral pancreatic anlage UBERON:0003924 ventral pancreatic bud http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png EHDAA2 WP pancreatic bud that gives rise to the major pancreatic duct. In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001429 VHOG DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000) pancreas ventral primordium duct bud EHDAA2:0001389 A duct that is part of a digestive system [Automatically generated definition]. TAO:0005162 ZFA:0005162 duct of digestive system duct of gastrointestinal system gastrointestinal system duct uberon UBERON:0003928 digestive system duct A duct that is part of a digestive system [Automatically generated definition]. OBOL:automatic duct of digestive system OBOL:automatic duct of gastrointestinal system OBOL:automatic gastrointestinal system duct OBOL:automatic An epithelium that lines the lumen of the digestive tract. Epithelium lining the lumen of the gut.[TAO] BTO:0000956 EHDAA2:0004567 EMAPA:32928 MA:0003201 NCIT:C12963 TAO:0005123 UMLS:C0836205 XAO:0003200 ZFA:0005123 digestive tract epithelial tissue epithelial tissue of digestive tract epithelial tissue of gut epithelium of digestive tract epithelium of gut gastrodermis gut epithelial tissue gut epithelium uberon alimentary tract epithelium UBERON:0003929 digestive tract epithelium An epithelium that lines the lumen of the digestive tract. Epithelium lining the lumen of the gut.[TAO] 2012-08-14 TAO:0005123 TAO ZFIN:curator UMLS:C0836205 ncithesaurus:Gut_Epithelium digestive tract epithelial tissue OBOL:automatic epithelial tissue of digestive tract OBOL:automatic epithelial tissue of gut OBOL:automatic epithelium of digestive tract OBOL:automatic epithelium of gut OBOL:automatic gastrodermis BGEE:ANN NCBITaxon:6073 gut epithelial tissue OBOL:automatic gut epithelium EHDAA2:0004567 MA:0003201 ZFA:0005123 alimentary tract epithelium OBOL:automatic A cartilage element of chondrocranium. Example: neurocranial trabecula. EFO:0003690 TAO:0001461 ZFA:0001461 cartilage of chondrocranium cartilaginous element of chondrocranium chondrocranium cartilage neurocranium cartilage uberon UBERON:0003932 cartilage element of chondrocranium A cartilage element of chondrocranium. Example: neurocranial trabecula. cartilage of chondrocranium OBOL:accepted cartilaginous element of chondrocranium OBOL:accepted chondrocranium cartilage ZFA:0001461 neurocranium cartilage ZFA:0001461 A cartilage element that is part of the cranial skeleton. Cartilage which is part of the cranium.[TAO] TAO:0001458 ZFA:0001458 cartilage of cranium cranium cartilage uberon cranial cartilages UBERON:0003933 cranial cartilage A cartilage element that is part of the cranial skeleton. ZFA:0001458 Cartilage which is part of the cranium.[TAO] 2012-08-14 TAO:0001458 TAO ZFIN:curator cartilage of cranium OBOL:automatic cranium cartilage OBOL:automatic cranial cartilages ZFA:0001458 Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MA:0001751 genitalia gland gland of genitalia gland of reproductive system reproductive gland reproductive system gland sex gland uberon UBERON:0003937 reproductive gland Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MP:0000653 genitalia gland OBOL:automatic gland of genitalia MP:0000653 gland of reproductive system OBOL:automatic reproductive gland MA:0001751 reproductive system gland OBOL:automatic sex gland MP:0000653 The sensory system for the sense of touch and pain. The neural tissue involved in the transmission of sensory signals MP defines this in a may more appropriate to somatosensory cortex UBERON:0014511 EMAPA:37954 NLXANAT:090818 somatic sensory system somatosensory system system for detection of somatic senses uberon UBERON:0003942 somatic sensory system The sensory system for the sense of touch and pain. NLXANAT:090818 The neural tissue involved in the transmission of sensory signals MP:0000959 MP defines this in a may more appropriate to somatosensory cortex MP EMAPA:37954 MA:th somatosensory system NLXANAT:090818 The brain ventricles or their associated choroid plexuses TODO - check relationship between CP and BV. If this is part of then this class should be obsoleted TODO merge into BV uberon UBERON:0003947 brain ventricle/choroid plexus The brain ventricles or their associated choroid plexuses MP:0002200 The posterior concave interior of the eye, consisting of the retina, the choroid, the posterior segment of the sclera, the optic disk, and blood vessels, visible by an ophthalmoscope TODO - check relationships EMAPA:37916 GAID:908 MESH:D005654 NCIT:C13378 RETIRED_EHDAA2:0000583 UMLS:C0740422 galen:FundusOculi eye fundus fundus fundus oculi fundus of eye uberon UBERON:0003951 ocular fundus The posterior concave interior of the eye, consisting of the retina, the choroid, the posterior segment of the sclera, the optic disk, and blood vessels, visible by an ophthalmoscope MP:0002864 EMAPA:37916 MA:th UMLS:C0740422 ncithesaurus:Fundus fundus HP:0001098 The anterior segment of the lamellated connective tissue layer of the cornea anterior stroma EMAPA:37414 cornea anterior stroma uberon UBERON:0003952 anterior stroma of cornea lexical The anterior segment of the lamellated connective tissue layer of the cornea MP:0003093 anterior stroma MP:0003093 EMAPA:37414 MA:th cornea anterior stroma MP:0003093 The posterior segment of the lamellated connective tissue layer of the cornea posterior stroma EMAPA:37415 cornea posterior stroma uberon UBERON:0003953 posterior stroma of cornea lexical The posterior segment of the lamellated connective tissue layer of the cornea MP:0003094 posterior stroma MP:0003094 EMAPA:37415 MA:th cornea posterior stroma MP:0003094 The structures associated with drainage of the aqueous humor from the eye, that include the trabecular meshwork, Schlemm's canal, the uveoscleral network, and the aqueous veins EMAPA:37427 uberon UBERON:0003956 aqueous drainage system The structures associated with drainage of the aqueous humor from the eye, that include the trabecular meshwork, Schlemm's canal, the uveoscleral network, and the aqueous veins MP:0005198 EMAPA:37427 MA:th An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP]. add more specific classification e.g. anastomosing network - consider FMA:3726 EMAPA:18332 FMA:19834 GAID:399 MA:0003013 MESH:D012152 NCIT:C33467 UMLS:C0035278 Haller's rete uberon UBERON:0003959 rete testis http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg Wikipedia An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP]. MP:0006416 UMLS:C0035278 ncithesaurus:Rete_Testis Haller's rete FMA:19834 The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity EMAPA:37841 cutaneous elastic fiber dermal elastic fiber uberon UBERON:0003967 cutaneous elastic tissue The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity MP:0008418 EMAPA:37841 MA:th cutaneous elastic fiber MP:0008418 dermal elastic fiber MP:0008418 The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. BTO:0003099 FMA:45654 female internal genitalia internal female genital organ internal genitalia of female reproductive system uberon organa genitalia feminina interna UBERON:0003975 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 internal female genitalia The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. MP:0009209 female internal genitalia FMA:45654 internal female genital organ BTO:0003099 internal genitalia of female reproductive system OBOL:automatic organa genitalia feminina interna BTO:0003099 valvular EHDAA2:0004046 EHDAA:1892 EHDAA:4406 FMA:67611 OpenCyc:Mx4rvqiwE5wpEbGdrcN5Y29ycA galen:Valve anatomical valve uberon UBERON:0003978 valve anatomical valve FMA:67611 One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows BAMS:CBf DHBA:12828 EMAPA:37818 FMA:321547 HBA:9406 cerebellar fissure fissurae cerebelli uberon cerebellar fissures cerebellar fissures set cerebellar sulci cerebellar sulcus set of cerebellar fissures sulcus of cerebellum UBERON:0003980 cerebellum fissure One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows MP:0009267 EMAPA:37818 MA:th fissurae cerebelli FMA:77789 FMA:TA cerebellar fissures BAMS:CBf cerebellar fissures set FMA:77789 cerebellar sulci HBA:9406 set of cerebellar fissures FMA:77789 A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]. Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO] Kardong says absent in adult tetrapods, check AAO we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally AAO:0010250 uberon UBERON:0003983 conus arteriosus http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]. MP:0009464 Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO] 2012-06-20 AAO:0010250 AAO AAO:BJB we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally ISBN:0073040584 The funnel-like expansion of the abdominal extremity of the uterine tube[MP] The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]. infundibulum EMAPA:29897 FMA:18307 infundibulum of oviduct infundibulum of uterine tube infundibulum of fallopian tube uberon infundibulum tubae uterinae UBERON:0003984 uterine tube infundibulum Illu:cervix.jpg FMA The funnel-like expansion of the abdominal extremity of the uterine tube[MP] MP:0009466 The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]. infundibulum infundibulum of oviduct FMA:18307 infundibulum of uterine tube FMA:18307 infundibulum of fallopian tube FMA:18307 infundibulum tubae uterinae The dense region demarcating the thymus medulla from the surrounding cortex that is characterized by numerous blood vessels (predominantly arterioles) with some perivascular connective tissue, mature and immature T lymphocytes, dendritic cells, variable numbers of perivascular B-lymphocytes and plasma cells; site of entry of bone marrow stem cells and exit of mature, functional T cells EMAPA:37974 thymic cortico-medullary boundary thymic corticomedullary boundary thymic corticomedullary junction thymic corticomedullary zone thymus CMZ thymus cortico-medullary boundary thymus corticomedullary junction thymus corticomedullary zone uberon UBERON:0003988 thymus corticomedullary boundary The dense region demarcating the thymus medulla from the surrounding cortex that is characterized by numerous blood vessels (predominantly arterioles) with some perivascular connective tissue, mature and immature T lymphocytes, dendritic cells, variable numbers of perivascular B-lymphocytes and plasma cells; site of entry of bone marrow stem cells and exit of mature, functional T cells MP:0009543 EMAPA:37974 MA:th thymic cortico-medullary boundary MP:0009543 thymic corticomedullary boundary MP:0009543 thymic corticomedullary junction MP:0009543 thymic corticomedullary zone MP:0009543 thymus CMZ MP:0009543 thymus cortico-medullary boundary MP:0009543 thymus corticomedullary junction MP:0009543 thymus corticomedullary zone MP:0009543 The connection between the embryo proper and extraembryonic tissues uberon UBERON:0004015 embryonic-extraembryonic boundary The connection between the embryo proper and extraembryonic tissues MP:0003890 A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. Not to be confused with 'dermatome segment of skin'. AAO:0011028 AEO:0001017 EHDAA2_RETIRED:0003428 EHDAA:1719 EHDAA:1725 EHDAA:1731 EHDAA:1737 EMAPA:32838 FMA:295656 NCIT:C61572 UMLS:C0180383 XAO:0000220 cutis plate dermatomal mesenchyme uberon epimere mesoderm mesenchyma dermatomiale UBERON:0004016 dermatome http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. AEO:0001017 AEO:JB UMLS:C0180383 ncithesaurus:Dermatome cutis plate dermatomal mesenchyme mesenchyma dermatomiale The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047] germinal neuroepithelial layer germinal neuroepithelium original neural tube uberon UBERON:0004022 germinal neuroepithelium NCBIBook:NBK10047 The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells MP:0004261 germinal neuroepithelial layer germinal neuroepithelium NCBIBook:NBK10047 original neural tube NCBIBook:NBK10047 That portion of the chorionic wall in the region of its uterine attachment, which gives rise to chorionic villi; it consists of the mesoderm that lines the chorionic vesicle and, on the maternal side, of the trophoblast that lines the intervillous spaces; in the last half of gestation, the mesodermal connective tissue is largely replaced by fibrinoid material, and the amnionic membrane is adherent to the fetal side of the plate. BTO:0002879 EMAPA:31872 NCIT:C34123 UMLS:C0230972 uberon UBERON:0004027 chorionic plate That portion of the chorionic wall in the region of its uterine attachment, which gives rise to chorionic villi; it consists of the mesoderm that lines the chorionic vesicle and, on the maternal side, of the trophoblast that lines the intervillous spaces; in the last half of gestation, the mesodermal connective tissue is largely replaced by fibrinoid material, and the amnionic membrane is adherent to the fetal side of the plate. MP:0004560 UMLS:C0230972 ncithesaurus:Chorionic_Plate The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects SP DHBA:10522 EMAPA:32703 PBA:294021932 cerebral cortex subplate subplate subplate zone uberon UBERON:0004035 cortical subplate The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate MP:0008440 The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects WP SP BRAINSPAN:BRAINSPAN cerebral cortex subplate EMAPA:32833 subplate zone DHBA:10522 The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone IZ EMAPA:17545 EMAPA:32712 uberon cerebral cortex mantle layer cerebral cortex mantle zone cortical mantle layer UBERON:0004040 cortical intermediate zone The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone MP:0008457 IZ BRAINSPAN:BRAINSPAN cerebral cortex mantle layer EMAPA:17545 The external masculine genital organs, including the penis and scrotum BTO:0003097 EMAPA:30977 FMA:45642 galen:MaleExternalGenitalia external male genital organ male external genitalia uberon organa genitalia masculina externa UBERON:0004053 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 external male genitalia The external masculine genital organs, including the penis and scrotum MP:0009199 external male genital organ BTO:0003097 male external genitalia FMA:45642 organa genitalia masculina externa BTO:0003097 The internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands consider splitting genitalia from genital organ BTO:0003096 FMA:45655 internal male genital organ male internal genitalia uberon organa genitalia masculina interna UBERON:0004054 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 internal male genitalia The internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands MP:0009205 internal male genital organ BTO:0003096 male internal genitalia FMA:45655 organa genitalia masculina interna BTO:0003096 One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP] In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule) BTO:0002840 EMAPA:37440 TAO:0005164 ZFA:0005164 bile ductule biliary ductule ductuli biliferi uberon bile capillary biliary ductule cholangiole terminal cholangiole UBERON:0004058 biliary ductule BTO One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP] BTO:0002840 MP:0009494 In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule) ZFA EMAPA:37440 MA:th bile ductule BTO:0002840 biliary ductule ductuli biliferi bile capillary BTO:0002840 biliary ductule BTO:0002840 cholangiole BTO:0002840 terminal cholangiole The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure The layer of undifferentiated, proliferating cells that line the neural tube lumen ependymal layer EMAPA:17152 EMAPA:35362 EMAPA_RETIRED:16783 MA:0003193 neural tube ependymal layer neural tube ventricular germinal zone neural tube ventricular zone neural tube ependymal zone uberon UBERON:0004060 neural tube ventricular layer NCBIBook:NBK10047 NCBIBook:NBK10047 The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium MP:0009689 The layer of undifferentiated, proliferating cells that line the neural tube lumen MP:0009689 ependymal layer NCBIBook:NBK10047 neural tube ependymal layer NCBIBook:NBK10047 neural tube ventricular germinal zone NCBIBook:NBK10047 neural tube ventricular zone MP:0009689 neural tube ependymal zone MP:0009689 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. EMAPA:17148 EMAPA:35360 neural tube intermediate zone uberon future brain marginal layer UBERON:0004061 neural tube mantle layer NCBIBook:NBK10047 by division NCBIBook:NBK10047 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. MP:0009690 neural tube intermediate zone MP:0009690 future brain marginal layer EMAPA:35360 The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter EMAPA:17151 neural tube marginal zone uberon brain marginal zone UBERON:0004062 neural tube marginal layer forms from axons The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter MP:0009691 neural tube marginal zone MP:0009691 The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. AAO:0010561 EFO:0001904 NCIT:C34111 UMLS:C1511061 basal plate basal plate of neural tube spinal cord basal plate uberon motor part of neural tube ventral part of neural tube UBERON:0004064 neural tube basal plate Shh Swenson The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. MP:0009693 UMLS:C1511061 ncithesaurus:Basal_Plate basal plate of neural tube spinal cord basal plate MP:0009693 The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout. UBERON:0006237 EHDAA2:0000578 EHDAA:4778 EMAPA:16681 FMA:293101 NCIT:C34182 UMLS:C1517321 VHOG:0001319 embryonic frontonasal prominence uberon forebrain prominence frontonasal mass frontonasal process prominentia frontonasalis UBERON:0004066 frontonasal prominence http://upload.wikimedia.org/wikipedia/commons/9/98/Gray44.png The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout. MP:0009901 UMLS:C1517321 ncithesaurus:Frontonasal_Prominence embryonic frontonasal prominence forebrain prominence MP:0009901 frontonasal mass MP:0009901 frontonasal process MP:0009901 prominentia frontonasalis The lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it EHDAA2:0000916 EHDAA:4786 EMAPA:16805 FMA:295864 lateral nasal process latero-nasal process uberon lateral nasal swelling prominentia nasalis lateralis UBERON:0004067 lateral nasal prominence http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png EHDAA2 Wikipedia The lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it MP:0009902 lateral nasal process EHDAA2:0000916 latero-nasal process EMAPA:16805 lateral nasal swelling prominentia nasalis lateralis one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356]. FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies. BIRNLEX:1356 BTO:0001442 EFO:0001914 EMAPA:32674 FMA:78447 HBA:9418 MA:0000818 MESH:D002552 NCIT:C12356 OpenCyc:Mx4rvmTY65wpEbGdrcN5Y29ycA UMLS:C0007799 brain ventricles cerebral ventricle region of ventricular system of brain uberon UBERON:0004086 brain ventricle one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356]. BIRNLEX:1356 FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies. FMA UMLS:C0007799 ncithesaurus:Ventricle_Brain brain ventricles cerebral ventricle HP:0002118 region of ventricular system of brain FMA:78447 Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. AAO:0010215 BTO:0001438 EMAPA:18415 FMA:321896 GAID:547 MA:0000068 MESH:D014684 NCIT:C12817 OpenCyc:Mx4rkJQ4U6gEEdudWQACs5b6Bw UMLS:C0042460 uberon caval vein venae cavae UBERON:0004087 vena cava Heart:numlabels.png http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. UMLS:C0042460 ncithesaurus:Vena_Cava venae cavae The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye in HP covers eyelid, eyebrow. FMA:260119 content of orbital part of eye eye region orbital part of face uberon ocular and peri-ocular region ocular region orbital content orbital part of eye UBERON:0004088 orbital region The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present in HP covers eyelid, eyebrow. HP:0000284 content of orbital part of eye FMA:260119 eye region orbital part of face orbital content FMA:260119 orbital part of eye FMA:72951 The middle of the face including the nose and its associated bony structures[MW]. this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface. midfacial EMAPA:32806 FMA:285406 MA:0001910 uberon lower face midface/lower face snout UBERON:0004089 midface The middle of the face including the nose and its associated bony structures[MW]. HP:0000309 snout MA:0001910 . uberon UBERON:0004092 hypothalamus-pituitary axis . HP:0000864 Joint cavity shared by all the joints of the elbow. The elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis. All three share a joint cavity which is highly sinuated/scalloped/coved. Joint spaces of the elbow summarizes the joint cavity shared by all three adjoining joints of the elbow joint. FMA:38911 synovial cavity of elbow joint uberon UBERON:0004099 joint space of elbow Joint cavity shared by all the joints of the elbow. The elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis. All three share a joint cavity which is highly sinuated/scalloped/coved. Joint spaces of the elbow summarizes the joint cavity shared by all three adjoining joints of the elbow joint. HP:0003943 synovial cavity of elbow joint FMA:38911 The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone. FMA:265239 collecting duct system kidney collecting duct system uberon tubulus renalis colligens UBERON:0004100 renal collecting system http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone. HP:0004742 collecting duct system kidney collecting duct system tubulus renalis colligens 2 2 Any tube, opening or passage that connects two distinct anatomical spaces. FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 foramen foramina uberon opening ostia ostium UBERON:0004111 anatomical conduit Any tube, opening or passage that connects two distinct anatomical spaces. FMA has both conduit and conduit space. In EHDAA2 this is a surface feature FMA foramen EHDAA2:0003080 foramina ostia A muscle of the tympanic cavity that attaches to an auditory ossicle. attenuate low-frequency sounds, reduce masking of high-frequency sounds by low-frequency sounds, frequency-selection filter UBERON:0004112 EMAPA:37776 FMA:49026 MA:0000256 NCIT:C33148 UMLS:C1513769 auditory ossicles muscle muscle of auditory ossicles muscle of tympanic cavity ossicular muscle tympanic cavity muscle uberon muscle of middle ear UBERON:0004113 muscle of auditory ossicle FMA A muscle of the tympanic cavity that attaches to an auditory ossicle. EMAPA:37776 MA:th UMLS:C1513769 ncithesaurus:Muscle_of_the_Tympanum auditory ossicles muscle FMA:49026 muscle of auditory ossicles FMA:49026 ossicular muscle FMA:49026 tympanic cavity muscle MA:0000256 small cavity surrounding the bones of the middle ear. BTO:0002098 EHDAA2:0004119 EMAPA:37778 EV:0100358 FMA:56461 anatomical cavity of middle ear cavitas tympani cavity of middle ear middle ear cavity middle-ear cavity uberon cavitas tympanica tympanum UBERON:0004114 tympanic cavity http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png EHDAA2 EHDAA2 small cavity surrounding the bones of the middle ear. EMAPA:37778 MA:th anatomical cavity of middle ear OBOL:automatic cavitas tympani cavity of middle ear OBOL:automatic middle ear cavity OBOL:automatic middle-ear cavity OBOL:automatic cavitas tympanica BTO:0002098 tympanum BTO:0002098 A blood vessel that is part of a tympanic cavity [Automatically generated definition]. EMAPA:37775 MA:0001219 anatomical cavity of middle ear blood vessel blood vessel of anatomical cavity of middle ear blood vessel of cavity of middle ear blood vessel of middle ear anatomical cavity blood vessel of middle ear cavity cavity of middle ear blood vessel middle ear anatomical cavity blood vessel middle ear blood vessel middle ear cavity blood vessel tympanic cavity blood vessel uberon UBERON:0004115 blood vessel of tympanic cavity A blood vessel that is part of a tympanic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37775 MA:th anatomical cavity of middle ear blood vessel OBOL:automatic blood vessel of anatomical cavity of middle ear OBOL:automatic blood vessel of cavity of middle ear OBOL:automatic blood vessel of middle ear anatomical cavity OBOL:automatic blood vessel of middle ear cavity OBOL:automatic cavity of middle ear blood vessel OBOL:automatic middle ear anatomical cavity blood vessel OBOL:automatic middle ear cavity blood vessel OBOL:automatic A nerve that is part of a tympanic cavity [Automatically generated definition]. EMAPA:37777 MA:0001222 anatomical cavity of middle ear nerve cavity of middle ear nerve middle ear anatomical cavity nerve middle ear cavity nerve nerve of anatomical cavity of middle ear nerve of cavity of middle ear nerve of middle ear anatomical cavity nerve of middle ear cavity tympanic cavity nerve tympanic cavity nerves uberon UBERON:0004116 nerve of tympanic cavity A nerve that is part of a tympanic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37777 MA:th anatomical cavity of middle ear nerve OBOL:automatic cavity of middle ear nerve OBOL:automatic middle ear anatomical cavity nerve OBOL:automatic middle ear cavity nerve OBOL:automatic nerve of anatomical cavity of middle ear OBOL:automatic nerve of cavity of middle ear OBOL:automatic nerve of middle ear anatomical cavity OBOL:automatic nerve of middle ear cavity OBOL:automatic tympanic cavity nerves MA:0001222 An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches. Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] EMAPA also includes a distinct pouch endoderm AAO:0011113 EFO:0003627 EHDAA:1086 EHDAA:1669 EHDAA:579 EHDAA:617 EMAPA:32752 FMA:293063 NCIT:C34252 TAO:0001106 UMLS:C0231067 VHOG:0001203 XAO:0000282 ZFA:0001106 branchial pouch visceral pouch uberon pharyngeal pouches visceral pouches UBERON:0004117 The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389] pharyngeal pouch EHDAA2 ZFA An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches. ZFA:0001106 Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO] 2012-08-14 TAO:0001106 TAO ZFIN:curator A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0001203 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) EMAPA also includes a distinct pouch endoderm EMAPA UMLS:C0231067 ncithesaurus:Pharyngeal_Pouch branchial pouch visceral pouch pharyngeal pouches VHOG:0001203 visceral pouches VHOG:0001203 A vasculature that is part of a iris [Automatically generated definition]. ZFA:0005568 iris blood vessels iris vascular network iris vasculature vascular network of iris uberon UBERON:0004118 vasculature of iris A vasculature that is part of a iris [Automatically generated definition]. OBOL:automatic iris blood vessels ZFA:0005568 iris vascular network OBOL:automatic vascular network of iris OBOL:automatic An anatomical structure that develops (entirely or partially) from the endoderm. Grouping term for query purposes uberon UBERON:0004119 endoderm-derived structure An anatomical structure that develops (entirely or partially) from the endoderm. An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes FBbt:00025998 mesodermal derivative uberon UBERON:0004120 mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. mesodermal derivative FBbt:00025998 An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes FBbt:00025990 ectodermal deriviative uberon UBERON:0004121 ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. ectodermal deriviative FBbt:00025990 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] genitourinary urogenital AAO:0000624 BILA:0000122 BTO:0003091 EFO:0003864 EHDAA:1013 EMAPA:16367 EV:0100094 FMA:280610 GAID:362 MESH:D014566 NCIT:C12810 OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g UMLS:C0042066 VHOG:0000286 XAO:0000140 galen:GenitoUrinarySystem urogenital system uberon GU tract UG tract Urogenitalsystem genito-urinary system genitourinary tract urogenital tract UBERON:0004122 genitourinary system Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. VHOG:0000286 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] 2012-06-20 AAO:0000624 AAO AAO:EJS relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] 2012-06-20 AAO:0000624 AAO Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] 2012-09-17 VHOG:0000286 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633 UMLS:C0042066 ncithesaurus:Genitourinary_System Urogenitalsystem BTO:0003091 genito-urinary system FMA:280610 urogenital tract BTO:0003091 Any of the layers of the myocardium. Example: compact layer, trabecular layer. EMAPA:37475 MA:0000080 layer of myocardium myocardium layer uberon UBERON:0004123 myocardial layer Any of the layers of the myocardium. Example: compact layer, trabecular layer. EMAPA:37475 MA:th The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA]. The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO] EFO:0003706 MA:0002866 TAO:0005059 ZFA:0005059 myocardial trabecular layer trabecular layer uberon heart muscle trabecula heart muscle trabeculae myocardial trabeculae carneae trabecula of heart muscle trabeculae UBERON:0004124 myocardium trabecular layer The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA]. ZFA:0005059 The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO] 2012-08-14 TAO:0005059 TAO ZFIN:curator trabecular layer ZFA:0005059 heart muscle trabeculae myocardial trabeculae carneae trabeculae TAO:0005059 A myocardium trabecular layer that is part of a cardiac ventricle. TODO - check FMA FMA:83511 TAO:0005060 ZFA:0005060 myocardium of region of ventricle trabecular cardiac ventricle muscle ventricular trabecular myocardium uberon UBERON:0004126 trabecular layer of ventricle A myocardium trabecular layer that is part of a cardiac ventricle. OBOL:automatic myocardium of region of ventricle FMA:83511 trabecular cardiac ventricle muscle GO:0003222 ventricular trabecular myocardium GO:0003222 The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] AAO:0011039 EHDAA2:0001320 EMAPA:16540 FMA:293357 NCIT:C34236 TAO:0000050 UMLS:C0231106 VHOG:0000165 XAO:0000228 ZFA:0000050 uberon evagination eye vesicle ocular vesicle optic vesicles UBERON:0004128 Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288] optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png ZFA GO-def ZFA The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. GO:0003404 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] 2012-09-17 VHOG:0000165 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 UMLS:C0231106 ncithesaurus:Optic_Vesicle eye vesicle XAO:0000228 ocular vesicle VHOG:0000165 optic vesicles ZFA:0000050 A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo. BIRNLEX:880 EMAPA:35212 FMA:83141 MA:0000201 NCIT:C49137 UMLS:C1707522 cell layer of cerebellar cortex cytoarchitectural part of the cerebellar cortex gray matter layer of cerebellum layer of cerebellar cortex layer of cerebellum uberon UBERON:0004130 cerebellar layer A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo. ncithesaurus:Cortical_Cell_Layer_of_the_Cerebellum UMLS:C1707522 ncithesaurus:Cortical_Cell_Layer_of_the_Cerebellum cytoarchitectural part of the cerebellar cortex BIRNLEX:880 gray matter layer of cerebellum FMA:83141 . salivary nucleus uberon UBERON:0004133 salivatory nucleus . GO:0021751 salivary nucleus GO:0021751 The first recognizable structure derived from the heart field TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 myocardial plate uberon cardiac crescent cardiogenic crescent heart rudiment UBERON:0004139 cardiogenic plate The first recognizable structure derived from the heart field GO:0003142 (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] 2012-09-17 VHOG:0000975 VHOG PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) myocardial plate EHDAA2:0000215 cardiac crescent EMAPA:16106 cardiogenic crescent GO:0003142 A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field uberon FHF PHF heart field UBERON:0004140 primary heart field GO:0003128 BGEE:ann A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. GO:0003138 GOC:mtg_heart GOC:rl this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] GO first heart field XAO:0004185 primary heart field XAO:0004185 FHF XAO:0004185 PHF XAO:0004185 heart field XAO:0004185 An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 NCIT:C34161 TAO:0000360 XAO:0000337 ZFA:0000360 embryonic heart tube endocardial heart tube endocardial tube uberon UBERON:0004141 heart tube ZFA-modified An epithelial tube that will give rise to the mature heart. GO:0003143 GOC:mtg_heart the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. MP:0012700 embryonic heart tube GO:0003143 endocardial heart tube MP:0012700 endocardial tube XAO:0000337 The outflow tract septum is a partition in the outflow tract uberon UBERON:0004142 outflow tract septum The outflow tract septum is a partition in the outflow tract GO:0003148 The outflow tract is the portion of the heart through which blood flows into the arteries Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616] EHDAA2:0001351 EHDAA:464 EHDAA:798 EMAPA:16346 MA:0000100 VHOG:0000670 XAO:0004139 cardiac outflow tract heart outflow tract uberon arterial (outflow) pole UBERON:0004145 outflow tract The outflow tract is the portion of the heart through which blood flows into the arteries GO:0003151 cardiac outflow tract arterial (outflow) pole Vein of heart that drains the myocardium EHDAA2:0004507 EMAPA:37137 FMA:12846 NCIT:C12878 NCIT:C12882 UMLS:C0226654 UMLS:C0226737 ZFA:0005814 galen:CoronaryVein cardiac vein coronary vein heart vein vein of heart uberon coronary vein UBERON:0004148 cardiac vein FMA Vein of heart that drains the myocardium EMAPA:37137 MA:th UMLS:C0226654 ncithesaurus:Cardiac_Vein UMLS:C0226737 ncithesaurus:Coronary_Vein cardiac vein FMA:12846 coronary vein ZFA:0005814 heart vein OBOL:automatic vein of heart OBOL:automatic coronary vein A cardiac chamber surrounds an enclosed cavity within the heart FMA:7095 OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw chamber of heart heart chamber uberon UBERON:0004151 generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus cardiac chamber A cardiac chamber surrounds an enclosed cavity within the heart GO:0003205 An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium propepicardial Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA] EMAPA:36025 ZFA:0005808 proepicardial cluster proepicardial organ uberon UBERON:0004160 proepicardium todo check other taxa ZFA An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium GO:0003342 proepicardial cluster ZFA:0005808 proepicardial organ ZFIN:ZDB-PUB-080218-16 A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum EHDAA2:0001829 EHDAA:736 EMAPA:16318 FMA:295593 NCIT:C34296 UMLS:C0231004 VHOG:0000019 transverse septum uberon UBERON:0004161 septum transversum A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. VHOG:0000019 A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] 2012-09-17 VHOG:0000019 VHOG In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000019 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum EHDAA2 UMLS:C0231004 ncithesaurus:Septum_Transversum transverse septum The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals FMA:45652 internal genitalia internal genitals uberon internal reproductive organ internal sex organ UBERON:0004175 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 internal genitalia The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals GO:0035260 The external genitalia are the outer sex organs, such as the penis or vulva in mammals FMA:45643 external genitalia uberon external reproductive organ external sex organ UBERON:0004176 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 external genitalia The external genitalia are the outer sex organs, such as the penis or vulva in mammals GO:0035261 Organ that is part of the hematopoietic system. consider splitting out lymph organ, compare with lymph node the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. the FMA class 'lymphoid organ' is a general anatomical term BTO:0004605 EMAPA:37665 FMA:7143 MA:0000747 haematological system organ haemopoietic system organ hematopoeitic organ hematopoietic system organ organ of haematological system organ of haemopoietic system organ of hematopoietic system organ of organa haemopoietica organa haemopoietica organ hematopoeitic or lymphoid organ lymph organ lymphoid organ uberon UBERON:0004177 hemopoietic organ Organ that is part of the hematopoietic system. GOC:Obol the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. the FMA class 'lymphoid organ' is a general anatomical term FMA EMAPA:37665 MA:th haematological system organ OBOL:automatic haemopoietic system organ OBOL:automatic hematopoietic system organ OBOL:automatic organ of haematological system OBOL:automatic organ of haemopoietic system OBOL:automatic organ of hematopoietic system OBOL:automatic organ of organa haemopoietica OBOL:automatic organa haemopoietica organ OBOL:automatic lymph organ MA:0000747 lymphoid organ BTO:0004605 FMA:7143 the nonstriated, involuntary muscle tissue located in the wall of the aorta BTO:0001685 CALOHA:TS-0048 EFO:0002775 EMAPA:35135 MA:0000702 NCIT:C49191 UMLS:C1706825 aorta non-striated muscle aorta smooth muscle aortic smooth muscle uberon UBERON:0004178 aorta smooth muscle tissue the nonstriated, involuntary muscle tissue located in the wall of the aorta MGI:csmith MP:0009865 UMLS:C1706825 ncithesaurus:Aorta_Smooth_Muscle_Tissue aorta non-striated muscle OBOL:automatic aorta smooth muscle OBOL:automatic aortic smooth muscle BTO:0001685 The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland TODO - check also FMA Stroma of glandular part of prostate UBERON:0005084 EMAPA:35714 FMA:45719 MA:0002912 NCIT:C13104 UMLS:C1521760 prostate stroma prostatic stroma stroma of prostate stroma of prostate gland stroma of glandular part of prostate uberon UBERON:0004184 prostate gland stroma The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland GO:0060741 UMLS:C1521760 ncithesaurus:Prostatic_Stroma prostate stroma OBOL:automatic prostatic stroma FMA:45719 stroma of prostate OBOL:automatic stroma of prostate gland OBOL:automatic stroma of glandular part of prostate FMA:74349 OBOL:automatic A portions of the gut that is derived from endoderm. EMAPA:32930 endodermal gut gut endoderm uberon UBERON:0004185 endodermal part of digestive tract A portions of the gut that is derived from endoderm. GO:0061031 gut endoderm EMAPA:32930 Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) UBERON:0002449 UBERON:0005098 pyramid BTO:0003926 FMA:258870 MA:0001654 NCIT:C12886 NCIT:C33436 UMLS:C0227629 UMLS:C1514613 Malpighian pyramid renal pyramid uberon Malphigian pyramid Malpighian pyramid medullary pyramid pyramid of Malphigi pyramid of Malpighi pyramides renales pyramis renalis renal medullary region UBERON:0004200 kidney pyramid Kidney:PioM.png Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. GO:0072056 not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) FMA pyramid GO:0072056 UMLS:C0227629 ncithesaurus:Renal_Pyramid UMLS:C1514613 ncithesaurus:Pyramid_of_Malpighi Malpighian pyramid renal pyramid Malphigian pyramid BTO:0003926 pyramid of Malphigi ncithesaurus:Pyramid_of_Malpighi pyramid of Malpighi UBERON:cjm pyramides renales pyramis renalis BTO:0003926 renal medullary region FMA:258870 The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex UBERON:0005267 BTO:0002643 EMAPA:28130 MA:0002600 kidney cortex collecting duct uberon renal cortex collecting duct UBERON:0004203 cortical collecting duct The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex GO:0072059 kidney cortex collecting duct MA:0002600 renal cortex collecting duct MA:0002600 Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron mesenchyme of nephron nephron mesenchyme uberon UBERON:0004208 The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] nephrogenic mesenchyme Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron GO:0072076 mesenchyme of nephron OBOL:automatic nephron mesenchyme OBOL:automatic The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells. note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap stage I nephron uberon UBERON:0004209 renal vesicle EHDAA2 The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells. GO:0072077 stage I nephron ZFA:0005586 The nephron epithelium is a tissue that covers the surface of a nephron epithelial tissue of nephron epithelium of nephron nephron epithelial tissue uberon UBERON:0004211 nephron epithelium The nephron epithelium is a tissue that covers the surface of a nephron GO:0072088 epithelial tissue of nephron OBOL:automatic epithelium of nephron OBOL:automatic nephron epithelial tissue OBOL:automatic A nerve that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:37344 MA:0000685 hind limb stylopod nerve hindlimb stylopod nerve lower extremity stylopod nerve thigh RELATED uberon UBERON:0004214 upper leg nerve A nerve that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37344 MA:th hind limb stylopod nerve OBOL:automatic hindlimb stylopod nerve OBOL:automatic lower extremity stylopod nerve OBOL:automatic thigh RELATED OBOL:automatic A nerve that is part of a back [Automatically generated definition]. EMAPA:37268 MA:0000497 nerve of back uberon UBERON:0004215 back nerve A nerve that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37268 MA:th nerve of back OBOL:automatic A nerve that is part of a lower arm [Automatically generated definition]. EMAPA:37338 MA:0000601 uberon UBERON:0004216 lower arm nerve A nerve that is part of a lower arm [Automatically generated definition]. OBOL:automatic EMAPA:37338 MA:th A nerve that is part of a forelimb stylopod [Automatically generated definition]. EMAPA:37337 MA:0000607 uberon UBERON:0004217 upper arm nerve A nerve that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37337 MA:th A nerve that is part of a lower leg [Automatically generated definition]. EMAPA:37345 MA:0000679 uberon UBERON:0004218 lower leg nerve A nerve that is part of a lower leg [Automatically generated definition]. OBOL:automatic EMAPA:37345 MA:th A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]. EMAPA:36630 FMA:76909 MA:0001691 muscle layer of urethra muscular coat of urethra muscular layer of urethra smooth muscle of urethra smooth muscle tissue of urethra tunica muscularis urethrae urethra smooth muscle tissue uberon urethral smooth muscle UBERON:0004219 urethra smooth muscle layer A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]. OBOL:automatic muscle layer of urethra FMA:76909 muscular coat of urethra FMA:76909 muscular layer of urethra FMA:76909 smooth muscle of urethra OBOL:automatic smooth muscle tissue of urethra OBOL:automatic tunica muscularis urethrae FMA:TA urethra smooth muscle tissue OBOL:automatic urethral smooth muscle MA:0001691 A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35469 MA:0001547 involuntary muscle of large intestine large intestine involuntary muscle large intestine non-striated muscle large intestine smooth muscle tissue non-striated muscle of large intestine smooth muscle of large intestine smooth muscle tissue of large intestine uberon UBERON:0004220 large intestine smooth muscle MA consider merging A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA involuntary muscle of large intestine OBOL:automatic large intestine involuntary muscle OBOL:automatic large intestine non-striated muscle OBOL:automatic large intestine smooth muscle tissue OBOL:automatic non-striated muscle of large intestine OBOL:automatic smooth muscle of large intestine OBOL:automatic smooth muscle tissue of large intestine OBOL:automatic A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa BTO:0000643 EMAPA:35441 EMAPA:35443 MA:0001539 NCIT:C49243 UMLS:C1708547 bowel involuntary muscle bowel non-striated muscle bowel smooth muscle bowel smooth muscle tissue intestine involuntary muscle intestine non-striated muscle intestine smooth muscle tissue involuntary muscle of bowel involuntary muscle of intestine non-striated muscle of bowel non-striated muscle of intestine smooth muscle of bowel smooth muscle of intestine smooth muscle tissue of bowel smooth muscle tissue of intestine uberon intestinal muscularis intestinal smooth muscle UBERON:0004221 intestine smooth muscle consider merging A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA UMLS:C1708547 ncithesaurus:Intestinal_Smooth_Muscle_Tissue bowel involuntary muscle OBOL:automatic bowel non-striated muscle OBOL:automatic bowel smooth muscle OBOL:automatic bowel smooth muscle tissue OBOL:automatic intestine involuntary muscle OBOL:automatic intestine non-striated muscle OBOL:automatic intestine smooth muscle tissue OBOL:automatic involuntary muscle of bowel OBOL:automatic involuntary muscle of intestine OBOL:automatic non-striated muscle of bowel OBOL:automatic non-striated muscle of intestine OBOL:automatic smooth muscle of bowel OBOL:automatic smooth muscle of intestine OBOL:automatic smooth muscle tissue of bowel OBOL:automatic smooth muscle tissue of intestine OBOL:automatic intestinal muscularis EMAPA:35441 intestinal smooth muscle BTO:0000643 A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. BTO:0001818 EMAPA:35823 MA:0001627 involuntary muscle of stomach involuntary muscle of ventriculus non-striated muscle of stomach non-striated muscle of ventriculus smooth muscle of stomach smooth muscle of ventriculus smooth muscle tissue of stomach smooth muscle tissue of ventriculus stomach involuntary muscle stomach non-striated muscle stomach smooth muscle tissue ventriculus involuntary muscle ventriculus non-striated muscle ventriculus smooth muscle ventriculus smooth muscle tissue uberon gastric muscle gastric smooth muscle stomach muscle UBERON:0004222 stomach smooth muscle A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. OBOL:automatic involuntary muscle of stomach OBOL:automatic involuntary muscle of ventriculus OBOL:automatic non-striated muscle of stomach OBOL:automatic non-striated muscle of ventriculus OBOL:automatic smooth muscle of stomach OBOL:automatic smooth muscle of ventriculus OBOL:automatic smooth muscle tissue of stomach OBOL:automatic smooth muscle tissue of ventriculus OBOL:automatic stomach involuntary muscle OBOL:automatic stomach non-striated muscle OBOL:automatic stomach smooth muscle tissue OBOL:automatic ventriculus involuntary muscle OBOL:automatic ventriculus non-striated muscle OBOL:automatic ventriculus smooth muscle OBOL:automatic ventriculus smooth muscle tissue OBOL:automatic gastric muscle BTO:0001818 gastric smooth muscle MA:0001627 stomach muscle BTO:0001818 A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition]. BTO:0004999 EMAPA:30997 MA:0001733 involuntary muscle of vagina non-striated muscle of vagina smooth muscle of vagina smooth muscle tissue of vagina vagina involuntary muscle vagina non-striated muscle vagina smooth muscle tissue vaginal smooth muscle uberon vagina smooth muscle UBERON:0004223 vagina smooth muscle A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition]. OBOL:automatic involuntary muscle of vagina OBOL:automatic non-striated muscle of vagina OBOL:automatic smooth muscle of vagina OBOL:automatic smooth muscle tissue of vagina OBOL:automatic vagina involuntary muscle OBOL:automatic vagina non-striated muscle OBOL:automatic vagina smooth muscle tissue OBOL:automatic vaginal smooth muscle BTO:0004999 vagina smooth muscle BTO:0004999 A muscular coat that is part of a vas deferens [Automatically generated definition]. TODO - check MA and FMA classes mean the same thing EMAPA:29270 FMA:19239 MA:0001750 muscle layer of deferent duct muscle layer of ductus deferens muscle layer of vas deferens muscular coat of ductus deferens muscular layer of ductus deferens muscularis of vas deferens tunica muscularis (ductus deferens) tunica muscularis ductus deferentis uberon UBERON:0004224 muscular coat of vas deferens A muscular coat that is part of a vas deferens [Automatically generated definition]. OBOL:automatic muscle layer of deferent duct FMA:19239 muscle layer of ductus deferens FMA:19239 muscle layer of vas deferens FMA:19239 muscular coat of ductus deferens FMA:19239 muscular layer of ductus deferens FMA:19239 muscularis of vas deferens FMA:19239 tunica muscularis (ductus deferens) FMA:19239 tunica muscularis ductus deferentis FMA:19239 FMA:TA A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. BTO:0001660 EMAPA:35734 MA:0001830 respiratory smooth muscle smooth muscle of respiratory system uberon airway smooth muscle airway smooth muscle cell UBERON:0004225 respiratory system smooth muscle A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic respiratory smooth muscle BTO:0001660 smooth muscle of respiratory system OBOL:automatic airway smooth muscle BTO:0001660 airway smooth muscle cell BTO:0001660 A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. EMAPA:35117 MA:0001523 smooth muscle tissue of gastrointestinal system uberon UBERON:0004226 gastrointestinal system smooth muscle A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. OBOL:automatic smooth muscle tissue of gastrointestinal system OBOL:automatic the smooth muscle tissue surrounding the urothelium of the kidney pelvis EMAPA:28120 FMA:262022 MA:0002631 kidney pelvis smooth muscle renal pelvis smooth muscle smooth muscle tissue of renal pelvis uberon pelvic smooth muscle UBERON:0004227 kidney pelvis smooth muscle the smooth muscle tissue surrounding the urothelium of the kidney pelvis MGI:csmith MP:0011335 kidney pelvis smooth muscle EMAPA:28120 renal pelvis smooth muscle EMAPA:28120 smooth muscle tissue of renal pelvis FMA:262022 pelvic smooth muscle EMAPA:28120 A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition]. BTO:0001849 CALOHA:TS-1087 EMAPA:37791 MA:0001697 bladder involuntary muscle bladder non-striated muscle bladder smooth muscle bladder smooth muscle tissue involuntary muscle of bladder involuntary muscle of urinary bladder non-striated muscle of bladder non-striated muscle of urinary bladder smooth muscle of bladder smooth muscle of urinary bladder smooth muscle tissue of bladder smooth muscle tissue of urinary bladder urinary bladder involuntary muscle urinary bladder muscle urinary bladder non-striated muscle urinary bladder smooth muscle tissue uberon smooth muscle layer of bladder UBERON:0004228 urinary bladder smooth muscle A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition]. OBOL:automatic EMAPA:37791 MA:th bladder involuntary muscle OBOL:automatic bladder non-striated muscle OBOL:automatic bladder smooth muscle OBOL:automatic bladder smooth muscle tissue OBOL:automatic involuntary muscle of bladder OBOL:automatic involuntary muscle of urinary bladder OBOL:automatic non-striated muscle of bladder OBOL:automatic non-striated muscle of urinary bladder OBOL:automatic smooth muscle of bladder OBOL:automatic smooth muscle of urinary bladder OBOL:automatic smooth muscle tissue of bladder OBOL:automatic smooth muscle tissue of urinary bladder OBOL:automatic urinary bladder involuntary muscle OBOL:automatic urinary bladder muscle MA:0001697 urinary bladder non-striated muscle OBOL:automatic urinary bladder smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition]. EMAPA:30123 FMA:67990 MA:0001699 bladder neck involuntary muscle bladder neck non-striated muscle bladder neck smooth muscle bladder neck smooth muscle tissue involuntary muscle of bladder neck involuntary muscle of neck of bladder involuntary muscle of neck of urinary bladder involuntary muscle of urinary bladder neck involuntary muscle of vesical neck neck of bladder involuntary muscle neck of bladder non-striated muscle neck of bladder smooth muscle neck of bladder smooth muscle tissue neck of urinary bladder involuntary muscle neck of urinary bladder non-striated muscle neck of urinary bladder smooth muscle neck of urinary bladder smooth muscle tissue non-striated muscle of bladder neck non-striated muscle of neck of bladder non-striated muscle of neck of urinary bladder non-striated muscle of urinary bladder neck non-striated muscle of vesical neck smooth muscle of bladder neck smooth muscle of neck of bladder smooth muscle of neck of urinary bladder smooth muscle of urinary bladder neck smooth muscle of vesical neck smooth muscle tissue of bladder neck smooth muscle tissue of neck of bladder smooth muscle tissue of neck of urinary bladder smooth muscle tissue of urinary bladder neck smooth muscle tissue of vesical neck trigonal muscle trigonal muscle of urinary bladder urinary bladder neck involuntary muscle urinary bladder neck muscle urinary bladder neck non-striated muscle urinary bladder neck smooth muscle tissue vesical neck involuntary muscle vesical neck non-striated muscle vesical neck smooth muscle vesical neck smooth muscle tissue uberon UBERON:0004230 urinary bladder neck smooth muscle A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck involuntary muscle OBOL:automatic bladder neck non-striated muscle OBOL:automatic bladder neck smooth muscle OBOL:automatic bladder neck smooth muscle tissue OBOL:automatic involuntary muscle of bladder neck OBOL:automatic involuntary muscle of neck of bladder OBOL:automatic involuntary muscle of neck of urinary bladder OBOL:automatic involuntary muscle of urinary bladder neck OBOL:automatic involuntary muscle of vesical neck OBOL:automatic neck of bladder involuntary muscle OBOL:automatic neck of bladder non-striated muscle OBOL:automatic neck of bladder smooth muscle OBOL:automatic neck of bladder smooth muscle tissue OBOL:automatic neck of urinary bladder involuntary muscle OBOL:automatic neck of urinary bladder non-striated muscle OBOL:automatic neck of urinary bladder smooth muscle OBOL:automatic neck of urinary bladder smooth muscle tissue OBOL:automatic non-striated muscle of bladder neck OBOL:automatic non-striated muscle of neck of bladder OBOL:automatic non-striated muscle of neck of urinary bladder OBOL:automatic non-striated muscle of urinary bladder neck OBOL:automatic non-striated muscle of vesical neck OBOL:automatic smooth muscle of bladder neck OBOL:automatic smooth muscle of neck of bladder OBOL:automatic smooth muscle of neck of urinary bladder OBOL:automatic smooth muscle of urinary bladder neck OBOL:automatic smooth muscle of vesical neck OBOL:automatic smooth muscle tissue of bladder neck OBOL:automatic smooth muscle tissue of neck of bladder OBOL:automatic smooth muscle tissue of neck of urinary bladder OBOL:automatic smooth muscle tissue of urinary bladder neck OBOL:automatic smooth muscle tissue of vesical neck OBOL:automatic trigonal muscle FMA:67990 trigonal muscle of urinary bladder FMA:67990 urinary bladder neck involuntary muscle OBOL:automatic urinary bladder neck muscle MA:0001699 urinary bladder neck non-striated muscle OBOL:automatic urinary bladder neck smooth muscle tissue OBOL:automatic vesical neck involuntary muscle OBOL:automatic vesical neck non-striated muscle OBOL:automatic vesical neck smooth muscle OBOL:automatic vesical neck smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37394 MA:0001532 anal part of perineum involuntary muscle anal part of perineum non-striated muscle anal part of perineum smooth muscle anal part of perineum smooth muscle tissue anal region involuntary muscle anal region non-striated muscle anal region smooth muscle tissue anal triangle involuntary muscle anal triangle non-striated muscle anal triangle smooth muscle anal triangle smooth muscle tissue involuntary muscle of anal part of perineum involuntary muscle of anal region involuntary muscle of anal triangle non-striated muscle of anal part of perineum non-striated muscle of anal region non-striated muscle of anal triangle smooth muscle of anal part of perineum smooth muscle of anal region smooth muscle of anal triangle smooth muscle tissue of anal part of perineum smooth muscle tissue of anal region smooth muscle tissue of anal triangle uberon UBERON:0004231 anal region smooth muscle A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37394 MA:th anal part of perineum involuntary muscle OBOL:automatic anal part of perineum non-striated muscle OBOL:automatic anal part of perineum smooth muscle OBOL:automatic anal part of perineum smooth muscle tissue OBOL:automatic anal region involuntary muscle OBOL:automatic anal region non-striated muscle OBOL:automatic anal region smooth muscle tissue OBOL:automatic anal triangle involuntary muscle OBOL:automatic anal triangle non-striated muscle OBOL:automatic anal triangle smooth muscle OBOL:automatic anal triangle smooth muscle tissue OBOL:automatic involuntary muscle of anal part of perineum OBOL:automatic involuntary muscle of anal region OBOL:automatic involuntary muscle of anal triangle OBOL:automatic non-striated muscle of anal part of perineum OBOL:automatic non-striated muscle of anal region OBOL:automatic non-striated muscle of anal triangle OBOL:automatic smooth muscle of anal part of perineum OBOL:automatic smooth muscle of anal region OBOL:automatic smooth muscle of anal triangle OBOL:automatic smooth muscle tissue of anal part of perineum OBOL:automatic smooth muscle tissue of anal region OBOL:automatic smooth muscle tissue of anal triangle OBOL:automatic A portion of smooth muscle tissue that is part of a lymphatic vessel [Automatically generated definition]. EMAPA:36313 FMA:262026 MA:0000751 NCIT:C49260 UMLS:C1708791 involuntary muscle of lymph vessel involuntary muscle of lymphatic vessel lymph vessel involuntary muscle lymph vessel non-striated muscle lymph vessel smooth muscle lymph vessel smooth muscle tissue lymphatic vessel involuntary muscle lymphatic vessel non-striated muscle lymphatic vessel smooth muscle tissue non-striated muscle of lymph vessel non-striated muscle of lymphatic vessel smooth muscle of lymph vessel smooth muscle of lymphatic vessel smooth muscle tissue of lymph vessel smooth muscle tissue of lymphatic vessel uberon UBERON:0004232 lymphatic vessel smooth muscle A portion of smooth muscle tissue that is part of a lymphatic vessel [Automatically generated definition]. OBOL:automatic UMLS:C1708791 ncithesaurus:Lymphatic_Vessel_Smooth_Muscle_Tissue involuntary muscle of lymph vessel OBOL:automatic involuntary muscle of lymphatic vessel OBOL:automatic lymph vessel involuntary muscle OBOL:automatic lymph vessel non-striated muscle OBOL:automatic lymph vessel smooth muscle OBOL:automatic lymph vessel smooth muscle tissue OBOL:automatic lymphatic vessel involuntary muscle OBOL:automatic lymphatic vessel non-striated muscle OBOL:automatic lymphatic vessel smooth muscle tissue OBOL:automatic non-striated muscle of lymph vessel OBOL:automatic non-striated muscle of lymphatic vessel OBOL:automatic smooth muscle of lymph vessel OBOL:automatic smooth muscle of lymphatic vessel OBOL:automatic smooth muscle tissue of lymph vessel OBOL:automatic smooth muscle tissue of lymphatic vessel OBOL:automatic A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:35520 MA:0002410 involuntary muscle of lower respiratory tract lower respiratory tract involuntary muscle lower respiratory tract non-striated muscle lower respiratory tract smooth muscle tissue non-striated muscle of lower respiratory tract smooth muscle of lower respiratory tract smooth muscle tissue of lower respiratory tract uberon UBERON:0004233 lower respiratory tract smooth muscle A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic involuntary muscle of lower respiratory tract OBOL:automatic lower respiratory tract involuntary muscle OBOL:automatic lower respiratory tract non-striated muscle OBOL:automatic lower respiratory tract smooth muscle tissue OBOL:automatic non-striated muscle of lower respiratory tract OBOL:automatic smooth muscle of lower respiratory tract OBOL:automatic smooth muscle tissue of lower respiratory tract OBOL:automatic A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. see notes for muscle of iris. BTO:0000655 EMAPA:35448 FMA:312338 MA:0001270 involuntary muscle of iris iridial smooth muscle iris involuntary muscle iris non-striated muscle iris smooth muscle tissue non-striated muscle of iris smooth muscle of iris smooth muscle tissue of iris uberon UBERON:0004234 iris smooth muscle MA A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. OBOL:automatic involuntary muscle of iris OBOL:automatic iridial smooth muscle iris involuntary muscle OBOL:automatic iris non-striated muscle OBOL:automatic iris smooth muscle tissue OBOL:automatic non-striated muscle of iris OBOL:automatic smooth muscle of iris OBOL:automatic smooth muscle tissue of iris OBOL:automatic A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. EMAPA:36287 FMA:312251 MA:0000706 uberon UBERON:0004236 arteriole smooth muscle A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. OBOL:automatic smooth muscle found within, and composing the majority of the wall of blood vessels. Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension. UBERON:0010508 BTO:0001431 CALOHA:TS-1107 EMAPA:35177 MA:0000710 MESH:D009131 NCIT:C33853 TAO:0005321 UMLS:C1519956 ZFA:0005321 blood vessel involuntary muscle blood vessel non-striated muscle blood vessel smooth muscle tissue involuntary muscle of blood vessel non-striated muscle of blood vessel smooth muscle of blood vessel smooth muscle tissue of blood vessel vascular smooth muscle vascular smooth muscle tissue uberon UBERON:0004237 blood vessel smooth muscle smooth muscle found within, and composing the majority of the wall of blood vessels. UMLS:C1519956 ncithesaurus:Vascular_Smooth_Muscle_Tissue blood vessel involuntary muscle OBOL:automatic blood vessel non-striated muscle OBOL:automatic blood vessel smooth muscle tissue OBOL:automatic involuntary muscle of blood vessel OBOL:automatic non-striated muscle of blood vessel OBOL:automatic smooth muscle of blood vessel OBOL:automatic smooth muscle tissue of blood vessel OBOL:automatic vascular smooth muscle ZFA:0005321 A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition]. EMAPA:35807 MA:0000757 involuntary muscle of spleen non-striated muscle of spleen smooth muscle of spleen smooth muscle tissue of spleen spleen involuntary muscle spleen non-striated muscle spleen smooth muscle tissue uberon UBERON:0004238 spleen smooth muscle A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition]. OBOL:automatic involuntary muscle of spleen OBOL:automatic non-striated muscle of spleen OBOL:automatic smooth muscle of spleen OBOL:automatic smooth muscle tissue of spleen OBOL:automatic spleen involuntary muscle OBOL:automatic spleen non-striated muscle OBOL:automatic spleen smooth muscle tissue OBOL:automatic A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35783 MA:0001559 involuntary muscle of small bowel involuntary muscle of small intestine non-striated muscle of small bowel non-striated muscle of small intestine small bowel involuntary muscle small bowel non-striated muscle small bowel smooth muscle small bowel smooth muscle tissue small intestine involuntary muscle small intestine non-striated muscle small intestine smooth muscle tissue smooth muscle of small bowel smooth muscle of small intestine smooth muscle tissue of small bowel smooth muscle tissue of small intestine uberon UBERON:0004239 small intestine smooth muscle consider merging A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA involuntary muscle of small bowel OBOL:automatic involuntary muscle of small intestine OBOL:automatic non-striated muscle of small bowel OBOL:automatic non-striated muscle of small intestine OBOL:automatic small bowel involuntary muscle OBOL:automatic small bowel non-striated muscle OBOL:automatic small bowel smooth muscle OBOL:automatic small bowel smooth muscle tissue OBOL:automatic small intestine involuntary muscle OBOL:automatic small intestine non-striated muscle OBOL:automatic small intestine smooth muscle tissue OBOL:automatic smooth muscle of small bowel OBOL:automatic smooth muscle of small intestine OBOL:automatic smooth muscle tissue of small bowel OBOL:automatic smooth muscle tissue of small intestine OBOL:automatic A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition]. EMAPA:35373 MA:0001635 NCIT:C49483 UMLS:C1708179 gall bladder involuntary muscle gall bladder non-striated muscle gall bladder smooth muscle tissue gallbladder involuntary muscle gallbladder non-striated muscle gallbladder smooth muscle gallbladder smooth muscle tissue involuntary muscle of gall bladder involuntary muscle of gallbladder non-striated muscle of gall bladder non-striated muscle of gallbladder smooth muscle of gall bladder smooth muscle of gallbladder smooth muscle tissue of gall bladder smooth muscle tissue of gallbladder uberon biliary smooth muscle UBERON:0004240 gall bladder smooth muscle A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition]. OBOL:automatic UMLS:C1708179 ncithesaurus:Gallbladder_Smooth_Muscle_Tissue gall bladder involuntary muscle OBOL:automatic gall bladder non-striated muscle OBOL:automatic gall bladder smooth muscle tissue OBOL:automatic gallbladder involuntary muscle OBOL:automatic gallbladder non-striated muscle OBOL:automatic gallbladder smooth muscle OBOL:automatic gallbladder smooth muscle tissue OBOL:automatic involuntary muscle of gall bladder OBOL:automatic involuntary muscle of gallbladder OBOL:automatic non-striated muscle of gall bladder OBOL:automatic non-striated muscle of gallbladder OBOL:automatic smooth muscle of gall bladder OBOL:automatic smooth muscle of gallbladder OBOL:automatic smooth muscle tissue of gall bladder OBOL:automatic smooth muscle tissue of gallbladder OBOL:automatic biliary smooth muscle MA:0001635 A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition]. BTO:0004401 EMAPA:35195 MA:0001840 NCIT:C49213 UMLS:C1707055 bronchi involuntary muscle bronchi non-striated muscle bronchi smooth muscle bronchi smooth muscle tissue bronchial trunk involuntary muscle bronchial trunk non-striated muscle bronchial trunk smooth muscle bronchial trunk smooth muscle tissue bronchus involuntary muscle bronchus non-striated muscle bronchus smooth muscle tissue involuntary muscle of bronchi involuntary muscle of bronchial trunk involuntary muscle of bronchus non-striated muscle of bronchi non-striated muscle of bronchial trunk non-striated muscle of bronchus smooth muscle of bronchi smooth muscle of bronchial trunk smooth muscle of bronchus smooth muscle tissue of bronchi smooth muscle tissue of bronchial trunk smooth muscle tissue of bronchus uberon bronchial smooth muscle UBERON:0004242 bronchus smooth muscle A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition]. OBOL:automatic UMLS:C1707055 ncithesaurus:Bronchus_Smooth_Muscle_Tissue bronchi involuntary muscle OBOL:automatic bronchi non-striated muscle OBOL:automatic bronchi smooth muscle OBOL:automatic bronchi smooth muscle tissue OBOL:automatic bronchial trunk involuntary muscle OBOL:automatic bronchial trunk non-striated muscle OBOL:automatic bronchial trunk smooth muscle OBOL:automatic bronchial trunk smooth muscle tissue OBOL:automatic bronchus involuntary muscle OBOL:automatic bronchus non-striated muscle OBOL:automatic bronchus smooth muscle tissue OBOL:automatic involuntary muscle of bronchi OBOL:automatic involuntary muscle of bronchial trunk OBOL:automatic involuntary muscle of bronchus OBOL:automatic non-striated muscle of bronchi OBOL:automatic non-striated muscle of bronchial trunk OBOL:automatic non-striated muscle of bronchus OBOL:automatic smooth muscle of bronchi OBOL:automatic smooth muscle of bronchial trunk OBOL:automatic smooth muscle of bronchus OBOL:automatic smooth muscle tissue of bronchi OBOL:automatic smooth muscle tissue of bronchial trunk OBOL:automatic smooth muscle tissue of bronchus OBOL:automatic bronchial smooth muscle EMAPA:35195 A portion of smooth muscle tissue that is part of a prostate gland [Automatically generated definition]. BTO:0003159 EMAPA:35713 FMA:74245 MA:0001741 involuntary muscle of prostate involuntary muscle of prostate gland muscular tissue of prostate non-striated muscle of prostate non-striated muscle of prostate gland prostate gland involuntary muscle prostate gland non-striated muscle prostate gland smooth muscle tissue prostate involuntary muscle prostate non-striated muscle prostate smooth muscle prostate smooth muscle tissue smooth muscle of prostate smooth muscle of prostate gland smooth muscle tissue of prostate smooth muscle tissue of prostate gland substantia muscularis prostatae uberon UBERON:0004243 prostate gland smooth muscle A portion of smooth muscle tissue that is part of a prostate gland [Automatically generated definition]. OBOL:automatic involuntary muscle of prostate OBOL:automatic involuntary muscle of prostate gland OBOL:automatic muscular tissue of prostate FMA:74245 non-striated muscle of prostate OBOL:automatic non-striated muscle of prostate gland OBOL:automatic prostate gland involuntary muscle OBOL:automatic prostate gland non-striated muscle OBOL:automatic prostate gland smooth muscle tissue OBOL:automatic prostate involuntary muscle OBOL:automatic prostate non-striated muscle OBOL:automatic prostate smooth muscle OBOL:automatic prostate smooth muscle tissue OBOL:automatic smooth muscle of prostate OBOL:automatic smooth muscle of prostate gland OBOL:automatic smooth muscle tissue of prostate OBOL:automatic smooth muscle tissue of prostate gland OBOL:automatic substantia muscularis prostatae FMA:74245 FMA:TA A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition]. EMAPA:29046 MA:0001721 fallopian tube involuntary muscle fallopian tube non-striated muscle fallopian tube smooth muscle fallopian tube smooth muscle tissue involuntary muscle of fallopian tube non-striated muscle of fallopian tube smooth muscle of fallopian tube smooth muscle tissue of fallopian tube uberon UBERON:0004245 oviduct smooth muscle A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition]. OBOL:automatic fallopian tube involuntary muscle OBOL:automatic fallopian tube non-striated muscle OBOL:automatic fallopian tube smooth muscle OBOL:automatic fallopian tube smooth muscle tissue OBOL:automatic involuntary muscle of fallopian tube OBOL:automatic non-striated muscle of fallopian tube OBOL:automatic smooth muscle of fallopian tube OBOL:automatic smooth muscle tissue of fallopian tube OBOL:automatic A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. EMAPA:37708 MA:0000492 involuntary muscle of outflow tract non-striated muscle of outflow tract outflow tract involuntary muscle outflow tract non-striated muscle outflow tract smooth muscle tissue smooth muscle of outflow tract smooth muscle tissue of outflow tract uberon UBERON:0004246 outflow tract smooth muscle A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. OBOL:automatic EMAPA:37708 MA:th involuntary muscle of outflow tract OBOL:automatic non-striated muscle of outflow tract OBOL:automatic outflow tract involuntary muscle OBOL:automatic outflow tract non-striated muscle OBOL:automatic outflow tract smooth muscle tissue OBOL:automatic smooth muscle of outflow tract OBOL:automatic smooth muscle tissue of outflow tract OBOL:automatic A bone that is part of the dorsal region of an animal. this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:37248 MA:0000494 uberon back bone bone of back dorsal region bone UBERON:0004247 bone of dorsum A bone that is part of the dorsal region of an animal. EMAPA:37248 MA:th back bone MA:0000494 bone of back OBOL:automatic dorsal region bone A bone that is part of a hindlimb digit. Typically phalanges but may include sesamoids. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:37309 MA:0000646 bone of digit of foot digit of foot bone digital bone of foot digital bone of pes digitus pedis bone digitus pedis bone organ foot digit bone foot digit bone organ hind limb digit bone toe bone toe bone organ foot digit bone uberon UBERON:0004248 pedal digit bone A bone that is part of a hindlimb digit. Typically phalanges but may include sesamoids. EMAPA:37309 MA:th bone of digit of foot OBOL:automatic digit of foot bone OBOL:automatic digitus pedis bone OBOL:automatic digitus pedis bone organ OBOL:automatic foot digit bone MA:0000646 foot digit bone organ OBOL:automatic hind limb digit bone OBOL:accepted toe bone OBOL:automatic toe bone organ OBOL:automatic foot digit bone NCBITaxon:9606 OBOL:accepted A bone that is part of a forelimb digit. Typically phalanges but may include sesamoids. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:37305 MA:0000622 digital bone of hand digital bone of manus finger bone fore limb digit bone hand digit bone hand digit bone uberon UBERON:0004249 manual digit bone A bone that is part of a forelimb digit. Typically phalanges but may include sesamoids. EMAPA:37305 MA:th finger bone OBOL:automatic fore limb digit bone OBOL:accepted hand digit bone MA:0000622 hand digit bone NCBITaxon:9606 OBOL:accepted A bone that is part of a forelimb stylopod [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:35892 MA:0000604 humerus uberon UBERON:0004250 May be merged into humerus. See: https://sourceforge.net/tracker/index.php?func=detail&aid=3586533&group_id=76834&atid=1205376 upper arm bone A bone that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic humerus A bone that is part of a lower leg [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:35519 MA:0000676 bone of hind limb middle limb segment bone of hind limb zeugopod bone of hindlimb middle limb segment bone of hindlimb zeugopod bone of inferior member middle limb segment bone of inferior member zeugopod bone of intermediate segment of free lower limb bone of lower extremity middle limb segment bone of lower extremity zeugopod bone of lower leg bone of middle limb segment of hind limb bone of middle limb segment of hindlimb bone of middle limb segment of inferior member bone of middle limb segment of lower extremity bone of zeugopod of hind limb bone of zeugopod of hindlimb bone of zeugopod of inferior member bone of zeugopod of leg bone of zeugopod of lower extremity bone organ of hind limb middle limb segment bone organ of hind limb zeugopod bone organ of hindlimb middle limb segment bone organ of hindlimb zeugopod bone organ of inferior member middle limb segment bone organ of inferior member zeugopod bone organ of intermediate segment of free lower limb bone organ of lower extremity middle limb segment bone organ of lower extremity zeugopod bone organ of lower leg bone organ of middle limb segment of hind limb bone organ of middle limb segment of hindlimb bone organ of middle limb segment of inferior member bone organ of middle limb segment of lower extremity bone organ of zeugopod of hind limb bone organ of zeugopod of hindlimb bone organ of zeugopod of inferior member bone organ of zeugopod of leg bone organ of zeugopod of lower extremity hind limb middle limb segment bone hind limb middle limb segment bone organ hind limb zeugopod bone hind limb zeugopod bone organ hindlimb middle limb segment bone hindlimb middle limb segment bone organ hindlimb zeugopod bone hindlimb zeugopod bone organ inferior member middle limb segment bone inferior member middle limb segment bone organ inferior member zeugopod bone inferior member zeugopod bone organ intermediate segment of free lower limb bone intermediate segment of free lower limb bone organ lower extremity middle limb segment bone lower extremity middle limb segment bone organ lower extremity zeugopod bone lower extremity zeugopod bone organ lower leg bone middle limb segment of hind limb bone middle limb segment of hind limb bone organ middle limb segment of hindlimb bone middle limb segment of hindlimb bone organ middle limb segment of inferior member bone middle limb segment of inferior member bone organ middle limb segment of lower extremity bone middle limb segment of lower extremity bone organ zeugopod of hind limb bone zeugopod of hind limb bone organ zeugopod of hindlimb bone zeugopod of hindlimb bone organ zeugopod of inferior member bone zeugopod of inferior member bone organ zeugopod of leg bone zeugopod of leg bone organ zeugopod of lower extremity bone zeugopod of lower extremity bone organ uberon UBERON:0004251 hindlimb zeugopod bone A bone that is part of a lower leg [Automatically generated definition]. OBOL:automatic bone of hind limb middle limb segment OBOL:automatic bone of hind limb zeugopod OBOL:automatic bone of hindlimb middle limb segment OBOL:automatic bone of hindlimb zeugopod OBOL:automatic bone of inferior member middle limb segment OBOL:automatic bone of inferior member zeugopod OBOL:automatic bone of intermediate segment of free lower limb OBOL:automatic bone of lower extremity middle limb segment OBOL:automatic bone of lower extremity zeugopod OBOL:automatic bone of lower leg OBOL:automatic bone of middle limb segment of hind limb OBOL:automatic bone of middle limb segment of hindlimb OBOL:automatic bone of middle limb segment of inferior member OBOL:automatic bone of middle limb segment of lower extremity OBOL:automatic bone of zeugopod of hind limb OBOL:automatic bone of zeugopod of hindlimb OBOL:automatic bone of zeugopod of inferior member OBOL:automatic bone of zeugopod of leg OBOL:automatic bone of zeugopod of lower extremity OBOL:automatic bone organ of hind limb middle limb segment OBOL:automatic bone organ of hind limb zeugopod OBOL:automatic bone organ of hindlimb middle limb segment OBOL:automatic bone organ of hindlimb zeugopod OBOL:automatic bone organ of inferior member middle limb segment OBOL:automatic bone organ of inferior member zeugopod OBOL:automatic bone organ of intermediate segment of free lower limb OBOL:automatic bone organ of lower extremity middle limb segment OBOL:automatic bone organ of lower extremity zeugopod OBOL:automatic bone organ of lower leg OBOL:automatic bone organ of middle limb segment of hind limb OBOL:automatic bone organ of middle limb segment of hindlimb OBOL:automatic bone organ of middle limb segment of inferior member OBOL:automatic bone organ of middle limb segment of lower extremity OBOL:automatic bone organ of zeugopod of hind limb OBOL:automatic bone organ of zeugopod of hindlimb OBOL:automatic bone organ of zeugopod of inferior member OBOL:automatic bone organ of zeugopod of leg OBOL:automatic bone organ of zeugopod of lower extremity OBOL:automatic hind limb middle limb segment bone OBOL:automatic hind limb middle limb segment bone organ OBOL:automatic hind limb zeugopod bone OBOL:automatic hind limb zeugopod bone organ OBOL:automatic hindlimb middle limb segment bone OBOL:automatic hindlimb middle limb segment bone organ OBOL:automatic hindlimb zeugopod bone OBOL:automatic hindlimb zeugopod bone organ OBOL:automatic inferior member middle limb segment bone OBOL:automatic inferior member middle limb segment bone organ OBOL:automatic inferior member zeugopod bone OBOL:automatic inferior member zeugopod bone organ OBOL:automatic intermediate segment of free lower limb bone OBOL:automatic intermediate segment of free lower limb bone organ OBOL:automatic lower extremity middle limb segment bone OBOL:automatic lower extremity middle limb segment bone organ OBOL:automatic lower extremity zeugopod bone OBOL:automatic lower extremity zeugopod bone organ OBOL:automatic lower leg bone MA:0000676 middle limb segment of hind limb bone OBOL:automatic middle limb segment of hind limb bone organ OBOL:automatic middle limb segment of hindlimb bone OBOL:automatic middle limb segment of hindlimb bone organ OBOL:automatic middle limb segment of inferior member bone OBOL:automatic middle limb segment of inferior member bone organ OBOL:automatic middle limb segment of lower extremity bone OBOL:automatic middle limb segment of lower extremity bone organ OBOL:automatic zeugopod of hind limb bone OBOL:automatic zeugopod of hind limb bone organ OBOL:automatic zeugopod of hindlimb bone OBOL:automatic zeugopod of hindlimb bone organ OBOL:automatic zeugopod of inferior member bone OBOL:automatic zeugopod of inferior member bone organ OBOL:automatic zeugopod of leg bone OBOL:automatic zeugopod of leg bone organ OBOL:automatic zeugopod of lower extremity bone OBOL:automatic zeugopod of lower extremity bone organ OBOL:automatic Any muscle organ that is part of a hindlimb stylopod (upper leg)[Automatically generated definition]. UBERON:0000374 BTO:0001367 EMAPA:19144 FMA:22470 MA:0000684 muscle of thigh thigh muscle upper leg muscle uberon UBERON:0004252 hindlimb stylopod muscle prolog Any muscle organ that is part of a hindlimb stylopod (upper leg)[Automatically generated definition]. OBOL:automatic muscle of thigh FMA:22470 thigh muscle FMA:22470 upper leg muscle MA:0000684 Any muscle organ that is part of a skin of body [Automatically generated definition]. review as part of general integumentary system review - part of skin, or more generally, integumental system in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only UBERON:0015797 EMAPA:18187 EMAPA:35776 MA:0002710 MA:0003139 integumental system muscle muscle of integumental system muscle organ of skin skin muscle organ uberon UBERON:0004253 skin muscle Any muscle organ that is part of a skin of body [Automatically generated definition]. OBOL:automatic in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only MA integumental system muscle MA:0003139 muscle of integumental system EMAPA:18187 muscle organ of skin OBOL:automatic skin muscle organ OBOL:automatic Any muscle organ that is part of a forelimb zeugopod (lower arm)[Automatically generated definition]. EMAPA:32622 FMA:37371 MA:0000600 forearm muscle lower arm muscle muscle of forearm wing zeugopod muscle uberon UBERON:0004254 forelimb zeugopod muscle prolog Any muscle organ that is part of a forelimb zeugopod (lower arm)[Automatically generated definition]. OBOL:automatic forearm muscle FMA:37371 lower arm muscle MA:0000600 muscle of forearm FMA:37371 wing zeugopod muscle NCBITaxon:8782 OBOL:automatic Any muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition]. the FMA class 'muscle of arm' belongs here, do not move See notes on UBERON:0001460 for possible terminological confusion over term 'arm' EMAPA:19107 FMA:37370 MA:0000606 muscle of upper arm upper arm muscle wing stylopod muscle uberon muscle of arm skeletal muscle of upper arm UBERON:0004255 forelimb stylopod muscle prolog Any muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition]. OBOL:automatic muscle of upper arm MA:0000606 upper arm muscle MA:0000606 wing stylopod muscle NCBITaxon:8782 OBOL:automatic muscle of arm FMA:37370 skeletal muscle of upper arm EMAPA:19107 Any muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]. the FMA class 'muscle of leg' belongs here, do not move[cjm] See notes on UBERON:0000978 for possible terminological confusion over term 'leg' EMAPA:19318 FMA:22471 MA:0000678 lower leg muscle uberon calf muscle muscle of leg UBERON:0004256 hindlimb zeugopod muscle prolog Any muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]. OBOL:automatic lower leg muscle MA:0000678 calf muscle OBOL:automatic muscle of leg FMA:22471 A blood vessel that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:37299 MA:0000681 blood vessel of stylopod of hind limb blood vessel of stylopod of hindlimb blood vessel of thigh blood vessel of upper leg hind limb stylopod blood vessel hindlimb stylopod blood vessel thigh blood vessel uberon UBERON:0004257 upper leg blood vessel A blood vessel that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37299 MA:th blood vessel of stylopod of hind limb OBOL:automatic blood vessel of stylopod of hindlimb OBOL:automatic blood vessel of thigh OBOL:automatic blood vessel of upper leg OBOL:automatic hind limb stylopod blood vessel OBOL:automatic hindlimb stylopod blood vessel OBOL:automatic thigh blood vessel OBOL:automatic A blood vessel that is part of a back [Automatically generated definition]. EMAPA:37243 MA:0000493 blood vessel of back uberon UBERON:0004258 back blood vessel A blood vessel that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37243 MA:th blood vessel of back OBOL:automatic A blood vessel that is part of a lower arm [Automatically generated definition]. EMAPA:37295 MA:0000597 forelimb zeugopod blood vessel uberon UBERON:0004259 lower arm blood vessel A blood vessel that is part of a lower arm [Automatically generated definition]. OBOL:automatic EMAPA:37295 MA:th forelimb zeugopod blood vessel A blood vessel that is part of a forelimb stylopod [Automatically generated definition]. EMAPA:37294 MA:0000603 forelimb stylopod blood vessel uberon UBERON:0004260 upper arm blood vessel A blood vessel that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37294 MA:th forelimb stylopod blood vessel A blood vessel that is part of a lower leg [Automatically generated definition]. EMAPA:37300 MA:0000675 hindlimb zeugopod blood vessel uberon UBERON:0004261 lower leg blood vessel A blood vessel that is part of a lower leg [Automatically generated definition]. OBOL:automatic EMAPA:37300 MA:th hindlimb zeugopod blood vessel A zone of skin that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:18159 FMA:37790 MA:0000686 hind limb stylopod skin hindlimb stylopod skin skin of upper leg uberon skin of thigh thigh skin UBERON:0004262 upper leg skin A zone of skin that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic hind limb stylopod skin OBOL:automatic hindlimb stylopod skin OBOL:automatic skin of upper leg OBOL:automatic skin of thigh OBOL:automatic thigh skin OBOL:automatic A zone of skin that is part of a forelimb stylopod [Automatically generated definition]. EMAPA:18062 FMA:37721 MA:0000608 arm stylopod skin skin of arm stylopod skin of upper arm uberon UBERON:0004263 upper arm skin A zone of skin that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic arm stylopod skin OBOL:automatic skin of arm stylopod OBOL:automatic skin of upper arm OBOL:automatic A zone of skin that is part of a lower leg [Automatically generated definition]. EMAPA:18156 MA:0000680 hind limb middle limb segment skin hind limb zeugopod skin uberon UBERON:0004264 lower leg skin A zone of skin that is part of a lower leg [Automatically generated definition]. OBOL:automatic hind limb middle limb segment skin OBOL:automatic hind limb zeugopod skin OBOL:automatic A myocardium that is part of a outflow tract [Automatically generated definition]. (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] EHDAA2:0001358 EMAPA:35623 MA:0000489 VHOG:0000603 cardiac muscle of outflow tract heart muscle of outflow tract heart myocardium of outflow tract muscle of heart of outflow tract myocardium of outflow tract outflow tract cardiac muscle outflow tract heart muscle outflow tract heart myocardium outflow tract muscle of heart uberon UBERON:0004265 outflow tract myocardium A myocardium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] 2012-09-17 VHOG:0000603 VHOG PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997) cardiac muscle of outflow tract OBOL:automatic heart muscle of outflow tract OBOL:automatic heart myocardium of outflow tract OBOL:automatic muscle of heart of outflow tract OBOL:automatic myocardium of outflow tract OBOL:automatic outflow tract cardiac muscle OBOL:automatic outflow tract heart muscle OBOL:automatic outflow tract heart myocardium OBOL:automatic outflow tract muscle of heart OBOL:automatic A portion of connective tissue that is part of a hindlimb stylopod [Automatically generated definition]. EMAPA:37325 MA:0000683 uberon UBERON:0004266 upper leg connective tissue A portion of connective tissue that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37325 MA:th A portion of connective tissue that is part of a back [Automatically generated definition]. EMAPA:37256 MA:0000495 uberon mesenchyne of back UBERON:0004267 back connective tissue A portion of connective tissue that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37256 MA:th mesenchyne of back OBOL:automatic A portion of connective tissue that is part of a lower arm [Automatically generated definition]. EMAPA:37319 MA:0000599 uberon UBERON:0004268 lower arm connective tissue A portion of connective tissue that is part of a lower arm [Automatically generated definition]. OBOL:automatic EMAPA:37319 MA:th A portion of connective tissue that is part of a forelimb stylopod [Automatically generated definition]. EMAPA:37317 MA:0000605 uberon UBERON:0004269 upper arm connective tissue A portion of connective tissue that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic EMAPA:37317 MA:th A portion of connective tissue that is part of a lower leg [Automatically generated definition]. EMAPA:37327 MA:0000677 uberon UBERON:0004270 lower leg connective tissue A portion of connective tissue that is part of a lower leg [Automatically generated definition]. OBOL:automatic EMAPA:37327 MA:th A pericardium that is part of a outflow tract [Automatically generated definition]. EMAPA:37707 MA:0000491 pericardium of outflow tract uberon UBERON:0004271 outflow tract pericardium A pericardium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic EMAPA:37707 MA:th pericardium of outflow tract OBOL:automatic A cranial suture that is part of a cartilaginous joint [Automatically generated definition]. EMAPA:37463 MA:0001498 articulatio cartilaginea cranial suture articulatio cartilaginea cranial sutures articulatio cartilaginea cranial sutures set articulatio cartilaginea cranium suture articulatio cartilaginea suture of cranium cartilaginous joint cranial suture cartilaginous joint cranial sutures cartilaginous joint cranial sutures set cartilaginous joint cranium suture cartilaginous joint suture of cranium cranial suture of articulatio cartilaginea cranial suture of cartilaginous joint cranial sutures of articulatio cartilaginea cranial sutures of cartilaginous joint cranial sutures set of articulatio cartilaginea cranial sutures set of cartilaginous joint cranium suture of articulatio cartilaginea cranium suture of cartilaginous joint suture of cranium of articulatio cartilaginea suture of cranium of cartilaginous joint uberon UBERON:0004273 cartilaginous joint suture A cranial suture that is part of a cartilaginous joint [Automatically generated definition]. OBOL:automatic EMAPA:37463 MA:th articulatio cartilaginea cranial suture OBOL:automatic articulatio cartilaginea cranial sutures OBOL:automatic articulatio cartilaginea cranial sutures set OBOL:automatic articulatio cartilaginea cranium suture OBOL:automatic articulatio cartilaginea suture of cranium OBOL:automatic cartilaginous joint cranial suture OBOL:automatic cartilaginous joint cranial sutures OBOL:automatic cartilaginous joint cranial sutures set OBOL:automatic cartilaginous joint cranium suture OBOL:automatic cartilaginous joint suture of cranium OBOL:automatic cranial suture of articulatio cartilaginea OBOL:automatic cranial suture of cartilaginous joint OBOL:automatic cranial sutures of articulatio cartilaginea OBOL:automatic cranial sutures of cartilaginous joint OBOL:automatic cranial sutures set of articulatio cartilaginea OBOL:automatic cranial sutures set of cartilaginous joint OBOL:automatic cranium suture of articulatio cartilaginea OBOL:automatic cranium suture of cartilaginous joint OBOL:automatic suture of cranium of articulatio cartilaginea OBOL:automatic suture of cranium of cartilaginous joint OBOL:automatic A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition]. EHDAA2:0004450 FMA:242815 MA:0000962 NCIT:C49248 UMLS:C1711323 chorioid plexus of cerebral hemisphere epithelial tissue of lateral ventricle chorioid plexus of cerebral hemisphere epithelium of lateral ventricle choroid plexus epithelial tissue of lateral ventricle choroid plexus epithelium of lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere of lateral ventricle epithelial tissue of choroid plexus of lateral ventricle epithelium of chorioid plexus of cerebral hemisphere of lateral ventricle epithelium of choroid plexus of lateral ventricle lateral ventricle chorioid plexus of cerebral hemisphere epithelial tissue lateral ventricle chorioid plexus of cerebral hemisphere epithelium lateral ventricle choroid plexus epithelial tissue lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere lateral ventricle epithelial tissue of choroid plexus lateral ventricle epithelium of chorioid plexus of cerebral hemisphere lateral ventricle epithelium of choroid plexus uberon UBERON:0004274 lateral ventricle choroid plexus epithelium A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition]. OBOL:automatic UMLS:C1711323 ncithesaurus:Choroid_Plexus_Epithelium_of_the_Lateral_Ventricle chorioid plexus of cerebral hemisphere epithelial tissue of lateral ventricle OBOL:automatic chorioid plexus of cerebral hemisphere epithelium of lateral ventricle OBOL:automatic choroid plexus epithelial tissue of lateral ventricle OBOL:automatic choroid plexus epithelium of lateral ventricle OBOL:automatic epithelial tissue of chorioid plexus of cerebral hemisphere of lateral ventricle OBOL:automatic epithelial tissue of choroid plexus of lateral ventricle OBOL:automatic epithelium of chorioid plexus of cerebral hemisphere of lateral ventricle OBOL:automatic epithelium of choroid plexus of lateral ventricle OBOL:automatic lateral ventricle chorioid plexus of cerebral hemisphere epithelial tissue OBOL:automatic lateral ventricle chorioid plexus of cerebral hemisphere epithelium OBOL:automatic lateral ventricle choroid plexus epithelial tissue OBOL:automatic lateral ventricle epithelial tissue of chorioid plexus of cerebral hemisphere OBOL:automatic lateral ventricle epithelial tissue of choroid plexus OBOL:automatic lateral ventricle epithelium of chorioid plexus of cerebral hemisphere OBOL:automatic lateral ventricle epithelium of choroid plexus OBOL:automatic A choroid plexus epithelium that is part of a fourth ventricle [Automatically generated definition]. FMA:242823 MA:0000984 NCIT:C49230 UMLS:C1707392 chorioid plexus of cerebral hemisphere epithelial tissue of fourth ventricle chorioid plexus of cerebral hemisphere epithelium of fourth ventricle choroid plexus epithelial tissue of fourth ventricle choroid plexus epithelium of fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere of fourth ventricle epithelial tissue of choroid plexus of fourth ventricle epithelium of chorioid plexus of cerebral hemisphere of fourth ventricle epithelium of choroid plexus of fourth ventricle fourth ventricle chorioid plexus of cerebral hemisphere epithelial tissue fourth ventricle chorioid plexus of cerebral hemisphere epithelium fourth ventricle choroid plexus epithelial tissue fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere fourth ventricle epithelial tissue of choroid plexus fourth ventricle epithelium of chorioid plexus of cerebral hemisphere fourth ventricle epithelium of choroid plexus uberon UBERON:0004276 fourth ventricle choroid plexus epithelium A choroid plexus epithelium that is part of a fourth ventricle [Automatically generated definition]. OBOL:automatic UMLS:C1707392 ncithesaurus:Choroid_Plexus_Epithelium_of_the_Fourth_Ventricle chorioid plexus of cerebral hemisphere epithelial tissue of fourth ventricle OBOL:automatic chorioid plexus of cerebral hemisphere epithelium of fourth ventricle OBOL:automatic choroid plexus epithelial tissue of fourth ventricle OBOL:automatic choroid plexus epithelium of fourth ventricle OBOL:automatic epithelial tissue of chorioid plexus of cerebral hemisphere of fourth ventricle OBOL:automatic epithelial tissue of choroid plexus of fourth ventricle OBOL:automatic epithelium of chorioid plexus of cerebral hemisphere of fourth ventricle OBOL:automatic epithelium of choroid plexus of fourth ventricle OBOL:automatic fourth ventricle chorioid plexus of cerebral hemisphere epithelial tissue OBOL:automatic fourth ventricle chorioid plexus of cerebral hemisphere epithelium OBOL:automatic fourth ventricle choroid plexus epithelial tissue OBOL:automatic fourth ventricle epithelial tissue of chorioid plexus of cerebral hemisphere OBOL:automatic fourth ventricle epithelial tissue of choroid plexus OBOL:automatic fourth ventricle epithelium of chorioid plexus of cerebral hemisphere OBOL:automatic fourth ventricle epithelium of choroid plexus OBOL:automatic A muscle that is part of the eye region. AAO:0000156 EMAPA:35335 MA:0000271 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA uberon UBERON:0004277 eye muscle MA A muscle that is part of the eye region. OBOL:automatic Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 EMAPA:17213 FMA:23875 GAID:177 MA:0003006 MAT:0000032 MESH:D012863 MIAA:0000032 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA VSAO:0000026 XAO:0004053 galen:Skeleton set of all bones set of bones of body uberon UBERON:0004288 skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] 2012-08-14 VSAO:0000026 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 The bilaminar epithelium formed from the myotome and dermatome. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] Portion of somites that gives rise to dermis and muscles.[AAO] all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] AAO:0010572 AEO:0000214 EHDAA2:0003259 EMAPA:31109 FMA:295654 NCIT:C34140 TAO:0001513 UMLS:C1511786 VHOG:0000676 ZFA:0001513 uberon dermamyotome dermomyotomes UBERON:0004290 dermomyotome AEO AEO EHDAA2 ZFA The bilaminar epithelium formed from the myotome and dermatome. AEO:0000214 Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] 2012-08-14 TAO:0001513 TAO ZFIN:curator Portion of somites that gives rise to dermis and muscles.[AAO] 2012-06-20 AAO:0010572 AAO AAO:EJS all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] 2012-09-17 VHOG:0000676 VHOG DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006) UMLS:C1511786 ncithesaurus:Dermomyotome dermamyotome VHOG:0000676 dermomyotomes VHOG:0000676 A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone rudimentary heart uberon UBERON:0004291 heart rudiment A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] 2012-08-14 TAO:0000115 TAO ZFIN:curator heart cone GO:0003313 rudimentary heart ZFA:0000115 Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP] EMAPA:36645 FMA:9496 cardiac fibrous skeleton fibrous skeleton of heart heart fibrous skeleton skeleton of heart uberon anulus fibrosus dexter cordis anulus fibrosus sinister cordis trigona fibrosa trigonum fibrosum dextrum cordis trigonum fibrosum sinistrum cordis UBERON:0004292 cardiac skeleton http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. GO:0003204 cardiac fibrous skeleton EMAPA:36645 heart fibrous skeleton GO:0003204 skeleton of heart FMA:9496 anulus fibrosus dexter cordis anulus fibrosus sinister cordis trigona fibrosa trigonum fibrosum dextrum cordis trigonum fibrosum sinistrum cordis A nerve that is part of a parasympathetic nervous system [Automatically generated definition]. EHDAA2:0001401 EMAPA:17271 MA:0000224 VHOG:0000641 nerve of parasympathetic nervous system uberon UBERON:0004293 parasympathetic nerve NCBIBook:NBK10065 NCBIBook:NBK10065 A nerve that is part of a parasympathetic nervous system [Automatically generated definition]. OBOL:automatic nerve of parasympathetic nervous system OBOL:automatic A nerve trunk that is part of a sympathetic nervous system [Automatically generated definition]. EHDAA2:0001970 EMAPA:35845 MA:0000227 nerve trunk of sympathetic nervous system nerve trunk of sympathetic part of autonomic division of nervous system sympathetic nervous system nerve trunk uberon UBERON:0004295 sympathetic nerve trunk A nerve trunk that is part of a sympathetic nervous system [Automatically generated definition]. OBOL:automatic nerve trunk of sympathetic nervous system OBOL:automatic nerve trunk of sympathetic part of autonomic division of nervous system OBOL:automatic sympathetic nervous system nerve trunk OBOL:automatic A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. EMAPA:37582 MA:0001826 smooth muscle of lymph vessel of respiratory system uberon UBERON:0004296 respiratory system lymphatic vessel smooth muscle A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37582 MA:th smooth muscle of lymph vessel of respiratory system OBOL:automatic A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. EMAPA:37573 MA:0001806 smooth muscle tissue of blood vessel of respiratory system uberon UBERON:0004297 respiratory system blood vessel smooth muscle A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37573 MA:th smooth muscle tissue of blood vessel of respiratory system OBOL:automatic Distal-most phalanx within a digit. In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans. AAO:0010676 EMAPA:35287 MA:0002914 phalanx distalis terminal phalanx ungual phalanx uberon phalanx distalis UBERON:0004300 distal phalanx http://upload.wikimedia.org/wikipedia/commons/a/ab/Scheme_human_hand_bones-en.svg Distal-most phalanx within a digit. phalanx distalis terminal phalanx AAO:0010676 ungual phalanx phalanx distalis A phalanx located between proximal and distal phalanges. consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin in some groups such as whales, there are multiple intermediate phalanges AAO:0010677 EMAPA:35572 MA:0002915 intermediate phalanx uberon medial phalanx penultimate phalanx phalanx 2 phalanx II UBERON:0004301 middle phalanx A phalanx located between proximal and distal phalanges. Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin WP penultimate phalanx AAO:0010677 Proximal-most phalanx within a digit. Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone) 1 AAO:0010680 EMAPA:35716 MA:0002916 phalanx 1 phalanx I proximal-most phalanx uberon UBERON:0004302 proximal phalanx Proximal-most phalanx within a digit. Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone) WP proximal-most phalanx AAO:0010680 A distal phalanx that is part of a hand digit 5 [Automatically generated definition]. FMA:23949 5th digit of hand distal phalanx 5th finger distal phalanx distal phalanx of 5th digit of hand distal phalanx of 5th finger distal phalanx of fifth digit of hand distal phalanx of fifth finger distal phalanx of little finger distal phalanx of manual digit V fifth distal phalanx of hand fifth finger distal phalanx hand digit 5 distal phalanx uberon UBERON:0004314 distal phalanx of manual digit 5 A distal phalanx that is part of a hand digit 5 [Automatically generated definition]. OBOL:automatic 5th digit of hand distal phalanx OBOL:automatic 5th finger distal phalanx OBOL:automatic distal phalanx of 5th digit of hand OBOL:automatic distal phalanx of 5th finger OBOL:automatic distal phalanx of fifth digit of hand FMA:23949 distal phalanx of fifth finger OBOL:automatic distal phalanx of little finger FMA:23949 distal phalanx of manual digit V fifth distal phalanx of hand FMA:23949 fifth finger distal phalanx OBOL:automatic hand digit 5 distal phalanx OBOL:automatic A distal phalanx that is part of a foot digit 1 [Automatically generated definition]. FMA:32627 distal phalanx of big toe distal phalanx of first digit of foot distal phalanx of foot digit 1 distal phalanx of great toe distal phalanx of hallux distal phalanx of pedal digit I first distal phalanx of foot foot digit 1 distal phalanx hallux distal phalanx uberon UBERON:0004315 distal phalanx of pedal digit 1 A distal phalanx that is part of a foot digit 1 [Automatically generated definition]. OBOL:automatic distal phalanx of big toe FMA:32627 distal phalanx of first digit of foot FMA:32627 distal phalanx of foot digit 1 OBOL:automatic distal phalanx of great toe FMA:32627 distal phalanx of hallux OBOL:automatic distal phalanx of pedal digit I first distal phalanx of foot FMA:32627 foot digit 1 distal phalanx OBOL:automatic hallux distal phalanx OBOL:automatic A distal phalanx that is part of a foot digit 5 [Automatically generated definition]. FMA:32631 5th toe distal phalanx distal phalanx of 5th toe distal phalanx of fifth digit of foot distal phalanx of fifth toe distal phalanx of foot digit 5 distal phalanx of little toe distal phalanx of pedal digit V distal phalanx of the 5th toe fifth distal phalanx of foot foot digit 5 distal phalanx uberon UBERON:0004319 distal phalanx of pedal digit 5 A distal phalanx that is part of a foot digit 5 [Automatically generated definition]. OBOL:automatic 5th toe distal phalanx OBOL:automatic distal phalanx of 5th toe OBOL:automatic distal phalanx of fifth digit of foot FMA:32631 distal phalanx of fifth toe FMA:32631 distal phalanx of foot digit 5 OBOL:automatic distal phalanx of little toe FMA:32631 distal phalanx of pedal digit V distal phalanx of the 5th toe OBOL:automatic fifth distal phalanx of foot FMA:32631 foot digit 5 distal phalanx OBOL:automatic A middle phalanx that is part of a hand digit 5 [Automatically generated definition]. FMA:23936 5th digit of hand intermediate phalanx 5th digit of hand middle phalanx 5th finger intermediate phalanx 5th finger middle phalanx fifth finger intermediate phalanx fifth finger middle phalanx fifth middle phalanx of hand hand digit 5 intermediate phalanx hand digit 5 middle phalanx intermediate phalanx of 5th digit of hand intermediate phalanx of 5th finger intermediate phalanx of fifth finger intermediate phalanx of hand digit 5 middle phalanx of 5th digit of hand middle phalanx of 5th finger middle phalanx of fifth digit of hand middle phalanx of fifth finger middle phalanx of little finger middle phalanx of manual digit V uberon UBERON:0004323 middle phalanx of manual digit 5 A middle phalanx that is part of a hand digit 5 [Automatically generated definition]. OBOL:automatic 5th digit of hand intermediate phalanx OBOL:automatic 5th digit of hand middle phalanx OBOL:automatic 5th finger intermediate phalanx OBOL:automatic 5th finger middle phalanx OBOL:automatic fifth finger intermediate phalanx OBOL:automatic fifth finger middle phalanx OBOL:automatic fifth middle phalanx of hand FMA:23936 hand digit 5 intermediate phalanx OBOL:automatic hand digit 5 middle phalanx OBOL:automatic intermediate phalanx of 5th digit of hand OBOL:automatic intermediate phalanx of 5th finger OBOL:automatic intermediate phalanx of fifth finger OBOL:automatic intermediate phalanx of hand digit 5 OBOL:automatic middle phalanx of 5th digit of hand OBOL:automatic middle phalanx of 5th finger OBOL:automatic middle phalanx of fifth digit of hand FMA:23936 middle phalanx of fifth finger OBOL:automatic middle phalanx of little finger OBOL:automatic middle phalanx of manual digit V A middle phalanx that is part of a pedal digit 5 [Automatically generated definition]. FMA:230984 5th toe intermediate phalanx 5th toe middle phalanx foot digit 5 intermediate phalanx foot digit 5 middle phalanx intermediate phalanx of 5th toe intermediate phalanx of foot digit 5 middle phalanx of 5th toe middle phalanx of foot digit 5 middle phalanx of little toe middle phalanx of pedal digit V middle phalanx of the 5th toe uberon UBERON:0004327 middle phalanx of pedal digit 5 A middle phalanx that is part of a pedal digit 5 [Automatically generated definition]. OBOL:automatic 5th toe intermediate phalanx OBOL:automatic 5th toe middle phalanx OBOL:automatic foot digit 5 intermediate phalanx OBOL:automatic foot digit 5 middle phalanx OBOL:automatic intermediate phalanx of 5th toe OBOL:automatic intermediate phalanx of foot digit 5 OBOL:automatic middle phalanx of 5th toe OBOL:automatic middle phalanx of foot digit 5 OBOL:automatic middle phalanx of little toe OBOL:automatic middle phalanx of pedal digit V middle phalanx of the 5th toe OBOL:automatic A proximal phalanx that is part of a hand digit 5 [Automatically generated definition]. FMA:23922 5th digit of hand proximal phalanx 5th finger proximal phalanx fifth finger proximal phalanx fifth proximal phalanx of hand hand digit 5 proximal phalanx manual digit 5 proximal phalanx manual phalanx V-1 proximal phalanx of 5th digit of hand proximal phalanx of 5th finger proximal phalanx of fifth digit of hand proximal phalanx of fifth finger proximal phalanx of little finger proximal phalanx of manual digit V uberon UBERON:0004331 proximal phalanx of manual digit 5 A proximal phalanx that is part of a hand digit 5 [Automatically generated definition]. OBOL:automatic 5th digit of hand proximal phalanx OBOL:automatic 5th finger proximal phalanx OBOL:automatic fifth finger proximal phalanx OBOL:automatic fifth proximal phalanx of hand FMA:23922 hand digit 5 proximal phalanx OBOL:automatic manual digit 5 proximal phalanx PHENOSCAPE:wd manual phalanx V-1 PHENOSCAPE:wd proximal phalanx of 5th digit of hand OBOL:automatic proximal phalanx of 5th finger OBOL:automatic proximal phalanx of fifth digit of hand FMA:23922 proximal phalanx of fifth finger OBOL:automatic proximal phalanx of little finger FMA:23922 proximal phalanx of manual digit V A proximal phalanx that is part of a pedal digit 1 [Automatically generated definition]. FMA:43252 foot digit 1 proximal phalanx hallux proximal phalanx pedal phalanx I-1 predal digit 1 proximal phalanx proximal phalanx of big toe proximal phalanx of foot digit 1 proximal phalanx of great toe proximal phalanx of hallux proximal phalanx of pedal digit I proximal phalanx of the 1st toe uberon UBERON:0004332 proximal phalanx of pedal digit 1 A proximal phalanx that is part of a pedal digit 1 [Automatically generated definition]. OBOL:automatic foot digit 1 proximal phalanx OBOL:automatic hallux proximal phalanx OBOL:automatic pedal phalanx I-1 PHENOSCAPE:wd predal digit 1 proximal phalanx PHENOSCAPE:wd proximal phalanx of big toe FMA:43252 proximal phalanx of foot digit 1 OBOL:automatic proximal phalanx of great toe FMA:43252 proximal phalanx of hallux OBOL:automatic proximal phalanx of pedal digit I A proximal phalanx that is part of a pedal digit 5 [Automatically generated definition]. FMA:32621 5th toe proximal phalanx fifth proximal phalanx of foot foot digit 5 proximal phalanx pedal phalanx V-1 predal digit 5 proximal phalanx proximal phalanx of 5th toe proximal phalanx of fifth digit of foot proximal phalanx of fifth toe proximal phalanx of foot digit 5 proximal phalanx of little toe proximal phalanx of pedal digit V proximal phalanx of the 5th toe uberon UBERON:0004336 proximal phalanx of pedal digit 5 A proximal phalanx that is part of a pedal digit 5 [Automatically generated definition]. OBOL:automatic 5th toe proximal phalanx OBOL:automatic fifth proximal phalanx of foot FMA:32621 foot digit 5 proximal phalanx OBOL:automatic pedal phalanx V-1 PHENOSCAPE:wd predal digit 5 proximal phalanx PHENOSCAPE:wd proximal phalanx of 5th toe OBOL:automatic proximal phalanx of fifth digit of foot FMA:32621 proximal phalanx of fifth toe FMA:32621 proximal phalanx of foot digit 5 OBOL:automatic proximal phalanx of little toe OBOL:automatic proximal phalanx of pedal digit V A distal phalanx that is part of a hand digit 1 [Automatically generated definition]. The human pollical distal phalanx (PDP) has a pronounced insertion for the flexor pollicis longus (asymmetric towards the radial side), an ungual fossa, and a pair of dissymmetric ungual spines (the ulnar being more prominent). This asymmetry is necessary to ensure that the thumb pulp is always facing the pulps of the other digits, an osteological configuration which provides the maximum contact surface with held objects. FMA:23945 PDP distal phalanx of first digit of hand distal phalanx of manual digit I distal phalanx of thumb first distal phalanx of hand manual digit 1 distal phalanx pollical distal phalanx thumb distal phalanx uberon UBERON:0004337 distal phalanx of manual digit 1 A distal phalanx that is part of a hand digit 1 [Automatically generated definition]. OBOL:automatic The human pollical distal phalanx (PDP) has a pronounced insertion for the flexor pollicis longus (asymmetric towards the radial side), an ungual fossa, and a pair of dissymmetric ungual spines (the ulnar being more prominent). This asymmetry is necessary to ensure that the thumb pulp is always facing the pulps of the other digits, an osteological configuration which provides the maximum contact surface with held objects. WP PDP distal phalanx of first digit of hand FMA:23945 distal phalanx of manual digit I distal phalanx of thumb OBOL:automatic first distal phalanx of hand FMA:23945 manual digit 1 distal phalanx PHENOSCAPE:wd pollical distal phalanx thumb distal phalanx OBOL:automatic A proximal phalanx that is part of a hand digit 1 [Automatically generated definition]. FMA:23918 first proximal phalanx of hand manual digit 1 proximal phalanx manual phalanx I-1 proximal phalanx of first digit of hand proximal phalanx of manual digit I proximal phalanx of thumb thumb proximal uberon UBERON:0004338 proximal phalanx of manual digit 1 A proximal phalanx that is part of a hand digit 1 [Automatically generated definition]. OBOL:automatic first proximal phalanx of hand FMA:23918 manual digit 1 proximal phalanx PHENOSCAPE:wd manual phalanx I-1 PHENOSCAPE:wd proximal phalanx of first digit of hand FMA:23918 proximal phalanx of manual digit I proximal phalanx of thumb OBOL:automatic thumb proximal OBOL:automatic Upper part of skull, consisting of parietals, frontals, post-parietals, and in some species the squamosal and a portion of the alisphenoid We follow http://www.ncbi.nlm.nih.gov/pubmed/11523816 (Morriss-Kay) in definingenumerating the components of the skull vault. Note that there is a conflict with Kardong; e.g. in fig 7.10, Kardong places the squamosal in the temporal series. We cannot place the vault as entirely part of the dermatocranium as it has a small splanchnocranium contribution and a sclerotomal contribution The earliest tetrapods arose from rhipidistian ancestors and retained many of their skull features, including most of the bones of the dermatocranium.[well established][VHOG] EHDAA2:0002167 EHDAA:9538 EMAPA:18016 FMA:52800 NCIT:C81188 UMLS:C0205950 VHOG:0000331 ZFA:0005606 calva cranial vault skull vault skull roof uberon calvaria calvarium skullcap UBERON:0004339 Terminology notes. we include calvarium as a synonym, but Gray's Anatomy's list includes the Ethmoid and Sphenoid bone in the Calvaria. Some books (and HPO) state that calvaria consists of just the frontal bone, parietal bone, temporal bone, and occipital bone. Note vault may not be precisely equivalent to calvaria vault of skull small pharyngeal arch and sclerotomal contribution Upper part of skull, consisting of parietals, frontals, post-parietals, and in some species the squamosal and a portion of the alisphenoid MP:0000076 The earliest tetrapods arose from rhipidistian ancestors and retained many of their skull features, including most of the bones of the dermatocranium.[well established][VHOG] 2012-09-17 VHOG:0000331 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256 UMLS:C0205950 ncithesaurus:Skullcap calva FMA:52800 cranial vault ZFA:0005606 calvaria ZFA:0005606 skullcap ZFA:0005606 A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]. A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG] Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] allantoic a diverticulum of the hindgut endoderm [ISBN:0073040584 (Vertebrates, Kardong)] part_of embryo in EHDAA2 - note differences in humans BTO:0000474 EHDAA2:0001504 EMAPA:16107 EMAPA_RETIRED:16084 MESH:A16.254.403.147 NCIT:C34101 RETIRED_EHDAA2:0000114 UMLS:C0002084 VHOG:0000738 uberon allantoic bud UBERON:0004340 allantois http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png EHDAA2-modified Hymans hindgut diverticulum endoderm ISBN:0073040584 ISBN:0073040584 A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]. VHOG:0000738 A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG] 2012-09-17 VHOG:0000738 VHOG Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] 2012-09-17 VHOG:0000738 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187 part_of embryo in EHDAA2 - note differences in humans EHDAA2 UMLS:C0002084 ncithesaurus:Allantois allantoic bud EMAPA:16107 The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP] (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 EHDAA2:0001525 EHDAA:185 EMAPA:16072 FMA:293110 NCIT:C28402 UMLS:C0033153 VHOG:0001202 primitive streak - blastopore - germ ring uberon UBERON:0004341 primitive streak http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png EHDAA2 The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP] MP:0002231 (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] 2012-09-17 VHOG:0001202 VHOG PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139 VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 VHOG UMLS:C0033153 ncithesaurus:Primitive_Streak primitive streak - blastopore - germ ring VHOG:0001202 outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition distinction between trophectoderm and trophoblast unclear/inconsistent in many sources The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG] (...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG] trophectodermal BTO has this has part of the trophoblast BTO:0001840 EHDAA2:0002091 EHDAA:56 EMAPA:16046 VHOG:0000979 uberon UBERON:0004345 trophectoderm EHDAA2 EHDAA2 EHDAA2 outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition MP:0005028 The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG] 2012-09-17 VHOG:0000979 VHOG (...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000979 VHOG ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106 BTO has this has part of the trophoblast BTO An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. Early outgrowth of presumptive limb.[AAO] AAO:0010375 BTO:0001640 EMAPA:35944 FMA:296780 GAID:1307 MESH:A16.254.462 NCIT:C34203 UMLS:C0282505 XAO:0003161 limb buds limbbud uberon gemmae membrorum UBERON:0004347 developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm limb bud ISBN:9780878932504 An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. ISBN:9780878932504 MP:0005650 Early outgrowth of presumptive limb.[AAO] 2012-06-20 AAO:0010375 AAO AAO:EJS UMLS:C0282505 ncithesaurus:Limb_Bud limb buds limbbud GO:0060174 gemmae membrorum The embryonic structure that gives rise to the corneal ectoderm EHDAA:938 EMAPA:16322 RETIRED_EHDAA2:0001308 VHOG:0001296 uberon UBERON:0004348 optic eminence The embryonic structure that gives rise to the corneal ectoderm MP:0006305 multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. note that media, dorsal fins etc have AERs. Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] Proliferative region that is part of the developing fin fold or fin.[TAO] relationship loss: subclass proliferative region (TAO:0000098)[TAO] The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop AAO:0010760 EMAPA:32744 NCIT:C34109 TAO:0002146 UMLS:C1516037 XAO:0004121 ZFA:0001702 apical epidermal ridge uberon AER crista ectodermalis apicalis UBERON:0004356 apical ectodermal ridge http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. MP:0001676 Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] 2012-06-20 AAO:0010760 AAO AAO:EJS Proliferative region that is part of the developing fin fold or fin.[TAO] 2012-08-14 TAO:0002146 TAO ZFIN:curator relationship loss: subclass proliferative region (TAO:0000098)[TAO] 2012-08-14 TAO:0002146 TAO The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold UMLS:C1516037 ncithesaurus:Apical_Ectodermal_Ridge apical epidermal ridge XAO:0004121 AER MP:0001676 crista ectodermalis apicalis An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] VHOG:0001258 limb - fin bud paired appendage bud paired limb/fin bud uberon UBERON:0004357 Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056] paired limb/fin bud An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. ISBN:9780878932504 MP:0005650 The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] 2012-09-17 VHOG:0001258 VHOG DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001) limb - fin bud VHOG:0001258 paired limb/fin bud VHOG:0001258 The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 1 AAO:0010364 CALOHA:TS-2089 EHDAA2:0000006 EHDAA:573 EMAPA:16118 FMA:293019 MFMO:0000095 NCIT:C34175 TAO:0001595 UMLS:C1517197 VHOG:0000296 XAO:0000097 ZFA:0001612 1st pharyngeal arch branchial arch 1 first branchial arch first pharyngeal arch first visceral arch mandibular arch visceral arch 1 uberon 1st arch 1st visceral arch arcus pharyngeus primus UBERON:0004362 pharyngeal arch 1 http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010364 AAO XAO:EJS the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery MP:0006337,MGI:smb A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000296 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) UMLS:C1517197 ncithesaurus:First_Pharyngeal_Arch branchial arch 1 first branchial arch first visceral arch visceral arch 1 1st arch EHDAA2:0000006 1st visceral arch VHOG:0000296 arcus pharyngeus primus One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] add specific artery derivatives Do not confuse with arch of aorta. Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches UBERON:0004342 AAO:0010414 EFO:0003695 EHDAA2:0000186 EHDAA:398 EHDAA:7327 EMAPA:16684 NCIT:C32123 TAO:0005004 UMLS:C0003489 VHOG:0000122 XAO:0000341 ZFA:0005004 PAA aortic arch aortic arches branchial aortic arches branchial arch artery embryonic aortic arch artery pharyngeal arch artery uberon a. arcuum pharyngeorum aortic arch artery arteriae arcuum pharyngeorum branchial aortic arches pharyngeal arch arteries pharyngeal arch artery UBERON:0004363 pharyngeal arch artery http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png ZFA One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] MP:0002672 Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] 2012-09-17 VHOG:0000122 VHOG When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000122 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 UMLS:C0003489 ncithesaurus:Aortic_Arch PAA MP:0002672 aortic arch ZFA:0005004 aortic arches ZFA:0005004 branchial aortic arches ZFIN:ZDB-PUB-080512-6 branchial arch artery EMAPA:16684 embryonic aortic arch artery EMAPA:16684 MP:0002672 pharyngeal arch artery MP:0002672 a. arcuum pharyngeorum aortic arch artery EMAPA:16684 arteriae arcuum pharyngeorum branchial aortic arches ZFA:0005004 ZFIN:ZDB-PUB-080512-6 pharyngeal arch arteries pharyngeal arch artery VHOG:0000122 blood vessel that is connected to the yolk sac. EMAPA:36494 uberon UBERON:0004365 vitelline blood vessel blood vessel that is connected to the yolk sac. A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] EMAPA:18804 FMA:58309 GAID:894 MA:0001246 MESH:D003886 NCIT:C32454 TAO:0002157 UMLS:C0011665 ZFA:0001686 Descemet membrane Descemet's posterior elastic lamina lamina limitans posterior lamina limitans posterior corneae posterior limiting lamina posterior limiting lamina of cornea posterior limiting membrane uberon UBERON:0004367 The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed) Descemet's membrane https://github.com/obophenotype/uberon/issues/15 Cline et al lexical A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. MP:0004285 Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] 2016-05-01 TAO:0002157 ZFIN ORCiD:0000-0001-9114-8737 ZFIN:ZDB-PUB-061010-3 UMLS:C0011665 ncithesaurus:Descemet_s_Membrane Descemet's posterior elastic lamina FMA:58309 lamina limitans posterior FMA:58309 lamina limitans posterior corneae FMA:58309 FMA:TA posterior limiting lamina MA:0001246 posterior limiting lamina of cornea FMA:58309 posterior limiting membrane ZFA:0001686 A continuous cartilaginous formation in mesenchyme of the second pharyngeal arch in the embryo. The longer cranial or styloid segment is continuous with the otic capsule; its inferior end is angulated and is situated very close to the oropharynx. The smaller caudal segment is in contact with the body and greater horn of the hyoid cartilaginous structure Classically defined as: a structure... develop the stapes, the styloid processes, the stylohyoid ligaments, and the lesser cornua of the hyoid bone; its proximal end gives rise to the stylohyoid ligament. Relationship to stapes disputed. in EHDAA2 this also develops from 3rd arch Mes from NC EHDAA2:0000793 EMAPA:17622 FMA:295800 Reichert cartilage hyaloid cartilage hyoid cartilage second branchial arch cartilage second pharyngeal arch cartilage uberon UBERON:0004368 Reichert's cartilage EHDAA2 A continuous cartilaginous formation in mesenchyme of the second pharyngeal arch in the embryo. The longer cranial or styloid segment is continuous with the otic capsule; its inferior end is angulated and is situated very close to the oropharynx. The smaller caudal segment is in contact with the body and greater horn of the hyoid cartilaginous structure MP:0004916 in EHDAA2 this also develops from 3rd arch Mes from NC EHDAA2 hyaloid cartilage MP:0004916 hyoid cartilage EHDAA2:0000793 second pharyngeal arch cartilage MP:0004916 A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals FMA:58273 MA:0001240 NCIT:C32226 TAO:0002155 UMLS:C0229127 ZFA:0001684 Bowman's anterior elastic lamina Bowman's layer Bowman's membrane anterior elastic lamina anterior limiting lamina anterior limiting lamina of cornea lamina limitans anterior (cornea) lamina limitans anterior corneae uberon Reichert's membrane anterior limiting membrane UBERON:0004370 anterior limiting lamina of cornea lexical A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. ncithesaurus:Bowman_s_Membrane Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] 2012-08-14 TAO:0002155 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0229127 ncithesaurus:Bowman_s_Membrane Bowman's anterior elastic lamina FMA:58273 Bowman's layer FMA:58273 Bowman's membrane FMA:58273 anterior elastic lamina ZFA:0001684 anterior limiting lamina MA:0001240 anterior limiting lamina of cornea FMA:58273 lamina limitans anterior (cornea) FMA:58273 lamina limitans anterior corneae FMA:58273 FMA:TA Reichert's membrane anterior limiting membrane ZFA:0001684 vascular network that is connected to the yolk sac. uberon omphalomesenteric system vitelline bloos vessel system vitelline system UBERON:0004374 vitelline vasculature vascular network that is connected to the yolk sac. omphalomesenteric system vitelline bloos vessel system vitelline system A bone that is part of an appendage [Automatically generated definition]. appendage bone bone of appendage bone of free segment of appendicular skeleton uberon UBERON:0004375 bone of free limb or fin A bone that is part of an appendage [Automatically generated definition]. OBOL:automatic A metaphysis that is in the distal side of a diaphysis. FMA:32824 distal diaphyseal end of long bone uberon UBERON:0004377 distal metaphysis A metaphysis that is in the distal side of a diaphysis. OBOL:automatic distal diaphyseal end of long bone FMA:32824 A metaphysis that is in the proximal side of a diaphysis. FMA:32823 proximal diaphyseal end of long bone uberon UBERON:0004378 proximal metaphysis A metaphysis that is in the proximal side of a diaphysis. OBOL:automatic proximal diaphyseal end of long bone FMA:32823 An epiphysis that is on the distal side of the bone. FMA:32822 distal end of long bone uberon UBERON:0004379 distal epiphysis An epiphysis that is on the distal side of the bone. distal end of long bone FMA:32822 An epiphysis that is on the proximal side of the bone. FMA:32821 proximal end of long bone uberon UBERON:0004380 proximal epiphysis An epiphysis that is on the proximal side of the bone. proximal end of long bone FMA:32821 The collection of all skeletal elements in an individual limb. Skeletal subdivision that is part of the limb.[VSAO] EHDAA2 considers hip and shoulder joints part of limb skeleton. EHDAA2:0002221 EMAPA:32702 VSAO:0000300 free limb skeleton limb skeleton set of bones of limb uberon UBERON:0004381 skeleton of limb The collection of all skeletal elements in an individual limb. Skeletal subdivision that is part of the limb.[VSAO] 2012-08-14 VSAO:0000300 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 EHDAA2 considers hip and shoulder joints part of limb skeleton. EHDAA2 free limb skeleton VSAO:0000300 limb skeleton EHDAA2:0002221 An epiphysis that is part of a humerus [Automatically generated definition]. FMA:32825 humeral epiphysis uberon UBERON:0004382 epiphysis of humerus An epiphysis that is part of a humerus [Automatically generated definition]. OBOL:automatic humeral epiphysis OBOL:automatic An epiphysis that is part of a femur [Automatically generated definition]. EMAPA:37539 FMA:32838 MA:0003056 femoral epiphysis uberon UBERON:0004384 epiphysis of femur An epiphysis that is part of a femur [Automatically generated definition]. OBOL:automatic EMAPA:37539 MA:th femoral epiphysis FMA:32838 An epiphysis that is part of a phalanx of a manus [Automatically generated definition]. FMA:240707 epiphysis of phalanx of finger uberon epiphysis of phalanx of hand UBERON:0004387 epiphysis of phalanx of manus An epiphysis that is part of a phalanx of a manus [Automatically generated definition]. OBOL:automatic epiphysis of phalanx of hand FMA:240707 An epiphysis that is part of a metatarsal bone [Automatically generated definition]. FMA:33814 epiphysis of metatarsal metatarsal bone epiphysis metatarsal epiphysis uberon UBERON:0004389 epiphysis of metatarsal bone An epiphysis that is part of a metatarsal bone [Automatically generated definition]. OBOL:automatic metatarsal bone epiphysis FMA:33814 An epiphysis that is part of a metacarpal bone [Automatically generated definition]. FMA:33792 epiphysis of metacarpal metacarpal bone epiphysis metacarpal epiphysis uberon UBERON:0004390 epiphysis of metacarpal bone An epiphysis that is part of a metacarpal bone [Automatically generated definition]. OBOL:automatic metacarpal bone epiphysis FMA:33792 An epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition]. FMA:33793 first metacarpal bone epiphysis metacarpal 1 epiphysis uberon UBERON:0004391 epiphysis of first metacarpal bone An epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition]. OBOL:automatic first metacarpal bone epiphysis FMA:33793 An epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition]. FMA:33815 first metatarsal bone epiphysis metatarsal 1 epiphysis uberon UBERON:0004395 epiphysis of first metatarsal bone An epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition]. OBOL:automatic first metatarsal bone epiphysis FMA:33815 An epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition]. FMA:86315 fifth metatarsal bone epiphysis metatarsal 5 epiphysis uberon UBERON:0004399 epiphysis of fifth metatarsal bone An epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition]. OBOL:automatic fifth metatarsal bone epiphysis FMA:86315 A portion of bone tissue that is part of a epiphysis [Automatically generated definition]. FMA:241364 uberon UBERON:0004400 bone tissue of epiphysis A portion of bone tissue that is part of a epiphysis [Automatically generated definition]. OBOL:automatic A portion of bone tissue that is part of a distal epiphysis [Automatically generated definition]. FMA:241374 uberon UBERON:0004401 bone tissue of distal epiphysis A portion of bone tissue that is part of a distal epiphysis [Automatically generated definition]. OBOL:automatic A portion of bone tissue that is part of a proximal epiphysis [Automatically generated definition]. FMA:241372 uberon UBERON:0004402 bone tissue of proximal epiphysis A portion of bone tissue that is part of a proximal epiphysis [Automatically generated definition]. OBOL:automatic A distal epiphysis that is part of a humerus [Automatically generated definition]. FMA:32826 distal end of humerus lower end of humerus uberon UBERON:0004404 distal epiphysis of humerus A distal epiphysis that is part of a humerus [Automatically generated definition]. OBOL:automatic distal end of humerus FMA:32826 lower end of humerus FMA:32826 A distal epiphysis that is part of a femur [Automatically generated definition]. Head of the femur that articulates with the tibia and fibula.[AAO] AAO:0000893 FMA:32844 distal femoral epiphysis uberon distal head of femur UBERON:0004406 distal epiphysis of femur A distal epiphysis that is part of a femur [Automatically generated definition]. OBOL:automatic Head of the femur that articulates with the tibia and fibula.[AAO] 2012-06-20 AAO:0000893 AAO AAO:LAP distal femoral epiphysis OBOL:automatic distal head of femur AAO:0000893 A distal epiphysis that is part of a phalanx of manus [Automatically generated definition]. FMA:226577 distal epiphysis of phalanx of finger uberon distal end of phalanx of hand distal epiphysis of phalanx of hand head of phalanx of finger head of phalanx of hand ungual tuberosity of distal phalanx of finger UBERON:0004409 distal epiphysis of phalanx of manus A distal epiphysis that is part of a phalanx of manus [Automatically generated definition]. OBOL:automatic distal end of phalanx of hand FMA:226577 distal epiphysis of phalanx of hand FMA:226577 head of phalanx of finger FMA:226577 head of phalanx of hand FMA:226577 ungual tuberosity of distal phalanx of finger FMA:226577 The upper extremity of the humerus (proximal humerus) consists of a large rounded head joined to the body by a constricted portion called the neck, and two eminences, the greater and lesser tubercles. FMA:23362 proximal end of humerus proximal humeral epiphysis upper end of humerus uberon head of the humerus humeral head proximal humerus upper extremity of humerus UBERON:0004411 proximal epiphysis of humerus http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray207.png The upper extremity of the humerus (proximal humerus) consists of a large rounded head joined to the body by a constricted portion called the neck, and two eminences, the greater and lesser tubercles. proximal end of humerus FMA:23362 proximal humeral epiphysis OBOL:automatic upper end of humerus FMA:23362 head of the humerus humeral head proximal humerus upper extremity of humerus A proximal epiphysis that is part of a femur [Automatically generated definition]. FMA:32841 proximal femoral epiphysis uberon capital femoral epiphysis UBERON:0004412 proximal epiphysis of femur A proximal epiphysis that is part of a femur [Automatically generated definition]. OBOL:automatic proximal femoral epiphysis OBOL:automatic capital femoral epiphysis A proximal epiphysis that is part of a phalanx of manus [Automatically generated definition]. FMA:226482 basal epiphysis of phalanx of finger base of phalanx of finger basis phalangis manus proximal epiphysis of phalanx of finger uberon proximal epiphysis of phalanx of hand UBERON:0004414 proximal epiphysis of phalanx of manus A proximal epiphysis that is part of a phalanx of manus [Automatically generated definition]. OBOL:automatic basal epiphysis of phalanx of finger FMA:226482 base of phalanx of finger FMA:226482 basis phalangis manus FMA:226482 FMA:TA proximal epiphysis of phalanx of hand FMA:226482 A proximal epiphysis that is part of a metatarsal bone [Automatically generated definition]. FMA:33817 base of metatarsal bone basis ossis metatarsi proximal end of metatarsal bone upper end of metatarsal bone uberon UBERON:0004415 proximal epiphysis of metatarsal bone A proximal epiphysis that is part of a metatarsal bone [Automatically generated definition]. OBOL:automatic base of metatarsal bone FMA:33817 basis ossis metatarsi FMA:33817 FMA:TA proximal end of metatarsal bone FMA:33817 upper end of metatarsal bone FMA:33817 A proximal epiphysis that is part of a metacarpal bone [Automatically generated definition]. FMA:33795 base of metacarpal bone basis ossis metacarpi metacarpal bone base proximal end of metacarpal bone upper end of metacarpal bone uberon UBERON:0004416 proximal epiphysis of metacarpal bone A proximal epiphysis that is part of a metacarpal bone [Automatically generated definition]. OBOL:automatic base of metacarpal bone FMA:33795 basis ossis metacarpi FMA:33795 FMA:TA metacarpal bone base FMA:33795 proximal end of metacarpal bone FMA:33795 upper end of metacarpal bone FMA:33795 A proximal epiphysis that is part of a manual digit 1 phalanx [Automatically generated definition]. FMA:37489 basal epiphysis of phalanx of thumb base of phalanx of first digit of hand base of phalanx of thumb proximal epiphysis of phalanx of manual digit 1 proximal epiphysis of phalanx of manual digit I proximal epiphysis of phalanx of thumb uberon UBERON:0004417 proximal epiphysis of phalanx of manual digit 1 A proximal epiphysis that is part of a manual digit 1 phalanx [Automatically generated definition]. OBOL:automatic basal epiphysis of phalanx of thumb FMA:37489 base of phalanx of first digit of hand FMA:37489 base of phalanx of thumb FMA:37489 proximal epiphysis of phalanx of manual digit I proximal epiphysis of phalanx of thumb FMA:37489 NCBITaxon:9606 A proximal epiphysis that is part of a manual digit 5 phalanx [Automatically generated definition]. FMA:37534 basal epiphysis of phalanx of fifth finger basal epiphysis of phalanx of little finger base of phalanx of fifth digit of hand base of phalanx of fifth finger base of phalanx of little finger proximal epiphysis of phalanx of manual digit 5 proximal epiphysis of phalanx of manual digit V proximal epiphysis of phalanx of little finger uberon UBERON:0004421 proximal epiphysis of phalanx of manual digit 5 A proximal epiphysis that is part of a manual digit 5 phalanx [Automatically generated definition]. OBOL:automatic basal epiphysis of phalanx of fifth finger FMA:37534 basal epiphysis of phalanx of little finger FMA:37534 base of phalanx of fifth digit of hand FMA:37534 base of phalanx of fifth finger FMA:37534 base of phalanx of little finger FMA:37534 proximal epiphysis of phalanx of manual digit V proximal epiphysis of phalanx of little finger FMA:37534 NCBITaxon:9606 A proximal epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition]. FMA:42788 base of first metacarpal bone first metacarpal bone base proximal epiphysis of metacarpal 1 uberon UBERON:0004422 proximal epiphysis of first metacarpal bone A proximal epiphysis that is part of a metacarpal bone of digit 1 [Automatically generated definition]. OBOL:automatic base of first metacarpal bone FMA:42788 first metacarpal bone base FMA:42788 A proximal epiphysis that is part of a metacarpal bone of digit 5 [Automatically generated definition]. FMA:42800 base of fifth metacarpal bone fifth metacarpal bone base proximal end of fifth metacarpal bone proximal epiphysis of metacarpal 5 uberon UBERON:0004426 proximal epiphysis of fifth metacarpal bone A proximal epiphysis that is part of a metacarpal bone of digit 5 [Automatically generated definition]. OBOL:automatic base of fifth metacarpal bone FMA:42800 fifth metacarpal bone base FMA:42800 proximal end of fifth metacarpal bone FMA:42800 A proximal epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition]. FMA:42963 base of first metatarsal bone proximal end of first metatarsal bone proximal epiphysis of metatarsal 1 uberon UBERON:0004427 proximal epiphysis of first metatarsal bone A proximal epiphysis that is part of a metatarsal bone of digit 1 [Automatically generated definition]. OBOL:automatic base of first metatarsal bone FMA:42963 proximal end of first metatarsal bone FMA:42963 A proximal epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition]. FMA:42967 base of fifth metatarsal bone proximal end of fifth metatarsal bone proximal epiphysis of metatarsal 5 uberon UBERON:0004431 proximal epiphysis of fifth metatarsal bone A proximal epiphysis that is part of a metatarsal bone of digit 5 [Automatically generated definition]. OBOL:automatic base of fifth metatarsal bone FMA:42967 proximal end of fifth metatarsal bone FMA:42967 A proximal epiphysis that is part of a distal phalanx of manual digit 5 [Automatically generated definition]. FMA:37541 basal epiphysis of distal phalanx of fifth finger basal epiphysis of distal phalanx of little finger base of distal phalanx of fifth digit of hand base of distal phalanx of fifth finger base of distal phalanx of little finger proximal epiphysis of distal phalanx of manual digit V proximal epiphysis of distal phalanx of little finger uberon UBERON:0004435 proximal epiphysis of distal phalanx of manual digit 5 A proximal epiphysis that is part of a distal phalanx of manual digit 5 [Automatically generated definition]. OBOL:automatic basal epiphysis of distal phalanx of fifth finger FMA:37541 basal epiphysis of distal phalanx of little finger FMA:37541 base of distal phalanx of fifth digit of hand FMA:37541 base of distal phalanx of fifth finger FMA:37541 base of distal phalanx of little finger FMA:37541 proximal epiphysis of distal phalanx of manual digit V proximal epiphysis of distal phalanx of little finger FMA:37541 NCBITaxon:9606 A proximal epiphysis that is part of a middle phalanx of manual digit 5 [Automatically generated definition]. FMA:37538 basal epiphysis of middle phalanx of fifth finger basal epiphysis of middle phalanx of little finger base of middle phalanx of fifth digit of hand base of middle phalanx of fifth finger base of middle phalanx of little finger proximal epiphysis of middle phalanx of manual digit V proximal epiphysis of middle phalanx of little finger uberon UBERON:0004439 proximal epiphysis of middle phalanx of manual digit 5 A proximal epiphysis that is part of a middle phalanx of manual digit 5 [Automatically generated definition]. OBOL:automatic basal epiphysis of middle phalanx of fifth finger FMA:37538 basal epiphysis of middle phalanx of little finger FMA:37538 base of middle phalanx of fifth digit of hand FMA:37538 base of middle phalanx of fifth finger FMA:37538 base of middle phalanx of little finger FMA:37538 proximal epiphysis of middle phalanx of manual digit V proximal epiphysis of middle phalanx of little finger FMA:37538 NCBITaxon:9606 A proximal epiphysis that is part of a proximal phalanx of manual digit 5 [Automatically generated definition]. FMA:37535 basal epiphysis of proximal phalanx of little finger base of proximal phalanx of fifth digit of hand base of proximal phalanx of fifth finger base of proximal phalanx of little finger proximal epiphysis of proximal phalanx of manual digit V proximal epiphysis of proximal phalanx of little finger uberon UBERON:0004443 proximal epiphysis of proximal phalanx of manual digit 5 A proximal epiphysis that is part of a proximal phalanx of manual digit 5 [Automatically generated definition]. OBOL:automatic basal epiphysis of proximal phalanx of little finger FMA:37535 base of proximal phalanx of fifth digit of hand FMA:37535 base of proximal phalanx of fifth finger FMA:37535 base of proximal phalanx of little finger FMA:37535 proximal epiphysis of proximal phalanx of manual digit V proximal epiphysis of proximal phalanx of little finger FMA:37535 NCBITaxon:9606 A proximal epiphysis that is part of a distal phalanx of manual digit 1 [Automatically generated definition]. FMA:37493 base of distal phalanx of thumb proximal epiphysis of distal phalanx of manual digit I proximal epiphysis of distal phalanx of thumb uberon UBERON:0004444 proximal epiphysis of distal phalanx of manual digit 1 A proximal epiphysis that is part of a distal phalanx of manual digit 1 [Automatically generated definition]. OBOL:automatic base of distal phalanx of thumb FMA:37493 proximal epiphysis of distal phalanx of manual digit I proximal epiphysis of distal phalanx of thumb FMA:37493 NCBITaxon:9606 A proximal epiphysis that is part of a proximal phalanx of manual digit 1 [Automatically generated definition]. FMA:37490 basal epiphysis of proximal phalanx of thumb base of proximal phalanx of thumb proximal epiphysis of proximal phalanx of manual digit I proximal epiphysis of proximal phalanx of thumb uberon UBERON:0004445 proximal epiphysis of proximal phalanx of manual digit 1 A proximal epiphysis that is part of a proximal phalanx of manual digit 1 [Automatically generated definition]. OBOL:automatic basal epiphysis of proximal phalanx of thumb FMA:37490 base of proximal phalanx of thumb FMA:37490 proximal epiphysis of proximal phalanx of manual digit I proximal epiphysis of proximal phalanx of thumb FMA:37490 NCBITaxon:9606 An epiphysis that is part of a phalanx [Automatically generated definition]. uberon UBERON:0004446 epiphysis of phalanx An epiphysis that is part of a phalanx [Automatically generated definition]. OBOL:automatic A proximal epiphysis that is part of a phalanx [Automatically generated definition]. uberon UBERON:0004447 proximal epiphysis of phalanx A proximal epiphysis that is part of a phalanx [Automatically generated definition]. OBOL:automatic A distal epiphysis that is part of a phalanx [Automatically generated definition]. head of phalanx uberon UBERON:0004448 distal epiphysis of phalanx A distal epiphysis that is part of a phalanx [Automatically generated definition]. OBOL:automatic One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain. Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO] relationship loss: part_of internal carotid (AAO:0010219)[AAO] in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required AAO:0010493 BTO:0005205 CALOHA:TS-0126 EHDAA2:0000233 EHDAA:5294 EMAPA:18613 GAID:484 MA:0002562 MESH:D002536 NCIT:C12691 UMLS:C0007770 XAO:0000367 uberon UBERON:0004449 cerebral artery One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain. Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO] 2012-06-20 AAO:0010493 AAO AAO:BJB relationship loss: part_of internal carotid (AAO:0010219)[AAO] 2012-06-20 AAO:0010493 AAO in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required AAO UMLS:C0007770 ncithesaurus:Cerebral_Artery A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra. In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar) it's not clear if the XAO class belongs here or below EMAPA:37722 MA:0002869 XAO:0003077 uberon presacral vertebra UBERON:0004451 trunk or cervical vertebra A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra. UBERONREF:0000006 it's not clear if the XAO class belongs here or below XAO EMAPA:37722 MA:th presacral vertebra MA:0002869 A mesopodium that is part of a manus. Includes as parts the carpal skeleton and associated tissues[cjm]. The anatomical region surrounding the carpus including the distal parts of the bones of the forearm and the proximal parts of the metacarpus or five metacarpal bones and the series of joints between these bones, thus referred to as wrist joints. This region also includes the carpal tunnel, the anatomical snuff box, the flexor retinaculum, and the extensor retinaculum[WP,unvetted] UBERON:0001462 EHDAA2:0000218 EHDAA:5196 EMAPA:19122 EMAPA:32784 FMA:24922 GAID:59 MA:0000039 MESH:D014953 NCIT:C111033 OpenCyc:Mx4rvVjncpwpEbGdrcN5Y29ycA galen:Wrist carpal limb segment carpal segment fore basipodium fore mesopodium hand mesopodium manus mesopodium regio carpalis wrist wrist region carpus of fore-paw uberon articulatio radiocarpea carpus UBERON:0004452 carpal region Hand:parts.jpg Human:wrist.png FMA A mesopodium that is part of a manus. Includes as parts the carpal skeleton and associated tissues[cjm]. The anatomical region surrounding the carpus including the distal parts of the bones of the forearm and the proximal parts of the metacarpus or five metacarpal bones and the series of joints between these bones, thus referred to as wrist joints. This region also includes the carpal tunnel, the anatomical snuff box, the flexor retinaculum, and the extensor retinaculum[WP,unvetted] fore basipodium MA:th fore mesopodium MA:th regio carpalis FMA:24922 FMA:TA wrist MA:0000039 carpus of fore-paw EMAPA:19122 articulatio radiocarpea carpus A metapodium region that is part of a manus. Note that along with FMA we treat this as a limb segment rather than a purely skeletal element metacarpal Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton CALOHA:TS-2218 EMAPA:32654 FMA:24925 MA:0000042 distal segment of hand proper metacarpal part of hand metacarpal part of manus metacarpal region metacarpus forelimb cannon region forelimb equine cannon region uberon UBERON:0004453 metacarpus region Metacarpals:numbered-en.svg FMA PHENOSCAPE:ni A metapodium region that is part of a manus. OBOL:automatic distal segment of hand proper FMA:24925 metacarpal part of hand FMA:24925 metacarpal region FMA:24925 metacarpus MA:0000042 forelimb cannon region NCBITaxon:9788 forelimb equine cannon region NCBITaxon:9788 mesopodial segment of the pes, including the tarsal skeleton and associated tissues. this term refers to the limb segment. See also: tarsal bones and tarsal skeleton MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin). UBERON:0002388 CALOHA:TS-2219 EFO:0001409 EMAPA:32783 FMA:9665 GAID:41 MA:0000043 MESH:A01.378.610.250.149 MESH:A13.473.821 OpenCyc:Mx4rvVi-R5wpEbGdrcN5Y29ycA galen:Ankle ankle ankle region tarsal limb segment uberon articulatio talocruralis hind basipodium hind mesopodium hock UBERON:0004454 tarsal region Ankle:en.svg mesopodial segment of the pes, including the tarsal skeleton and associated tissues. MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin). MA ankle MA:0000043 articulatio talocruralis hind basipodium MA:th hind mesopodium MA:th hock An embryo at the neurula stage. UBERON:0007013 BILA:0000061 BTO:0001766 NCIT:C34229 UMLS:C1518306 neurula uberon UBERON:0004455 neurula embryo An embryo at the neurula stage. UMLS:C1518306 ncithesaurus:Neurula neurula BTO:0001766 Sum of all sensory systems in an organism. note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon UBERON:0004456 entire sense organ system Sum of all sensory systems in an organism. sense organ system FMA:78499 Any collection of skeletal muscles that is part of a head [Automatically generated definition]. EMAPA:18171 FMA:71287 head musculature muscle group of head muscles of head musculi capitis set of muscles of head uberon UBERON:0004461 This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376 skeletal musculature of head https://github.com/obophenotype/mouse-anatomy-ontology/issues/4 https://github.com/obophenotype/uberon/issues/1405 Any collection of skeletal muscles that is part of a head [Automatically generated definition]. OBOL:automatic head musculature FMA:71287 muscle group of head FMA:71287 muscles of head FMA:71287 musculi capitis FMA:71287 FMA:TA set of muscles of head FMA:71287 Any collection of muscles that is part of a body wall [Automatically generated definition]. define generically to encompass both vertebrates and invertebrates BSA:0000058 BTO:0001863 EMAPA:37853 FMA:86931 WBbt:0005813 body wall musculature uberon body wall muscles UBERON:0004462 musculature of body wall Any collection of muscles that is part of a body wall [Automatically generated definition]. OBOL:automatic EMAPA:37853 MA:th body wall musculature FMA:86931 Any collection of muscles that is part of a hindlimb stylopod (upper leg / thigh)[Automatically generated definition]. FMA:50208 muscle group of thigh musculature of thigh set of muscles of thigh thigh musculature uberon UBERON:0004463 musculature of hindlimb stylopod Any collection of muscles that is part of a hindlimb stylopod (upper leg / thigh)[Automatically generated definition]. OBOL:automatic muscle group of thigh FMA:50208 musculature of thigh FMA:50208 set of muscles of thigh FMA:50208 thigh musculature FMA:50208 Any collection of muscles that is part of a thorax [Automatically generated definition]. BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO:0000508 EMAPA:37260 FMA:71293 muscle group of thorax muscles of thorax musculi thoracis set of muscles of thorax thoracic musculature uberon UBERON:0004464 musculature of thorax Any collection of muscles that is part of a thorax [Automatically generated definition]. OBOL:automatic BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO EMAPA:37260 MA:th muscle group of thorax FMA:71293 muscles of thorax FMA:71293 musculi thoracis FMA:71293 FMA:TA set of muscles of thorax FMA:71293 thoracic musculature FMA:71293 Any collection of muscles that is part of a neck [Automatically generated definition]. AAO:0000091 EMAPA:36050 FMA:71290 MESH:D009334 cervical muscles muscle group of neck muscles of neck musculi cervicis musculi colli neck musculature set of muscles of neck uberon UBERON:0004465 musculature of neck Any collection of muscles that is part of a neck [Automatically generated definition]. OBOL:automatic cervical muscles AAO:0000091 muscle group of neck FMA:71290 muscles of neck FMA:71290 musculi cervicis FMA:71290 FMA:TA musculi colli FMA:71290 FMA:TA neck musculature FMA:71290 set of muscles of neck FMA:71290 Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition]. see notes on UBERON:0000978 for possible confusion over the term 'leg'. This class represents the class-union of upper leg musculature and lower leg musculature (and thus may not mean precisely the same thing as the EHDAA2 class) UBERON:0005632 EHDAA2:0000973 leg muscle system uberon UBERON:0004466 musculature of leg Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition]. OBOL:automatic leg muscle system EHDAA2:0000973 FMA:33061 muscle group of vertebral column uberon UBERON:0004468 set of muscles of vertebral column muscle group of vertebral column FMA:33061 Any collection of muscles that is part of a back [Automatically generated definition]. FMA:71291 muscle group of back muscles of back musculi dorsi set of muscles of back uberon UBERON:0004469 musculature of back Any collection of muscles that is part of a back [Automatically generated definition]. OBOL:automatic muscle group of back FMA:71291 muscles of back FMA:71291 musculi dorsi FMA:71291 FMA:TA set of muscles of back FMA:71291 Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. we merge two FMA classes here UBERON:0004485 UBERON:0005633 AAO:0000427 EHDAA2:0001429 EMAPA:18184 FMA:50205 FMA:50248 muscle group of pelvic girdle muscle group of pelvis pelvic girdle muscle system pelvic girdle muscles pelvic girdle musculature set of muscles of pelvic girdle uberon muscular system of pelvis set of muscles of pelvis UBERON:0004470 musculature of pelvic girdle Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic we merge two FMA classes here FMA muscle group of pelvic girdle FMA:50205 muscle group of pelvis FMA:50248 pelvic girdle muscle system EHDAA2:0001429 pelvic girdle muscles AAO:0000427 pelvic girdle musculature FMA:50205 set of muscles of pelvic girdle FMA:50205 muscular system of pelvis FMA:50248 set of muscles of pelvis FMA:50248 A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles. AAO:0000423 EMAPA:37857 FMA:33519 muscle group of pectoral girdle pectoral girdle muscles pectoral girdle musculature set of muscles of pectoral girdle uberon UBERON:0004471 musculature of pectoral girdle A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles. EMAPA:37857 MA:th muscle group of pectoral girdle FMA:33519 pectoral girdle muscles AAO:0000423 pectoral girdle musculature FMA:33519 set of muscles of pectoral girdle FMA:33519 Any collection of muscles that is part of a face. originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose FMA:71288 entire facial musculature facial muscles muscle group of face musculi faciei uberon set of facial muscles set of muscles of face UBERON:0004473 musculature of face Any collection of muscles that is part of a face. OBOL:automatic entire facial musculature facial muscles FMA:71288 muscle group of face FMA:71288 musculi faciei FMA:71288 FMA:TA set of facial muscles FMA:71288 set of muscles of face FMA:71288 Any collection of muscles that is part of an arm [Automatically generated definition]. EHDAA2:0000141 arm muscle system arm musculature muscle group of arm set of muscles of arm uberon UBERON:0004474 musculature of arm Any collection of muscles that is part of an arm [Automatically generated definition]. OBOL:automatic arm muscle system EHDAA2:0000141 arm musculature FMA:50202 muscle group of arm FMA:50202 set of muscles of arm FMA:50202 The collection of muscles that form attachments to the hip skeleton. FMA:50227 hip musculature muscle group of hip set of muscles of hip uberon UBERON:0004475 musculature of hip The collection of muscles that form attachments to the hip skeleton. hip musculature FMA:50227 muscle group of hip FMA:50227 set of muscles of hip FMA:50227 The collection of muscles that form attachments to the shoulder skeleton. FMA:50220 muscle group of shoulder set of muscles of shoulder uberon UBERON:0004476 musculature of shoulder The collection of muscles that form attachments to the shoulder skeleton. muscle group of shoulder FMA:50220 set of muscles of shoulder FMA:50220 The collection of muscles that are part of the larynx. currently defined by location rather than attachment FMA:264611 FMA:46616 MESH:D007821 laryngeal muscles laryngeal muscles set muscle group of larynx set of laryngeal muscles set of muscles of larynx uberon UBERON:0004478 musculature of larynx The collection of muscles that are part of the larynx. laryngeal muscles FMA:46616 laryngeal muscles set FMA:46616 muscle group of larynx FMA:46616 set of laryngeal muscles FMA:46616 set of muscles of larynx FMA:264611 Any collection of muscles that is part of a trunk [Automatically generated definition]. currently defined by location rather than attachment AAO:0011572 EFO:0003531 FMA:50187 muscle group of trunk set of muscles of trunk uberon muscular system of trunk UBERON:0004479 musculature of trunk Any collection of muscles that is part of a trunk [Automatically generated definition]. OBOL:automatic muscle group of trunk FMA:50187 set of muscles of trunk FMA:50187 muscular system of trunk FMA:50187 Any collection of muscles that is part of a limb [Automatically generated definition]. currently defined by location rather than attachment UBERON:0005635 EHDAA2:0000995 EMAPA:32700 FMA:50188 limb muscle system limb musculature muscle group of limb set of muscles of limb uberon UBERON:0004480 musculature of limb Any collection of muscles that is part of a limb [Automatically generated definition]. OBOL:automatic limb muscle system EHDAA2:0000995 limb musculature FMA:50188 muscle group of limb FMA:50188 set of muscles of limb FMA:50188 Any collection of muscles that is part of a forelimb [Automatically generated definition]. currently defined by location rather than attachment FMA:50396 free upper limb musculature muscle group of free upper limb musculature of free upper limb set of muscles of free upper limb uberon UBERON:0004481 musculature of upper limb Any collection of muscles that is part of a forelimb [Automatically generated definition]. OBOL:automatic free upper limb musculature FMA:50396 muscle group of free upper limb FMA:50396 musculature of free upper limb FMA:50396 set of muscles of free upper limb FMA:50396 Any collection of muscles that is part of a hindlimb [Automatically generated definition]. currently defined by location rather than attachment FMA:50399 free lower limb musculature muscle group of free lower limb musculature of free lower limb set of muscles of free lower limb uberon UBERON:0004482 musculature of lower limb Any collection of muscles that is part of a hindlimb [Automatically generated definition]. OBOL:automatic free lower limb musculature FMA:50399 muscle group of free lower limb FMA:50399 musculature of free lower limb FMA:50399 set of muscles of free lower limb FMA:50399 Any collection of muscles that is part of a lower arm [Automatically generated definition]. FMA:39089 muscle group of forearm musculature of forearm set of muscles of forearm uberon UBERON:0004487 musculature of forelimb zeugopod Any collection of muscles that is part of a lower arm [Automatically generated definition]. OBOL:automatic muscle group of forearm FMA:39089 musculature of forearm FMA:39089 set of muscles of forearm FMA:39089 Any collection of muscles that is part of a foot [Automatically generated definition]. currently defined by location rather than attachment FMA:50214 foot musculature muscle group of foot musculature of foot set of muscles of foot uberon UBERON:0004488 musculature of pes Any collection of muscles that is part of a foot [Automatically generated definition]. OBOL:automatic foot musculature FMA:50214 muscle group of foot FMA:50214 musculature of foot FMA:50214 set of muscles of foot FMA:50214 Any collection of muscles that is part of a manus [Automatically generated definition]. currently defined by location rather than attachment FMA:42368 hand musculature muscle group of hand musculature of hand set of muscles of hand uberon UBERON:0004489 musculature of manus Any collection of muscles that is part of a manus [Automatically generated definition]. OBOL:automatic hand musculature FMA:42368 muscle group of hand FMA:42368 musculature of hand FMA:42368 set of muscles of hand FMA:42368 A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. FMA:7283 atrial cardiac muscle tissue atrial heart muscle cardiac atrium muscle uberon atrial myocardium UBERON:0004490 cardiac muscle tissue of atrium A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. OBOL:automatic in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. GO atrial cardiac muscle tissue GO:0055009 atrial heart muscle GO:0055009 cardiac atrium muscle GO:0055009 atrial myocardium GO:0055009 GOC:mtg_heart A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]. FMA:84083 interatrial septum cardiac muscle tissue interatrial septum heart muscle interatrial septum muscle interatrial septum myocardium uberon UBERON:0004491 cardiac muscle tissue of interatrial septum A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]. OBOL:automatic interatrial septum cardiac muscle tissue interatrial septum heart muscle interatrial septum muscle interatrial septum myocardium A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. FMA:226279 cardiac septum cardiac muscle tissue cardiac septum heart muscle cardiac septum muscle cardiac septum myocardium uberon UBERON:0004492 cardiac muscle tissue of cardiac septum A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. OBOL:automatic cardiac septum cardiac muscle tissue cardiac septum heart muscle cardiac septum muscle cardiac septum myocardium A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. Note placement of MA class based on parthood relationship EMAPA:32688 FMA:261726 MA:0002441 uberon UBERON:0004493 cardiac muscle tissue of myocardium MA A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. OBOL:automatic A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. FMA:261898 uberon UBERON:0004495 skeletal muscle tissue of diaphragm A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. OBOL:automatic A portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition]. FMA:261045 FMA:261081 smooth muscle tissue of lobular bronchiole uberon UBERON:0004515 smooth muscle tissue of bronchiole A portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition]. OBOL:automatic smooth muscle tissue of lobular bronchiole FMA:261081 A portion of smooth muscle tissue that is part of a terminal bronchiole [Automatically generated definition]. FMA:261051 uberon UBERON:0004516 smooth muscle tissue of terminal bronchiole A portion of smooth muscle tissue that is part of a terminal bronchiole [Automatically generated definition]. OBOL:automatic A muscle that is attached to a vertebra of the vertebral column. FMA:22594 vertebral column muscle uberon UBERON:0004518 muscle of vertebral column A muscle that is attached to a vertebra of the vertebral column. vertebral column muscle FMA:22594 A portion of striated muscle tissue that is part of a prostate gland [Automatically generated definition]. FMA:45716 uberon UBERON:0004520 striated muscle tissue of prostate A portion of striated muscle tissue that is part of a prostate gland [Automatically generated definition]. OBOL:automatic A vasculature that is part of a muscle organ [Automatically generated definition]. FMA:87123 muscular organ vasculature uberon UBERON:0004521 vasculature of muscle organ A vasculature that is part of a muscle organ [Automatically generated definition]. OBOL:automatic muscular organ vasculature FMA:87123 A vasculature that is part of a musculoskeletal system [Automatically generated definition]. FMA:239607 uberon UBERON:0004522 vasculature of musculoskeletal system A vasculature that is part of a musculoskeletal system [Automatically generated definition]. OBOL:automatic A projection or outgrowth of tissue from a larger body or organ. should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs) Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO] anatomical process process AAO:0010278 FMA:67601 HAO:0000822 NCIT:C61549 TAO:0001834 VSAO:0000180 XAO:0004020 galen:Ridge processus projection flange flanges lamella lamellae lamina laminae organ process papilla process of organ processes projection projections ridge ridges shelf shelves uberon anatomical protrusion protrusion spine UBERON:0004529 anatomical projection A projection or outgrowth of tissue from a larger body or organ. Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO] 2012-06-20 AAO:0010278 AAO AAO:BJB Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO] 2012-08-14 TAO:0001834 TAO TAO:wd Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO] 2012-08-14 VSAO:0000180 VSAO TAO:curator process VSAO:0000180 processus FMA:67601 FMA:TA flange VSAO:0000180 flanges VSAO:0000180 lamella VSAO:0000180 lamellae VSAO:0000180 lamina VSAO:0000180 laminae VSAO:0000180 processes VSAO:0000180 projection VSAO:0000180 projections VSAO:0000180 ridge VSAO:0000180 ridges VSAO:0000180 shelf VSAO:0000180 shelves VSAO:0000180 Anatomical projection that is composed of bone tissue. FMA:75433 ZFA:0001637 bone process projection of bone uberon bony projections UBERON:0004530 bony projection Anatomical projection that is composed of bone tissue. VSAO:wd bone process FMA:75433 bony projections ZFA:0001637 A testis that is in the left side of the genitalia [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37370 FMA:7212 MA:0001746 NCIT:C49323 UMLS:C0227998 left testicle uberon UBERON:0004533 left testis A testis that is in the left side of the genitalia [Automatically generated definition]. OBOL:automatic EMAPA:37370 MA:th UMLS:C0227998 ncithesaurus:Left_Testis left testicle MA:0001746 A testis that is in the right side of the genitalia [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37371 FMA:7211 MA:0001747 NCIT:C49326 OpenCyc:Mx4rvVjM25wpEbGdrcN5Y29ycA UMLS:C0227997 right testicle uberon UBERON:0004534 right testis A testis that is in the right side of the genitalia [Automatically generated definition]. OBOL:automatic EMAPA:37371 MA:th UMLS:C0227997 ncithesaurus:Right_Testis right testicle MA:0001747 Anatomical system that has as its parts the heart and blood vessels. we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 EHDAA2:0000216 EHDAA:394 EMAPA:16104 EMAPA:16370 EV:0100017 FMA:7161 GAID:467 MA:0000010 MAT:0000016 MESH:D002319 MIAA:0000016 NCIT:C12686 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA TAO:0000010 UMLS:C0007226 VHOG:0000302 WikipediaCategory:Cardiovascular_system XAO:0000100 XAO:0001010 ZFA:0000010 uberon CV system Herz und Gefaesssystem UBERON:0004535 cardiovascular system Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000302 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 UMLS:C0007226 ncithesaurus:Cardiovascular_System CV system BTO:0000088 Herz und Gefaesssystem BTO:0000088 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep. consider merging with parent A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] FMA:63815 TAO:0005105 ZFA:0005105 lymphatic trunks and ducts lymphatic vasculature lymphatic vessel network lymphatic vessels set set of lymphatic vessels trunci et ductus lymphatici uberon lymph vessels UBERON:0004536 lymph vasculature A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep. ZFA:0005105 A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] 2012-08-14 TAO:0005105 TAO ZFIN:curator lymphatic trunks and ducts FMA:63815 lymphatic vessels set FMA:63815 trunci et ductus lymphatici FMA:63815 FMA:TA lymph vessels ZFA:0005105 A vascular network consisting of blood vessels. TAO:0001079 ZFA:0001079 blood vascular network set of blood vessels uberon blood system blood vessel system blood vessels UBERON:0004537 blood vasculature A vascular network consisting of blood vessels. blood vessels TAO:0001079 A kidney that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:36589 FMA:7205 MA:0001655 NCIT:C34006 UMLS:C0227614 uberon UBERON:0004538 left kidney A kidney that is part of a left side of organism [Automatically generated definition]. OBOL:automatic UMLS:C0227614 ncithesaurus:Left_Kidney A kidney that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:36590 FMA:7204 MA:0001683 NCIT:C34005 UMLS:C0227613 uberon UBERON:0004539 right kidney A kidney that is part of a right side of organism [Automatically generated definition]. OBOL:automatic UMLS:C0227613 ncithesaurus:Right_Kidney the layer of secretory cells which lines the epididymis BTO:0005768 CALOHA:TS-2063 EMAPA:30445 FMA:19153 MA:0002825 epididymis epithelium epithelium of epididymis uberon UBERON:0004544 epididymis epithelium the layer of secretory cells which lines the epididymis MGI:csmith MP:0004933 epididymis epithelium FMA:19153 epithelium of epididymis FMA:19153 An eye that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37362 FMA:12515 MA:0002949 NCIT:C119334 left eyeball left orbital part of face left orbital region uberon UBERON:0004548 left eye An eye that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37362 MA:th left eyeball FMA:12515 left orbital part of face FMA:54450 left orbital region FMA:54450 An eye that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37363 FMA:12514 MA:0002950 NCIT:C119333 right eyeball right orbital part of face right orbital region uberon UBERON:0004549 right eye An eye that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37363 MA:th right eyeball FMA:12514 right orbital part of face FMA:54449 right orbital region FMA:54449 the thick circular layer of smooth gastric musculature encircling the gastroesophageal junction that functions to reduce backflow into the esophagus from the stomach TODO - split? check FMA:63048 ! circular muscle layer of abdominal part of esophagus EMAPA:18267 FMA:14915 MA:0002951 NCIT:C33009 UMLS:C0227192 galen:LowerEsophagealSphincter cardiac sphincter gastroesophageal sphincter gastroesophageal sphincter muscle inferior esophageal sphincter uberon LES cardiac sphincter constrictor cardiae esophageal sphincter esophageal sphincter%2c lower esophageal-cardiac junction esophagogastric junction gastro-esophageal junction gastro-esophageal sphincter gastro-oesophageal junction gastroesophageal junction gastroesophageal sphincter lower esophageal sphincter UBERON:0004550 gastroesophageal sphincter MA the thick circular layer of smooth gastric musculature encircling the gastroesophageal junction that functions to reduce backflow into the esophagus from the stomach ISBN:0-683-40008-8 MP:0010153 UMLS:C0227192 ncithesaurus:Lower_Esophageal_Sphincter cardiac sphincter MA:0002951 MP:0010153 gastroesophageal sphincter FMA:14915 inferior esophageal sphincter FMA:14915 LES cardiac sphincter constrictor cardiae MP:0010153 esophageal sphincter esophageal sphincter%2c lower esophageal-cardiac junction esophagogastric junction gastro-esophageal junction gastro-esophageal sphincter gastro-oesophageal junction gastroesophageal junction gastroesophageal sphincter lower esophageal sphincter lower esophageal sphincter MA:0002951 An artery that is part of a digit [Automatically generated definition]. check part_of - do we need term for digit + metacarpal/tarsal bones? EMAPA:37076 MA:0001941 uberon UBERON:0004552 digital artery An artery that is part of a digit [Automatically generated definition]. OBOL:automatic EMAPA:37076 MA:th A digital artery that is part of a forelimb [Automatically generated definition]. EMAPA:37210 MA:0001953 digital artery of manus forelimb digital arteries wing digital artery uberon UBERON:0004553 forelimb digital artery A digital artery that is part of a forelimb [Automatically generated definition]. OBOL:automatic EMAPA:37210 MA:th forelimb digital arteries MA:0001953 wing digital artery NCBITaxon:8782 OBOL:automatic A digital artery that is part of a hindlimb [Automatically generated definition]. EMAPA:37214 FMA:69713 MA:0001964 digital artery of foot hindlimb digital arteries uberon UBERON:0004554 hindlimb digital artery A digital artery that is part of a hindlimb [Automatically generated definition]. OBOL:automatic EMAPA:37214 MA:th digital artery of foot FMA:69713 hindlimb digital arteries MA:0001964 The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. FMA:45623 systemic arterial circulatory system uberon UBERON:0004571 systemic arterial system MA-inferred The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. systemic arterial circulatory system FMA:45623 The part of the cardiovascular system consisting of all arteries. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004690 EHDAA2:0000143 EHDAA:396 EMAPA:16201 EMAPA:16371 MA:0002719 VHOG:0000273 uberon UBERON:0004572 arterial system MA The part of the cardiovascular system consisting of all arteries. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000273 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. EMAPA:37126 FMA:66464 systemic arterial subtree uberon UBERON:0004573 systemic artery An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. EMAPA:37126 MA:th systemic arterial subtree FMA:66464 The part of the venous system that drains the general body tissues[Kardong] In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] FMA:45626 systemic venous circulatory system uberon UBERON:0004581 systemic venous system The part of the venous system that drains the general body tissues[Kardong] ISBN:0073040584 In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] FMA FMA:45626 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) systemic venous circulatory system FMA:45626 The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004692 EHDAA2:0002171 EHDAA:486 EMAPA:16240 MA:0002720 NCIT:C33858 UMLS:C1267406 VHOG:0000277 vein system uberon UBERON:0004582 venous system MA The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) UMLS:C1267406 ncithesaurus:Venous_System A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. FMA class is not a subtype of muscle FMA:75004 NCIT:C28381 UMLS:C1409894 sphincter uberon circular muscle UBERON:0004590 sphincter muscle A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. FMA class is not a subtype of muscle FMA UMLS:C1409894 ncithesaurus:Sphincter An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart BTO:0000766 CALOHA:TS-2155 EMAPA:35176 MA:0000709 NCIT:C53395 TAO:0005257 UMLS:C1706972 ZFA:0005257 uberon UBERON:0004638 blood vessel endothelium An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart UMLS:C1706972 ncithesaurus:Blood_Vessel_Endothelium the connective tissue that surrounds the spleen EMAPA:35802 FMA:15849 MA:0000753 NCIT:C33598 UMLS:C0229681 Malpighian capsule capsula splenica capsule of spleen fibroelastic coat of spleen fibrous capsule of spleen splenic capsule tunica fibrosa (splen)(lien) tunica fibrosa splenica uberon UBERON:0004641 spleen capsule the connective tissue that surrounds the spleen MGI:cwg MP:0002227 UMLS:C0229681 ncithesaurus:Splenic_Capsule Malpighian capsule FMA:15849 capsula splenica FMA:15849 FMA:TA capsule of spleen FMA:15849 fibroelastic coat of spleen FMA:15849 fibrous capsule of spleen FMA:15849 splenic capsule FMA:15849 tunica fibrosa (splen)(lien) FMA:15849 tunica fibrosa splenica FMA:15849 FMA:TA the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP] EMAPA:35499 FMA:14471 MA:0002494 NCIT:C32732 UMLS:C0227518 hepatic lobule lobuli hepatici lobulus hepaticus uberon lobules of liver lobuli hepatis UBERON:0004647 liver lobule FMA FMA MA the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein ISBN:0-683-40008-8 MP:0008987 UMLS:C0227518 ncithesaurus:Hepatic_Lobule hepatic lobule FMA:14471 lobuli hepatici lobulus hepaticus FMA:14471 lobules of liver lobuli hepatis A keratinized stratified squamous epithelium that is part of a tongue. FMA:74865 MA:0002787 keratinized epithelium of tongue uberon UBERON:0004650 tongue keratinized epithelium A keratinized stratified squamous epithelium that is part of a tongue. OBOL:automatic keratinized epithelium of tongue FMA:74865 The body or shaft of the humerus is almost cylindrical in the upper half of its extent, prismatic and flattened below, and has three borders and three surfaces. EMAPA:25051 FMA:13305 MA:0002807 NCIT:C120671 body of humerus corpus humeri diaphysis of humerus humeral diaphysis shaft of humerus uberon body of the humerus medial humerus shaft of the humerus UBERON:0004652 humerus diaphysis The body or shaft of the humerus is almost cylindrical in the upper half of its extent, prismatic and flattened below, and has three borders and three surfaces. body of humerus FMA:13305 corpus humeri FMA:13305 FMA:TA diaphysis of humerus FMA:13305 humeral diaphysis FMA:13305 shaft of humerus FMA:13305 body of the humerus medial humerus shaft of the humerus An anatomical wall that is part of an aorta, enclosing the luminal space. EMAPA:35139 FMA:14156 MA:0002901 aortic wall wall of aorta uberon UBERON:0004663 aorta wall An anatomical wall that is part of an aorta, enclosing the luminal space. aortic wall FMA:14156 wall of aorta FMA:14156 the outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers EMAPA:35136 FMA:14283 MA:0002902 tunica adventitia of aorta uberon UBERON:0004664 aorta tunica adventitia the outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers ISBN:0-683-40008-8 MP:0009871 tunica adventitia of aorta FMA:14283 A muscular coat that is part of a seminal vesicle [Automatically generated definition]. EMAPA:29773 FMA:19404 MA:0002913 muscle layer of seminal vesicle muscular coat of seminal gland muscular layer of seminal gland tunica muscularis (vesicula seminalis) tunica muscularis glandulae vesiculosae uberon UBERON:0004665 muscular coat of seminal vesicle A muscular coat that is part of a seminal vesicle [Automatically generated definition]. OBOL:automatic muscle layer of seminal vesicle FMA:19404 muscular coat of seminal gland FMA:19404 muscular layer of seminal gland FMA:19404 tunica muscularis (vesicula seminalis) FMA:19404 tunica muscularis glandulae vesiculosae FMA:19404 FMA:TA The membranous portion of the wall between the two lower chambers of the heart The membranous septum is the upper part of ventricular septum[GO:0003149]. UBERON:0004143 membranous septum ventricle membranous septum ventricular membranous septum EHDAA2:0004596 EMAPA:18246 FMA:7135 MA:0002939 VHOG:0000927 cardiac ventricular membranous septum membranous interventricular septum membranous part interventricular septum membranous part of interventricular septum membranous portion of interventricular septum pars membranacea (septi interventricularis) pars membranacea septi interventricularis uberon membranous interventricular septum UBERON:0004666 interventricular septum membranous part Wikipedia The membranous portion of the wall between the two lower chambers of the heart MP:0008823 The membranous septum is the upper part of ventricular septum[GO:0003149]. GO:0003149 membranous septum GO:0003149 ventricle membranous septum VT:0000018 ventricular membranous septum MP:0008823 cardiac ventricular membranous septum membranous interventricular septum FMA:7135 membranous part interventricular septum VHOG:0000927 membranous part of interventricular septum FMA:7135 membranous portion of interventricular septum FMA:7135 pars membranacea (septi interventricularis) FMA:7135 pars membranacea septi interventricularis FMA:7135 FMA:TA membranous interventricular septum MA:0002939 The muscular portion of the wall between the two lower chambers of the heart The muscular septum is the lower part of the ventricular septum[GO] UBERON:0004144 muscular septum EHDAA2:0000885 EHDAA:2607 EMAPA:18247 FMA:7134 MA:0002940 RETIRED_EHDAA2:0000888 cardiac ventricular muscular septum muscular interventricular septum muscular part interventricular septum muscular part of interventricular septum pars muscularis (septi interventricularis) pars muscularis septi interventricularis septum membranaceum ventricular muscular septum uberon muscular interventricular septum UBERON:0004667 interventricular septum muscular part The muscular portion of the wall between the two lower chambers of the heart The muscular septum is the lower part of the ventricular septum[GO] GO:0003150 muscular septum GO:0003150 cardiac ventricular muscular septum muscular interventricular septum FMA:7134 muscular part of interventricular septum FMA:7134 pars muscularis (septi interventricularis) FMA:7134 pars muscularis septi interventricularis FMA:7134 FMA:TA septum membranaceum muscular interventricular septum MA:0002940 One of: the 4th ventricle median or lateral apertures. FMA:242766 MA:0002945 aperture of 4th ventricle aperture of fourth ventricle uberon UBERON:0004668 fourth ventricle aperture One of: the 4th ventricle median or lateral apertures. aperture of fourth ventricle FMA:242766 The sensory system for the sense of balance. The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system]. FMA and NIF have no part information for this class. This is a GAT in FMA BTO:0003381 EMAPA:37986 FMA:7193 NLXANAT:090819 vestibular organ system vestibular system equilibrioception system vestibulomotor system uberon UBERON:0004681 vestibular system The sensory system for the sense of balance. NLXANAT:090819 The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system]. FMA and NIF have no part information for this class. This is a GAT in FMA FMA EMAPA:37986 MA:th vestibular organ system FMA:7193 vestibular system NLXANAT:090819 The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. BAMS:RA EMAPA:35721 FMA:84017 MA:0003147 MESH:A08.186.211.132.659.632 NCIT:C97335 NLXANAT:20090205 TAO:0001429 UMLS:C0034671 ZFA:0001429 nuclei raphes raphe nuclei raphe nuclei set uberon nuclei raphes raphe cluster raphe nucleus raphe of mesenchephalon set of raphe nuclei UBERON:0004684 we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei' raphe nuclei http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png GO Wikipedia The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. NLXANAT:20090205 UMLS:C0034671 ncithesaurus:Raphe_Nuclei nuclei raphes FMA:84017 FMA:TA raphe nuclei FMA:84017 raphe nuclei NLXANAT:20090205 raphe nuclei set FMA:84017 nuclei raphes raphe cluster raphe nucleus ZFA:0001429 raphe of mesenchephalon BAMS:RA set of raphe nuclei FMA:84017 The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. EMAPA:37496 FMA:10636 MA:0001939 costocervical trunk trunk of costocervical artery uberon truncus costocervicalis UBERON:0004688 costo-cervical trunk http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. EMAPA:37496 MA:th costocervical trunk FMA:10636 trunk of costocervical artery FMA:10636 truncus costocervicalis An epithelium that is part of an external naris [Automatically generated definition]. EMAPA:18596 MA:0001321 uberon UBERON:0004692 external naris epithelium An epithelium that is part of an external naris [Automatically generated definition]. OBOL:automatic A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. EMAPA:36503 MA:0000704 uberon UBERON:0004695 arterial system smooth muscle A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. OBOL:automatic A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. EMAPA:36613 MA:0000715 uberon UBERON:0004696 venous system smooth muscle A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. OBOL:automatic An endothelium that is part of a vena cava [Automatically generated definition]. EMAPA:37800 MA:0000713 NCIT:C49318 UMLS:C1710623 uberon UBERON:0004698 vena cava endothelium An endothelium that is part of a vena cava [Automatically generated definition]. OBOL:automatic EMAPA:37800 MA:th UMLS:C1710623 ncithesaurus:Vena_Cava_Endothelium An endothelium that is part of a outflow tract [Automatically generated definition]. It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] MA:0000490 VHOG:0001524 uberon UBERON:0004699 outflow tract endothelium An endothelium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] 2012-09-17 VHOG:0001524 VHOG DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001) An endothelium that is part of an arterial system [Automatically generated definition]. EMAPA:35145 MA:0000703 NCIT:C49329 UMLS:C1706849 uberon UBERON:0004700 arterial system endothelium An endothelium that is part of an arterial system [Automatically generated definition]. OBOL:automatic UMLS:C1706849 ncithesaurus:Arterial_System_Endothelium An endothelium that is part of a venous system [Automatically generated definition]. EMAPA:35907 MA:0000714 NCIT:C49320 UMLS:C1710626 uberon UBERON:0004701 venous system endothelium An endothelium that is part of a venous system [Automatically generated definition]. OBOL:automatic UMLS:C1710626 ncithesaurus:Venous_System_Endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. EMAPA:35732 MA:0001805 uberon UBERON:0004702 respiratory system blood vessel endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic A depression or hollow in a bone[WP]. Anatomical space that is a concavity, shallow depression, or groove on a bone.[TAO] General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named 'fossa' are cavities in FMA, hence placement here fossa AAO:0010439 FMA:45791 TAO:0001743 UMLS:C0836913 VSAO:0005069 ZFA:0005388 uberon concavities concavity depression depressions fossae groove UBERON:0004704 bone fossa FMA-implied A depression or hollow in a bone[WP]. Anatomical space that is a concavity, shallow depression, or groove on a bone.[TAO] 2012-08-14 TAO:0001743 TAO TAO:wd General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named 'fossa' are cavities in FMA, hence placement here FMA UMLS:C0836913 ncithesaurus:Fossa concavities TAO:0001743 concavity TAO:0001743 depression TAO:0001743 depressions TAO:0001743 fossae TAO:0001743 groove TAO:0001743 a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches TODO - check relationship to bulbus arteriosus A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] EHDAA2:0000197 EHDAA:438 EHDAA:768 EMAPA:16333 FMA:70300 NCIT:C34114 UMLS:C1284055 primitive right ventricle endocardium uberon UBERON:0004706 bulbus cordis http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches ISBN:0-683-40008-8 MP:0010568 A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] 2012-08-14 TAO:0000173 TAO ZFIN:curator UMLS:C1284055 ncithesaurus:Bulbus_Cordis primitive right ventricle endocardium EHDAA2:0000197 JB:def A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities. Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001) DrerDO:0000052 EFO:0001310 OGES:000006 ZFS:0000050 phylotypic stage uberon pharyngula UBERON:0004707 pharyngula stage A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities. An appendage that is part of an appendage girdle complex. this class is the union of the classes limb, pectoral fin and pelvic fin. UBERON:0009872 VSAO:0000067 girdle-associated appendage limb or fin limb/fin pectoral or pelvic appendage pelvic/pectoral appendage jointed paired lateral appendage paired appendage uberon UBERON:0004708 paired limb/fin VSAO VSAO definitional An appendage that is part of an appendage girdle complex. UBERON:cjm girdle-associated appendage limb or fin limb/fin pectoral or pelvic appendage pelvic/pectoral appendage jointed paired lateral appendage paired appendage VSAO:0000067 Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. UBERON:0009876 posterior appendage VSAO:0000126 hindlimb/pelvic fin pelvic appendage pelvic limb/fin posterior limb/fin posterior paired appendage uberon UBERON:0004709 pelvic appendage definitional lexical Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. VSAO:0000150 hindlimb/pelvic fin pelvic appendage VSAO:0000126 pelvic limb/fin posterior paired appendage VSAO:0000126 Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues. While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] UBERON:0009875 anterior appendage VHOG:0001753 VSAO:0000125 anterior limb/fin anterior paired appendage forelimb - pectoral fin forelimb or pectoral fin forelimb/pectoral fin pectoral limb/fin uberon UBERON:0004710 pectoral appendage definitional lexical Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues. VSAO:0000150-modified While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] 2012-09-17 VHOG:0001753 VHOG DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004) anterior limb/fin anterior paired appendage VSAO:0000148 forelimb - pectoral fin VHOG:0001753 forelimb or pectoral fin forelimb/pectoral fin pectoral limb/fin The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. BTO:0001744 CALOHA:TS-0497 EMAPA:18638 GAID:536 MA:0002154 MESH:D007601 NCIT:C12738 UMLS:C0022427 uberon jugular vena jugularis UBERON:0004711 jugular vein http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. UMLS:C0022427 ncithesaurus:Jugular_Vein vena jugularis BTO:0001744 The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus AEO:0000194 BTO:0003834 EHDAA2:0000001 EHDAA2:0003235 EMAPA:36040 NCIT:C34131 UMLS:C1516779 embryo plus adnexa uberon UBERON:0004716 conceptus The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. BTO:0003834 UMLS:C1516779 ncithesaurus:Conceptus A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted A metameric segment of the central nervous system.[ZFA] Melissa Haendel 2009-06-18T09:00:04Z NLX:147842 TAO:0001328 ZFA:0001328 neural tube metameric segment neural tube segment neuromere neuromeres uberon neural metamere neural segment UBERON:0004731 neuromere A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). A metameric segment of the central nervous system.[ZFA] 2012-08-14 TAO:0001328 TAO ZFIN:curator neural tube metameric segment neuromeres TAO:0001328 Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451) FBbt:00005140 uberon neuromere UBERON:0004732 segmental subdivision of nervous system Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. FBbt:00005140 neuromere FBbt:00005140 An organ subunit that is part of a hindbrain [Automatically generated definition]. FMA:61998 hindbrain segment segment of hindbrain uberon UBERON:0004733 segmental subdivision of hindbrain An organ subunit that is part of a hindbrain [Automatically generated definition]. OBOL:automatic hindbrain segment FMA:61998 segment of hindbrain FMA:61998 Organism at the gastrula stage. We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 FMA:293108 GAID:1302 MESH:A16.254.412 MIAA:0000179 NCIT:C34057 NCIT:C34058 UMLS:C0017199 UMLS:C1284022 gastrula embryo uberon blastocystis trilaminaris tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ UBERON:0004734 gastrula Organism at the gastrula stage. We explicitly merge the NCITA terms here NCIT UMLS:C0017199 ncithesaurus:Gastrula UMLS:C1284022 ncithesaurus:Trilaminar_Embryonic_Disc gastrula embryo BILA:0000060 blastocystis trilaminaris tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ A collecting duct of renal tubule that is part of a metanephros [Automatically generated definition]. VHOG:0000983 collecting duct of metanephros uberon metanephric collecting tubule UBERON:0004737 metanephric collecting duct true Wikipedia-abduced A collecting duct of renal tubule that is part of a metanephros [Automatically generated definition]. OBOL:automatic metanephric collecting tubule VHOG:0000983 The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]. Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO] Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO] The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG] relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO] Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG] In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular. AAO:0000124 EFO:0003508 TAO:0000191 VHOG:0001022 ZFA:0000191 dentaries dentary bone uberon dentale os dentale sur-angulaire UBERON:0004742 dentary ZFA mandibular series ISBN:0073040584 ZFA EHDAA2 EHDAA2-modified The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]. VHOG:0001022 Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO] 2012-08-14 TAO:0000191 TAO TAO:GA_TG Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO] 2012-06-20 AAO:0000124 AAO AAO:LAP The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG] 2012-09-17 VHOG:0001022 VHOG relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO] 2012-08-14 TAO:0000191 TAO Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG] 2012-09-17 VHOG:0001022 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248 dentaries TAO:0000191 dentary bone ZFA:0000191 dentale AAO:0000124 os dentale AAO:0000124 sur-angulaire AAO:0000124 Skeletal element that consists of the scapula and the coracoid[VSAO, modified]. todo - decide whether to create separate classes for cartilage & ossified. Wikipedia considers this absent in Therians, but if considered as a grouping of scapula and coracoid then it would be present Fused, ossified portions of the scapula, procoracoid, and coracoid.[AAO] Pectoral fin cartilage that consists of a paired cartilaginous plate of the embryonic primary pectoral girdle and from which the scapular and coracaoid bones ossify.[TAO] either a fusion of the scapula and coracoid (the two main bones of the shoulder girdle), or the scapula & coracoid considered as a single structural unit.[Palaeos] relationship loss: part_of scapular area (AAO:0000935)[AAO] ZFA defines as precursor to scapula and coracoid. Cartilage in TAO AAO:0000781 TAO:0001455 VSAO:0005002 ZFA:0001455 scapulocoracoideum coraco-scapular cartilage scapulo-coracoid cartilage scapulocoracoid cartilage uberon UBERON:0004753 scapulocoracoid VSAO Skeletal element that consists of the scapula and the coracoid[VSAO, modified]. VSAO:0005002 Fused, ossified portions of the scapula, procoracoid, and coracoid.[AAO] 2012-06-20 AAO:0000781 AAO AAO:LAP Pectoral fin cartilage that consists of a paired cartilaginous plate of the embryonic primary pectoral girdle and from which the scapular and coracaoid bones ossify.[TAO] 2012-08-14 TAO:0001455 TAO TAO:GA_TG ZFIN:curator either a fusion of the scapula and coracoid (the two main bones of the shoulder girdle), or the scapula & coracoid considered as a single structural unit.[Palaeos] 2012-09-10 relationship loss: part_of scapular area (AAO:0000935)[AAO] 2012-06-20 AAO:0000781 AAO ZFA defines as precursor to scapula and coracoid. Cartilage in TAO ZFA scapulocoracoideum VSAO:0005002 coraco-scapular cartilage ZFA:0001455 scapulo-coracoid cartilage TAO:0001455 scapulocoracoid cartilage TAO:0001455 A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 MA:0003047 VSAO:0000015 XAO:0004038 ZFA:0005619 uberon UBERON:0004755 Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue VSAO A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] GO_REF:0000034 PSPUB:0000170 VSAO:0000015 A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] 2012-08-14 VSAO:0000015 taken from version of VSAO used in TAO and used directly in Uberon VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 EMAPA:37744 MA:th dermis-derived entity that is made of skeletal tissue. dermal element uberon UBERON:0004756 dermal skeletal element dermis-derived entity that is made of skeletal tissue. dermal element VSAO:curator A gland that is part of an anal canal [Automatically generated definition]. EMAPA:27221 EMAPA:27233 EMAPA:27543 FMA:15720 FMA:15724 NCIT:C32068 UMLS:C0162322 gland of anal canal uberon anal gland anal sac gland of anus rectal gland UBERON:0004760 gland of anal canal A gland that is part of an anal canal [Automatically generated definition]. OBOL:automatic UMLS:C0162322 ncithesaurus:Anal_Gland gland of anal canal OBOL:automatic anal sac The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) AAO:0000094 AAO:0010153 EHDAA:6031 FMA:76621 NCIT:C34121 UMLS:C1516496 XAO:0003059 cartilaginous chondocranium cartiligionous skeletal structure of skull uberon cartilaginous skull chondocranium embryonic chondocranium neurocranium UBERON:0004761 cartilaginous neurocranium FMA PMC1571569 The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) FMA UMLS:C1516496 ncithesaurus:Chondrocranium chondocranium neurocranium Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure uberon UBERON:0004765 skeletal element VSAO Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] 2012-08-14 VSAO:0000128 VSAO PSPUB:0000170 Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] 2012-08-14 TAO:0001890 TAO TAO:VSAO_workshop A bone that is part of a cranium. here cranium = skull - mandible cranium bone uberon UBERON:0004766 cranial bone A bone that is part of a cranium. UBERON:automatic cranium bone UBERON:automatic Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular Do not manually classify under here - bones are automatically classified lower jaw bone uberon UBERON:0004768 bone of lower jaw Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified]. Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA]. The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, Wikipedia:Diaphysis]. EMAPA:35504 FMA:24013 GAID:189 MESH:D018483 body of long bone long bone diaphysis shaft of long bone uberon UBERON:0004769 diaphysis http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified]. FMA:24013 Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA]. FMA:24013 The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, Wikipedia:Diaphysis]. FMA:24013, Wikipedia:Diaphysis Anatomical system that consists of all the joints of the body. EMAPA:35150 FMA:23878 MA:0003007 VSAO:0000181 joint system set of all joints of body uberon set of all joints set of joints of body UBERON:0004770 articular system FMA Anatomical system that consists of all the joints of the body. VSAO:0000181 joint system FMA:23878 set of all joints of body FMA:23878 set of joints of body FMA:23878 Opening/conduit between the nasal cavity and the nasopharynx[AAO] The choanae are separated by the vomer[WP]. One of the paired openings from the nasal cavities into the pharynx. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-6, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Opening between the nasal cavity and the nasopharynx.[AAO] The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] Fish don't have choanae, instead they have two pairs of external nostrils In addition to tetrapods, the lungfish has internal nostrils too. In tetrapods the exhalant nostril (choana) empties into the buccal cavity. choana internal naris AAO:0000093 EHDAA2:0000242 EHDAA:7842 EMAPA:17849 FMA:53143 MA:0001323 VHOG:0000545 XAO:0000277 posterior nasal apperture uberon choanae nasopharyngeal naris posterior choana posterior naris UBERON:0004771 posterior nasal aperture http://upload.wikimedia.org/wikipedia/commons/8/87/Gray855.png Opening/conduit between the nasal cavity and the nasopharynx[AAO] The choanae are separated by the vomer[WP]. AAO:0000093 One of the paired openings from the nasal cavities into the pharynx. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-6, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000545 VHOG Opening between the nasal cavity and the nasopharynx.[AAO] 2012-06-20 AAO:0000093 AAO AAO:LAP The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] 2012-09-17 VHOG:0000545 VHOG DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004) Fish don't have choanae, instead they have two pairs of external nostrils WP choana XAO:0000277 internal naris MA:0001323 posterior nasal apperture XAO:0000277 choanae VHOG:0000545 posterior choana HP:0004496 posterior naris VHOG:0000545 A submucosa that is part of a respiratory system [Automatically generated definition]. EMAPA:37578 MA:0001822 apparatus respiratorius submucosa submucosa of apparatus respiratorius submucosa of respiratory system uberon UBERON:0004777 respiratory system submucosa A submucosa that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37578 MA:th apparatus respiratorius submucosa OBOL:automatic submucosa of apparatus respiratorius OBOL:automatic submucosa of respiratory system OBOL:automatic A submucosa that is part of a larynx [Automatically generated definition]. EMAPA:35474 FMA:321584 MA:0002728 submucosa of larynx uberon laryngeal submucosa UBERON:0004778 larynx submucosa A submucosa that is part of a larynx [Automatically generated definition]. OBOL:automatic submucosa of larynx OBOL:automatic laryngeal submucosa EMAPA:35474 A lamina propria that is part of a respiratory system [Automatically generated definition]. EMAPA:37576 MA:0001821 apparatus respiratorius lamina propria apparatus respiratorius lamina propria mucosa lamina propria mucosa of apparatus respiratorius lamina propria mucosa of respiratory system lamina propria of apparatus respiratorius lamina propria of respiratory system respiratory system lamina propria mucosa uberon UBERON:0004779 respiratory system lamina propria true A lamina propria that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37576 MA:th apparatus respiratorius lamina propria OBOL:automatic apparatus respiratorius lamina propria mucosa OBOL:automatic lamina propria mucosa of apparatus respiratorius OBOL:automatic lamina propria mucosa of respiratory system OBOL:automatic lamina propria of apparatus respiratorius OBOL:automatic lamina propria of respiratory system OBOL:automatic respiratory system lamina propria mucosa OBOL:automatic A lamina propria that is part of a gastrointestinal system. MA:0001899 NCIT:C49299 UMLS:C1708197 uberon UBERON:0004780 gastrointestinal system lamina propria true A lamina propria that is part of a gastrointestinal system. OBOL:automatic UMLS:C1708197 ncithesaurus:Gastrointestinal_Tract_Lamina_Propria A lamina propria that is part of a gallbladder [Automatically generated definition]. EMAPA:35371 FMA:278594 MA:0001633 NCIT:C49228 UMLS:C1708175 gall bladder lamina propria mucosa gallbladder lamina propria gallbladder lamina propria mucosa lamina propria mucosa of gall bladder lamina propria mucosa of gallbladder lamina propria of gall bladder lamina propria of gallbladder uberon biliary lamina propria UBERON:0004781 gall bladder lamina propria true A lamina propria that is part of a gallbladder [Automatically generated definition]. OBOL:automatic UMLS:C1708175 ncithesaurus:Gallbladder_Lamina_Propria gall bladder lamina propria mucosa OBOL:automatic gallbladder lamina propria OBOL:automatic gallbladder lamina propria mucosa OBOL:automatic lamina propria mucosa of gall bladder OBOL:automatic lamina propria mucosa of gallbladder OBOL:automatic lamina propria of gall bladder OBOL:automatic lamina propria of gallbladder OBOL:automatic biliary lamina propria MA:0001633 A serous membrane that is part of a digestive system [Automatically generated definition]. EMAPA:37592 MA:0001522 digestive system serosa digestive system serous membrane gastrointestinal system serous membrane serosa of digestive system serosa of gastrointestinal system serous membrane of digestive system serous membrane of gastrointestinal system uberon UBERON:0004782 gastrointestinal system serosa A serous membrane that is part of a digestive system [Automatically generated definition]. OBOL:automatic EMAPA:37592 MA:th digestive system serosa OBOL:automatic digestive system serous membrane OBOL:automatic gastrointestinal system serous membrane OBOL:automatic serosa of digestive system OBOL:automatic serosa of gastrointestinal system OBOL:automatic serous membrane of digestive system OBOL:automatic serous membrane of gastrointestinal system OBOL:automatic A serous membrane that is part of a gallbladder [Automatically generated definition]. EMAPA:35372 FMA:14659 MA:0001634 gall bladder serous membrane gallbladder serosa gallbladder serous membrane serosa of gall bladder serosa of gallbladder serous coat of gallbladder serous membrane of gall bladder serous membrane of gallbladder tunica serosa (vesica biliaris) tunica serosa vesicae biliaris uberon biliary serosa UBERON:0004783 gall bladder serosa A serous membrane that is part of a gallbladder [Automatically generated definition]. OBOL:automatic gall bladder serous membrane OBOL:automatic gallbladder serosa OBOL:automatic gallbladder serous membrane OBOL:automatic serosa of gall bladder OBOL:automatic serosa of gallbladder OBOL:automatic serous coat of gallbladder FMA:14659 serous membrane of gall bladder OBOL:automatic serous membrane of gallbladder OBOL:automatic tunica serosa (vesica biliaris) FMA:14659 tunica serosa vesicae biliaris FMA:14659 FMA:TA biliary serosa MA:0001634 An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. FMA:13884 MA:0002791 NCIT:C119295 anatomical wall of cardiac ventricle anatomical wall of heart ventricle anatomical wall of lower chamber of heart anatomical wall of ventricle of heart cardiac ventricle anatomical wall cardiac ventricle wall heart ventricle anatomical wall lower chamber of heart anatomical wall lower chamber of heart wall ventricle of heart anatomical wall ventricle of heart wall ventricular wall wall of cardiac ventricle wall of heart ventricle wall of lower chamber of heart wall of ventricle of heart uberon wall of ventricle UBERON:0004784 heart ventricle wall An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. OBOL:automatic anatomical wall of cardiac ventricle OBOL:automatic anatomical wall of heart ventricle OBOL:automatic anatomical wall of lower chamber of heart OBOL:automatic anatomical wall of ventricle of heart OBOL:automatic cardiac ventricle anatomical wall OBOL:automatic cardiac ventricle wall OBOL:automatic heart ventricle anatomical wall OBOL:automatic lower chamber of heart anatomical wall OBOL:automatic lower chamber of heart wall OBOL:automatic ventricle of heart anatomical wall OBOL:automatic ventricle of heart wall OBOL:automatic ventricular wall FMA:13884 wall of cardiac ventricle OBOL:automatic wall of heart ventricle OBOL:automatic wall of lower chamber of heart OBOL:automatic wall of ventricle of heart OBOL:automatic wall of ventricle MA:0002791 the mucous membrane lining the respiratory tract TODO - split respiratory tract mucosa from respiratory system mucosa BTO:0000973 EMAPA:18334 EMAPA:37577 FMA:302092 GAID:304 MA:0001827 MESH:D020545 apparatus respiratorius mucosa apparatus respiratorius mucosa of organ apparatus respiratorius mucous membrane mucosa of apparatus respiratorius mucosa of organ of apparatus respiratorius mucosa of organ of respiratory system mucosa of respiratory system mucous membrane of apparatus respiratorius mucous membrane of respiratory system respiratory system mucosa of organ respiratory system mucous membrane uberon laryngeal mucous membrane respiratory mucosa respiratory tract mucosa UBERON:0004785 respiratory system mucosa the mucous membrane lining the respiratory tract MESH:A04.760 MGI:cwg MP:0002277 EMAPA:37577 MA:th apparatus respiratorius mucosa OBOL:automatic apparatus respiratorius mucosa of organ OBOL:automatic apparatus respiratorius mucous membrane OBOL:automatic mucosa of apparatus respiratorius OBOL:automatic mucosa of organ of apparatus respiratorius OBOL:automatic mucosa of organ of respiratory system OBOL:automatic mucosa of respiratory system OBOL:automatic mucous membrane of apparatus respiratorius OBOL:automatic mucous membrane of respiratory system OBOL:automatic respiratory system mucosa of organ OBOL:automatic respiratory system mucous membrane OBOL:automatic laryngeal mucous membrane EMAPA:18334 respiratory mucosa BTO:0000973 A mucosa that is part of a gastrointestinal system. BTO:0000546 BTO:0005568 EMAPA:36591 MA:0001521 digestive tract mucosa gut mucosa gut mucuous membrane mucosa of gut uberon UBERON:0004786 The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 gastrointestinal system mucosa BTO-modified A mucosa that is part of a gastrointestinal system. OBOL:automatic digestive tract mucosa gut mucosa BTO:0000546 gut mucuous membrane mucosa of gut A mucous gland that is part of a larynx [Automatically generated definition]. EMAPA:37631 MA:0001767 mucous gland of larynx uberon UBERON:0004789 larynx mucous gland A mucous gland that is part of a larynx [Automatically generated definition]. OBOL:automatic EMAPA:37631 MA:th mucous gland of larynx OBOL:automatic A mucous gland that is part of the skin. See comments for 'skin mucus' EMAPA:35775 MA:0000148 mucous gland of entire skin mucous gland of skin of body skin mucus gland skin of body mucous gland uberon UBERON:0004790 skin mucous gland A mucous gland that is part of the skin. mucous gland of entire skin OBOL:automatic mucous gland of skin of body OBOL:automatic skin mucus gland OBOL:automatic skin of body mucous gland OBOL:automatic the thymic connective tissue which extends into the parenchyma MA:0002674 NCIT:C33773 UMLS:C1515431 thymic trabecula thymus gland trabecula trabecula of thymus trabecula of thymus gland uberon UBERON:0004791 thymus trabecula MA the thymic connective tissue which extends into the parenchyma ISBN:0-397-51047-0 MGI:cwg MP:0002370 UMLS:C1515431 ncithesaurus:Thymic_Trabecula thymic trabecula OBOL:automatic thymus gland trabecula OBOL:automatic trabecula of thymus OBOL:automatic trabecula of thymus gland OBOL:automatic A secretion that is part of a endocrine pancreas [Automatically generated definition]. MA:0002517 NCIT:C33255 UMLS:C1518866 endocrine pancreas secretion pancreatic endocrine secretion pars endocrina pancreatis secretion secretion of pars endocrina pancreatis uberon UBERON:0004792 secretion of endocrine pancreas A secretion that is part of a endocrine pancreas [Automatically generated definition]. OBOL:automatic UMLS:C1518866 ncithesaurus:Pancreatic_Endocrine_Secretion endocrine pancreas secretion OBOL:automatic pancreatic endocrine secretion ncithesaurus:Pancreatic_Endocrine_Secretion pars endocrina pancreatis secretion OBOL:automatic secretion of pars endocrina pancreatis OBOL:automatic A secretion that is part of a exocrine pancreas [Automatically generated definition]. MA:0002518 NCIT:C33256 UMLS:C1518867 exocrine pancreas secretion pancreatic exocrine secretion pars exocrina pancreatis secretion secretion of pars exocrina pancreatis uberon UBERON:0004793 secretion of exocrine pancreas A secretion that is part of a exocrine pancreas [Automatically generated definition]. OBOL:automatic UMLS:C1518867 ncithesaurus:Pancreatic_Exocrine_Secretion exocrine pancreas secretion OBOL:automatic pancreatic exocrine secretion ncithesaurus:Pancreatic_Exocrine_Secretion pars exocrina pancreatis secretion OBOL:automatic secretion of pars exocrina pancreatis OBOL:automatic A secretion that is part of a esophagus [Automatically generated definition]. FMA:79662 MA:0002514 NCIT:C52555 UMLS:C0227179 esophageal secretion gullet secretion oesophagus secretion secretion of esophagus secretion of gullet secretion of oesophagus uberon UBERON:0004794 esophagus secretion A secretion that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C0227179 ncithesaurus:Esophagus_Secretion esophageal secretion FMA:79662 gullet secretion OBOL:automatic oesophagus secretion OBOL:automatic secretion of esophagus OBOL:automatic secretion of gullet OBOL:automatic secretion of oesophagus OBOL:automatic A secretion that is part of a pancreas [Automatically generated definition]. MA:0002516 NCIT:C13270 UMLS:C0030296 pancreatic secretion secretion of pancreas uberon UBERON:0004795 pancreas secretion A secretion that is part of a pancreas [Automatically generated definition]. OBOL:automatic UMLS:C0030296 ncithesaurus:Pancreatic_Secretion pancreatic secretion OBOL:automatic secretion of pancreas OBOL:automatic A bodily secretion that is produced by the prostate gland. Prostatic secretions vary among species. They are generally composed of simple sugars and are often slightly alkaline. A secretion of the prostate this is slightly alkaline fluid, milky or white in appearance. Usually constitutes 20-30% of the volume of the semen along with spermatozoa and seminal vesicle fluid [Wikipedia:Prostate#Secretions] UBERON:0010142 EMAPA:36545 FMA:66884 MA:0002525 NCIT:C52553 UMLS:C1709733 prostate secretion prostatic fluid secretion of prostate secretion of prostate gland uberon prostate fluid UBERON:0004796 prostate gland secretion FMA A bodily secretion that is produced by the prostate gland. UMLS:C1709733 ncithesaurus:Prostate_Gland_Secretion prostate secretion OBOL:automatic prostatic fluid FMA:66884 secretion of prostate OBOL:automatic secretion of prostate gland OBOL:automatic prostate fluid BTO:0001232 Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. EMAPA:36296 MA:0002854 uberon UBERON:0004797 blood vessel layer Blood:vessels.svg Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. An epithelium that is part of a uterine cervix [Automatically generated definition]. The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium BTO:0000241 CALOHA:TS-0137 EFO:0001913 EMAPA:29929 MA:0001724 NCIT:C49218 UMLS:C1711358 cervical canal epithelial tissue cervical canal epithelium cervical epithelium cervix epithelial tissue epithelium of cervix uberon UBERON:0004801 cervix epithelium An epithelium that is part of a uterine cervix [Automatically generated definition]. OBOL:automatic The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium UMLS:C1711358 ncithesaurus:Cervix_Epithelium cervical canal epithelial tissue OBOL:automatic cervical canal epithelium OBOL:automatic cervical epithelium BTO:0000241 cervix epithelial tissue OBOL:automatic epithelium of cervix OBOL:automatic the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi BTO:0000419 CALOHA:TS-0023 EMAPA:32827 MA:0001480 VHOG:0000981 epithelial tissue of respiratory tract epithelium of respiratory tract respiratory tract epithelial tissue uberon airway epithelium respiratory epithelium UBERON:0004802 respiratory tract epithelium the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi ISBN:0-683-40008-8 MGI:anna MP:0010942 epithelial tissue of respiratory tract OBOL:automatic epithelium of respiratory tract OBOL:automatic respiratory tract epithelial tissue OBOL:automatic airway epithelium BTO:0000419 respiratory epithelium BTO:0000419 An epithelium that is part of a penis [Automatically generated definition]. EHDAA2:0004039 EMAPA:35674 MA:0001742 epithelial tissue of penis epithelium of penis penis epithelial tissue uberon UBERON:0004803 penis epithelium An epithelium that is part of a penis [Automatically generated definition]. OBOL:automatic epithelial tissue of penis OBOL:automatic epithelium of penis OBOL:automatic penis epithelial tissue OBOL:automatic An epithelium that is part of a oviduct [Automatically generated definition]. in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label BTO:0002402 CALOHA:TS-1316 EMAPA:29043 MA:0001718 epithelial tissue of oviduct epithelium of fallopian tube epithelium of oviduct epithelium of uterine tube oviduct epithelial tissue uberon columnar epithelium of the fallopian tube columnar epithelium of the oviduct fallopian tube epithelium UBERON:0004804 oviduct epithelium An epithelium that is part of a oviduct [Automatically generated definition]. OBOL:automatic in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA epithelial tissue of oviduct OBOL:automatic epithelium of fallopian tube OBOL:automatic epithelium of oviduct OBOL:automatic epithelium of uterine tube FMA:62016 oviduct epithelial tissue OBOL:automatic columnar epithelium of the fallopian tube BTO:0002402 columnar epithelium of the oviduct BTO:0002402 fallopian tube epithelium BTO:0002402 An epithelium that is part of a seminal vesicle [Automatically generated definition]. CALOHA:TS-2069 EMAPA:29771 MA:0001745 NCIT:C49295 UMLS:C1710049 epithelial tissue of seminal gland epithelial tissue of seminal vesicle epithelium of seminal gland epithelium of seminal vesicle seminal gland epithelial tissue seminal gland epithelium seminal vesicle epithelial tissue uberon UBERON:0004805 seminal vesicle epithelium An epithelium that is part of a seminal vesicle [Automatically generated definition]. OBOL:automatic UMLS:C1710049 ncithesaurus:Seminal_Vesicle_Epithelium epithelial tissue of seminal gland OBOL:automatic epithelial tissue of seminal vesicle OBOL:automatic epithelium of seminal gland OBOL:automatic epithelium of seminal vesicle OBOL:automatic seminal gland epithelial tissue OBOL:automatic seminal gland epithelium OBOL:automatic seminal vesicle epithelial tissue OBOL:automatic An epithelium that is part of a vas deferens [Automatically generated definition]. EMAPA:29274 FMA:225317 MA:0001749 NCIT:C49315 UMLS:C1710617 deferent duct epithelial tissue deferent duct epithelium ductus deferens epithelial tissue ductus deferens epithelium epithelial tissue of deferent duct epithelial tissue of ductus deferens epithelial tissue of sperm duct epithelial tissue of vas deferen epithelial tissue of vas deferens epithelium of deferent duct epithelium of ductus deferens epithelium of sperm duct epithelium of vas deferen epithelium of vas deferens sperm duct epithelial tissue sperm duct epithelium vas deferen epithelial tissue vas deferen epithelium vas deferens epithelial tissue uberon UBERON:0004806 vas deferens epithelium An epithelium that is part of a vas deferens [Automatically generated definition]. OBOL:automatic UMLS:C1710617 ncithesaurus:Vas_Deferens_Epithelium deferent duct epithelial tissue OBOL:automatic deferent duct epithelium OBOL:automatic ductus deferens epithelial tissue OBOL:automatic ductus deferens epithelium OBOL:automatic epithelial tissue of deferent duct OBOL:automatic epithelial tissue of ductus deferens OBOL:automatic epithelial tissue of sperm duct OBOL:automatic epithelial tissue of vas deferen OBOL:automatic epithelial tissue of vas deferens OBOL:automatic epithelium of deferent duct OBOL:automatic epithelium of ductus deferens OBOL:automatic epithelium of sperm duct OBOL:automatic epithelium of vas deferen OBOL:automatic epithelium of vas deferens OBOL:automatic sperm duct epithelial tissue OBOL:automatic sperm duct epithelium OBOL:automatic vas deferen epithelial tissue OBOL:automatic vas deferen epithelium OBOL:automatic vas deferens epithelial tissue OBOL:automatic An epithelium that is part of a respiratory system [Automatically generated definition]. CALOHA:TS-0023 EMAPA:32826 MA:0001823 VHOG:0000981 apparatus respiratorius epithelial tissue apparatus respiratorius epithelium epithelial tissue of apparatus respiratorius epithelial tissue of respiratory system epithelium of apparatus respiratorius epithelium of respiratory system respiratory system epithelial tissue uberon UBERON:0004807 respiratory system epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius epithelial tissue OBOL:automatic apparatus respiratorius epithelium OBOL:automatic epithelial tissue of apparatus respiratorius OBOL:automatic epithelial tissue of respiratory system OBOL:automatic epithelium of apparatus respiratorius OBOL:automatic epithelium of respiratory system OBOL:automatic respiratory system epithelial tissue OBOL:automatic An epithelium that is part of a digestive system [Automatically generated definition]. EMAPA:32683 MA:0001520 digestive system epithelial tissue digestive system epithelium epithelial tissue of digestive system epithelial tissue of gastrointestinal system epithelium of digestive system epithelium of gastrointestinal system gastrointestinal system epithelial tissue uberon UBERON:0004808 gastrointestinal system epithelium An epithelium that is part of a digestive system [Automatically generated definition]. OBOL:automatic digestive system epithelial tissue OBOL:automatic digestive system epithelium OBOL:automatic epithelial tissue of digestive system OBOL:automatic epithelial tissue of gastrointestinal system OBOL:automatic epithelium of digestive system OBOL:automatic epithelium of gastrointestinal system OBOL:automatic gastrointestinal system epithelial tissue OBOL:automatic An epithelium that is part of a salivary gland [Automatically generated definition]. BTO:0004421 CALOHA:TS-2067 EMAPA:32816 MA:0001587 epithelial tissue of salivary gland epithelium of salivary gland salivary gland epithelial tissue uberon UBERON:0004809 salivary gland epithelium An epithelium that is part of a salivary gland [Automatically generated definition]. OBOL:automatic epithelial tissue of salivary gland OBOL:automatic epithelium of salivary gland OBOL:automatic salivary gland epithelial tissue OBOL:automatic the cellular avascular layer of the renal tubule luminar surfaces See https://github.com/obophenotype/uberon/issues/1305 BTO:0005239 EMAPA:36524 MA:0001681 NCIT:C49276 UMLS:C1709902 kidney tubule epithelium uberon UBERON:0004810 nephron tubule epithelium the cellular avascular layer of the renal tubule luminar surfaces MGI:csmith MP:0009640 UMLS:C1709902 ncithesaurus:Renal_Tubule_Epithelium kidney tubule epithelium MA:0001681 An epithelium that is part of an endometrium [Automatically generated definition]. In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial) EMAPA:35307 MA:0002731 endometrium epithelial tissue epithelial tissue of endometrium epithelium of endometrium epithelium of tunica mucosa of endometrium uberon uterine epithelium UBERON:0004811 endometrium epithelium An epithelium that is part of an endometrium [Automatically generated definition]. OBOL:automatic In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial) endometrium epithelial tissue OBOL:automatic epithelial tissue of endometrium OBOL:automatic epithelium of endometrium OBOL:automatic epithelium of tunica mucosa of endometrium OBOL:automatic uterine epithelium An epithelium that is part of a prepuce of penis [Automatically generated definition]. NCITA term may be sex-neutral epithelial tissue of prepuce epithelium of prepuce prepuce epithelial tissue prepuce of penis epithelium EMAPA:30655 MA:0001753 NCIT:C49270 UMLS:C1709639 epithelial tissue of foreskin epithelial tissue of penile prepuce epithelial tissue of prepuce of penis epithelium of foreskin epithelium of penile prepuce epithelium of prepuce of penis foreskin epithelial tissue foreskin epithelium penile prepuce epithelial tissue penile prepuce epithelium prepuce epithelium prepuce of penis epithelial tissue uberon UBERON:0004812 male prepuce epithelium An epithelium that is part of a prepuce of penis [Automatically generated definition]. OBOL:automatic epithelial tissue of prepuce OBOL:automatic epithelium of prepuce OBOL:automatic prepuce epithelial tissue OBOL:automatic prepuce of penis epithelium OBOL:automatic UMLS:C1709639 ncithesaurus:Prepuce_Epithelium epithelial tissue of foreskin OBOL:automatic epithelial tissue of penile prepuce OBOL:automatic epithelial tissue of prepuce of penis OBOL:automatic epithelium of foreskin OBOL:automatic epithelium of penile prepuce OBOL:automatic epithelium of prepuce of penis OBOL:automatic foreskin epithelial tissue OBOL:automatic foreskin epithelium OBOL:automatic penile prepuce epithelial tissue OBOL:automatic penile prepuce epithelium OBOL:automatic prepuce epithelium MA:0001753 prepuce of penis epithelial tissue OBOL:automatic the stratified epithelial lining of the seminiferous tubules, consisting of the developing spermatozoa and the supporting Sertoli cells, which are tall, columnar type cells that line the tubule BTO:0001811 CALOHA:TS-0920 EHDAA:8148 EMAPA:35761 FMA:19885 GAID:401 MA:0001748 MESH:D012670 NCIT:C49296 RETIRED_EHDAA2:0002009 UMLS:C0036629 VHOG:0000631 epithelial tissue of seminiferous tubule epithelial tissue of seminiferous tubule of testis epithelium of seminiferous tubule epithelium of seminiferous tubule of testis germinal epithelium (male) male germinal epithelium seminiferous epithelium seminiferous tubule epithelial tissue testis germinal epithelium wall of seminiferous tubule uberon UBERON:0004813 seminiferous tubule epithelium the stratified epithelial lining of the seminiferous tubules, consisting of the developing spermatozoa and the supporting Sertoli cells, which are tall, columnar type cells that line the tubule MGI:csmith MP:0011750 UMLS:C0036629 ncithesaurus:Seminiferous_Epithelium epithelial tissue of seminiferous tubule OBOL:automatic epithelial tissue of seminiferous tubule of testis OBOL:automatic epithelium of seminiferous tubule OBOL:automatic epithelium of seminiferous tubule of testis OBOL:automatic germinal epithelium (male) male germinal epithelium seminiferous epithelium BTO:0001811 seminiferous tubule epithelial tissue OBOL:automatic testis germinal epithelium VHOG:0000631 wall of seminiferous tubule An epithelium that is part of a upper respiratory tract [Automatically generated definition]. EMAPA:35894 MA:0001912 epithelial tissue of upper respiratory tract epithelium of upper respiratory tract upper respiratory tract epithelial tissue uberon UBERON:0004814 upper respiratory tract epithelium An epithelium that is part of a upper respiratory tract [Automatically generated definition]. OBOL:automatic epithelial tissue of upper respiratory tract OBOL:automatic epithelium of upper respiratory tract OBOL:automatic upper respiratory tract epithelial tissue OBOL:automatic An epithelium that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37549 MA:0001481 epithelial tissue of lower respiratory tract epithelium of lower respiratory tract lower respiratory tract epithelial tissue uberon UBERON:0004815 lower respiratory tract epithelium An epithelium that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37549 MA:th epithelial tissue of lower respiratory tract OBOL:automatic epithelium of lower respiratory tract OBOL:automatic lower respiratory tract epithelial tissue OBOL:automatic An epithelium that is part of a larynx [Automatically generated definition]. composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0] EHDAA2:0004065 EMAPA:35472 MA:0001765 NCIT:C49247 UMLS:C0751258 epithelial tissue of larynx epithelium of larynx laryngeal epithelium larynx epithelial tissue uberon UBERON:0004816 larynx epithelium An epithelium that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C0751258 ncithesaurus:Laryngeal_Epithelium epithelial tissue of larynx OBOL:automatic epithelium of larynx OBOL:automatic laryngeal epithelium OBOL:automatic larynx epithelial tissue OBOL:automatic An epithelium that is part of a lacrimal gland [Automatically generated definition]. EMAPA:36515 MA:0001297 epithelial tissue of lacrimal gland epithelium of lacrimal gland lacrimal gland epithelial tissue uberon UBERON:0004817 lacrimal gland epithelium An epithelium that is part of a lacrimal gland [Automatically generated definition]. OBOL:automatic epithelial tissue of lacrimal gland OBOL:automatic epithelium of lacrimal gland OBOL:automatic lacrimal gland epithelial tissue OBOL:automatic the cellular avascular layer of the kidney luminar surfaces BTO:0000059 CALOHA:TS-0505 EMAPA:35457 MA:0002846 epithelial tissue of kidney epithelium of kidney kidney epithelial tissue uberon renal epithelium UBERON:0004819 kidney epithelium the cellular avascular layer of the kidney luminar surfaces MGI:csmith MP:0004967 epithelial tissue of kidney OBOL:automatic epithelium of kidney OBOL:automatic kidney epithelial tissue OBOL:automatic renal epithelium EMAPA:35457 Any epithelium that lines one of the bile ducts. The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium. BTO:0000417 MA:0001629 NCIT:C43616 UMLS:C1711208 biliary duct epithelium epithelium of bile duct epithelium of biliary duct uberon UBERON:0004820 bile duct epithelium Any epithelium that lines one of the bile ducts. The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium. BTO:0000417 UMLS:C1711208 ncithesaurus:Bile_Duct_Epithelium biliary duct epithelium OBOL:automatic epithelium of bile duct OBOL:automatic epithelium of biliary duct OBOL:automatic An epithelium that is part of a extrahepatic bile duct [Automatically generated definition]. EHDAA2:0000742 EHDAA:3051 MA:0002661 NCIT:C43618 UMLS:C1711347 epithelial tissue of extrahepatic bile duct epithelium of extrahepatic bile duct extrahepatic bile duct epithelial tissue uberon UBERON:0004822 extrahepatic bile duct epithelium An epithelium that is part of a extrahepatic bile duct [Automatically generated definition]. OBOL:automatic UMLS:C1711347 ncithesaurus:Extrahepatic_Bile_Duct_Epithelium epithelial tissue of extrahepatic bile duct OBOL:automatic epithelium of extrahepatic bile duct OBOL:automatic extrahepatic bile duct epithelial tissue OBOL:automatic An epithelium that is part of a intrahepatic bile duct [Automatically generated definition]. EHDAA2:0000743 EHDAA:3053 MA:0002662 NCIT:C43617 UMLS:C1708552 epithelial tissue of intrahepatic bile duct epithelium of intrahepatic bile duct intrahepatic bile duct epithelial tissue uberon UBERON:0004823 intrahepatic bile duct epithelium An epithelium that is part of a intrahepatic bile duct [Automatically generated definition]. OBOL:automatic UMLS:C1708552 ncithesaurus:Intrahepatic_Bile_Duct_Epithelium epithelial tissue of intrahepatic bile duct OBOL:automatic epithelium of intrahepatic bile duct OBOL:automatic intrahepatic bile duct epithelial tissue OBOL:automatic A medulla that is part of a thyroid [Automatically generated definition]. EMAPA:37768 MA:0000132 medulla of thyroid medulla of thyroid follicle medulla of thyroid gland medulla of thyroid gland follicle thyroid follicle medulla thyroid gland follicle medulla thyroid medulla uberon UBERON:0004827 thyroid gland medulla A medulla that is part of a thyroid [Automatically generated definition]. OBOL:automatic EMAPA:37768 MA:th medulla of thyroid OBOL:automatic medulla of thyroid follicle OBOL:automatic medulla of thyroid gland OBOL:automatic medulla of thyroid gland follicle OBOL:automatic thyroid follicle medulla OBOL:automatic thyroid gland follicle medulla OBOL:automatic thyroid medulla OBOL:automatic A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]. EMAPA:37788 MA:0001690 skeletal muscle of urethra skeletal muscle tissue of urethra urethra skeletal muscle tissue uberon urethra skeletal muscle urethral skeletal muscle UBERON:0004829 urethra skeletal muscle tissue A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]. OBOL:automatic EMAPA:37788 MA:th skeletal muscle of urethra OBOL:automatic skeletal muscle tissue of urethra OBOL:automatic urethra skeletal muscle tissue OBOL:automatic urethra skeletal muscle MA:0001690 urethral skeletal muscle MA:0001690 A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37583 MA:0001829 respiratory system skeletal muscle tissue skeletal muscle of apparatus respiratorius skeletal muscle of respiratory system skeletal muscle tissue of apparatus respiratorius skeletal muscle tissue of respiratory system uberon UBERON:0004830 respiratory system skeletal muscle A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37583 MA:th respiratory system skeletal muscle tissue OBOL:automatic skeletal muscle of apparatus respiratorius OBOL:automatic skeletal muscle of respiratory system OBOL:automatic skeletal muscle tissue of apparatus respiratorius OBOL:automatic skeletal muscle tissue of respiratory system OBOL:automatic A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. EMAPA:36523 MA:0001572 esophagus skeletal muscle tissue skeletal muscle of esophagus uberon UBERON:0004831 Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal esophagus skeletal muscle A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus skeletal muscle tissue OBOL:automatic skeletal muscle of esophagus OBOL:automatic A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37393 MA:0001530 anal part of perineum skeletal muscle anal part of perineum skeletal muscle tissue anal region skeletal muscle tissue anal triangle skeletal muscle anal triangle skeletal muscle tissue skeletal muscle of anal part of perineum skeletal muscle of anal region skeletal muscle of anal triangle skeletal muscle tissue of anal part of perineum skeletal muscle tissue of anal region skeletal muscle tissue of anal triangle uberon UBERON:0004832 anal region skeletal muscle A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37393 MA:th anal part of perineum skeletal muscle OBOL:automatic anal part of perineum skeletal muscle tissue OBOL:automatic anal region skeletal muscle tissue OBOL:automatic anal triangle skeletal muscle OBOL:automatic anal triangle skeletal muscle tissue OBOL:automatic skeletal muscle of anal part of perineum OBOL:automatic skeletal muscle of anal region OBOL:automatic skeletal muscle of anal triangle OBOL:automatic skeletal muscle tissue of anal part of perineum OBOL:automatic skeletal muscle tissue of anal region OBOL:automatic skeletal muscle tissue of anal triangle OBOL:automatic A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips EMAPA:37642 MA:0001578 lip skeletal muscle tissue skeletal muscle of lip skeletal muscle tissue of lip uberon UBERON:0004833 lip skeletal muscle A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37642 MA:th lip skeletal muscle tissue OBOL:automatic skeletal muscle of lip OBOL:automatic skeletal muscle tissue of lip OBOL:automatic Smooth muscle tissue in all or part of a hepatic duct. EMAPA:37598 MA:0001640 uberon UBERON:0004834 hepatic duct smooth muscle Smooth muscle tissue in all or part of a hepatic duct. EMAPA:37598 MA:th A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition]. EMAPA:30747 MA:0001736 epididymis involuntary muscle epididymis non-striated muscle epididymis smooth muscle tissue involuntary muscle of epididymis non-striated muscle of epididymis smooth muscle of epididymis smooth muscle tissue of epididymis uberon UBERON:0004835 epididymis smooth muscle A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition]. OBOL:automatic epididymis involuntary muscle OBOL:automatic epididymis non-striated muscle OBOL:automatic epididymis smooth muscle tissue OBOL:automatic involuntary muscle of epididymis OBOL:automatic non-striated muscle of epididymis OBOL:automatic smooth muscle of epididymis OBOL:automatic smooth muscle tissue of epididymis OBOL:automatic An endothelium of artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37566 MA:0001801 apparatus respiratorius arterial endothelium apparatus respiratorius artery endothelium apparatus respiratorius endothelium of artery arterial endothelium of apparatus respiratorius arterial endothelium of respiratory system artery endothelium of apparatus respiratorius artery endothelium of respiratory system endothelium of artery of apparatus respiratorius endothelium of artery of respiratory system respiratory system artery endothelium respiratory system endothelium of artery uberon UBERON:0004848 respiratory system arterial endothelium true An endothelium of artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37566 MA:th apparatus respiratorius arterial endothelium OBOL:automatic apparatus respiratorius artery endothelium OBOL:automatic apparatus respiratorius endothelium of artery OBOL:automatic arterial endothelium of apparatus respiratorius OBOL:automatic arterial endothelium of respiratory system OBOL:automatic artery endothelium of apparatus respiratorius OBOL:automatic artery endothelium of respiratory system OBOL:automatic endothelium of artery of apparatus respiratorius OBOL:automatic endothelium of artery of respiratory system OBOL:automatic respiratory system artery endothelium OBOL:automatic respiratory system endothelium of artery OBOL:automatic An endothelium of vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37585 MA:0001811 apparatus respiratorius endothelium of vein apparatus respiratorius vein endothelium apparatus respiratorius venous endothelium endothelium of vein of apparatus respiratorius endothelium of vein of respiratory system respiratory system endothelium of vein respiratory system vein endothelium vein endothelium of apparatus respiratorius vein endothelium of respiratory system venous endothelium of apparatus respiratorius venous endothelium of respiratory system uberon UBERON:0004849 respiratory system venous endothelium An endothelium of vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37585 MA:th apparatus respiratorius endothelium of vein OBOL:automatic apparatus respiratorius vein endothelium OBOL:automatic apparatus respiratorius venous endothelium OBOL:automatic endothelium of vein of apparatus respiratorius OBOL:automatic endothelium of vein of respiratory system OBOL:automatic respiratory system endothelium of vein OBOL:automatic respiratory system vein endothelium OBOL:automatic vein endothelium of apparatus respiratorius OBOL:automatic vein endothelium of respiratory system OBOL:automatic venous endothelium of apparatus respiratorius OBOL:automatic venous endothelium of respiratory system OBOL:automatic An endothelium that is part of a lymph node [Automatically generated definition]. EMAPA:35526 MA:0000741 endothelium of lymph node uberon UBERON:0004850 lymph node endothelium An endothelium that is part of a lymph node [Automatically generated definition]. OBOL:automatic endothelium of lymph node OBOL:automatic the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall BTO:0000394 CALOHA:TS-0047 EFO:0002597 EMAPA:35134 MA:0000701 NCIT:C49190 UMLS:C1706824 adult aorta endothelium endothelium of adult aorta endothelium of aorta endothelium of trunk of aortic tree endothelium of trunk of systemic arterial tree trunk of aortic tree endothelium trunk of systemic arterial tree endothelium uberon aortic endothelium UBERON:0004851 aorta endothelium the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall MGI:csmith MP:0009864 UMLS:C1706824 ncithesaurus:Aorta_Endothelium adult aorta endothelium OBOL:automatic endothelium of adult aorta OBOL:automatic endothelium of aorta OBOL:automatic endothelium of trunk of aortic tree OBOL:automatic endothelium of trunk of systemic arterial tree OBOL:automatic trunk of aortic tree endothelium OBOL:automatic trunk of systemic arterial tree endothelium OBOL:automatic aortic endothelium BTO:0000394 An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 MA:0000717 MESH:D004730 NCIT:C13053 TAO:0002171 UMLS:C0014261 VHOG:0001217 XAO:0000356 ZFA:0001639 uberon endothelia vascular endothelia UBERON:0004852 cardiovascular system endothelium An endothelium that is part of the cardiovascular system. Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001217 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 UMLS:C0014261 ncithesaurus:Vascular_Endothelium endothelia ZFA:0001639 vascular endothelia XAO:0000356 A mesentery that is part of a digestive system [Automatically generated definition]. EMAPA:37068 MA:0001900 digestive system mesentery mesentery of digestive system mesentery of gastrointestinal system uberon UBERON:0004854 gastrointestinal system mesentery A mesentery that is part of a digestive system [Automatically generated definition]. OBOL:automatic EMAPA:37068 MA:th digestive system mesentery OBOL:automatic mesentery of digestive system OBOL:automatic mesentery of gastrointestinal system OBOL:automatic A connective tissue that surrounds a skeletal muscle tissue. EMAPA:37743 MA:0002868 connective tissue of skeletal muscle connective tissue of skeletal muscle tissue portion of connective tissue of skeletal muscle portion of connective tissue of skeletal muscle tissue skeletal muscle portion of connective tissue skeletal muscle textus connectivus skeletal muscle tissue connective tissue skeletal muscle tissue portion of connective tissue skeletal muscle tissue textus connectivus textus connectivus of skeletal muscle textus connectivus of skeletal muscle tissue uberon skeletal muscle interstitial tissue skeletal muscle interstitum UBERON:0004857 skeletal muscle connective tissue A connective tissue that surrounds a skeletal muscle tissue. OBOL:automatic EMAPA:37743 MA:th connective tissue of skeletal muscle OBOL:automatic connective tissue of skeletal muscle tissue OBOL:automatic portion of connective tissue of skeletal muscle OBOL:automatic portion of connective tissue of skeletal muscle tissue OBOL:automatic skeletal muscle portion of connective tissue OBOL:automatic skeletal muscle textus connectivus OBOL:automatic skeletal muscle tissue connective tissue OBOL:automatic skeletal muscle tissue portion of connective tissue OBOL:automatic skeletal muscle tissue textus connectivus OBOL:automatic textus connectivus of skeletal muscle OBOL:automatic textus connectivus of skeletal muscle tissue OBOL:automatic skeletal muscle interstitial tissue MA:0002868 skeletal muscle interstitum MA:0002868 A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. EMAPA:35334 MA:0000267 eye-associated gland gland of eye uberon UBERON:0004859 Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands eye gland A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. eye-associated gland gland of eye OBOL:automatic A sympathetic nerve trunk that is part of a thorax [Automatically generated definition]. EMAPA:37657 FMA:6262 MA:0001165 NCIT:C52827 UMLS:C1710393 nerve trunk of sympathetic nervous system of thorax nerve trunk of sympathetic part of autonomic division of nervous system of thorax sympathetic nerve trunk of thorax sympathetic nervous system nerve trunk of thorax thoracic part of sympathetic trunk thoracic sympathetic chain thorax nerve trunk of sympathetic nervous system thorax nerve trunk of sympathetic part of autonomic division of nervous system thorax sympathetic nerve trunk thorax sympathetic nervous system nerve trunk uberon thoracic sympathetic trunk UBERON:0004863 thoracic sympathetic nerve trunk A sympathetic nerve trunk that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37657 MA:th UMLS:C1710393 ncithesaurus:Thoracic_Sympathetic_Nerve_Trunk nerve trunk of sympathetic nervous system of thorax OBOL:automatic nerve trunk of sympathetic part of autonomic division of nervous system of thorax OBOL:automatic sympathetic nerve trunk of thorax OBOL:automatic sympathetic nervous system nerve trunk of thorax OBOL:automatic thoracic part of sympathetic trunk FMA:6262 thoracic sympathetic chain FMA:6262 thorax nerve trunk of sympathetic nervous system OBOL:automatic thorax nerve trunk of sympathetic part of autonomic division of nervous system OBOL:automatic thorax sympathetic nerve trunk OBOL:automatic thorax sympathetic nervous system nerve trunk OBOL:automatic thoracic sympathetic trunk FMA:6262 A vasculature that is part of a retina [Automatically generated definition]. FMA:76552 MESH:D012171 XAO:0004153 retina vasculature retina vasculature of camera-type eye retinal blood vessels retinal blood vessels set retinal vasculature set of blood vessels of retina set of retinal blood vessels vasa sanguinea retinae uberon UBERON:0004864 vasculature of retina A vasculature that is part of a retina [Automatically generated definition]. OBOL:automatic retina vasculature GO:0061298 retina vasculature of camera-type eye GO:0061298 retinal blood vessels FMA:76552 retinal blood vessels set FMA:76552 retinal vasculature OBOL:automatic set of blood vessels of retina OBOL:automatic set of retinal blood vessels FMA:76552 vasa sanguinea retinae FMA:76552 FMA:TA A part of the epithalamus present in some animal species. The eye may be photoreceptive and is usually associated with the pineal gland, regulating circadian rhythmicity and hormone production for thermoregulation. The parietal eye is a part of the epithalamus, which can be divided into two major parts; the epiphysis (the pineal organ, or pineal gland if mostly endocrine) and the parietal organ (often called the parietal eye, or third eye if it is photoreceptive). It arises as an anterior evagination of the pineal organ or as a separate outgrowth of the roof of the diencephalon. In some species, it protrudes through the skull.[4] The parietal eye uses a different biochemical method of detecting light than rod cells or cone cells in a normal vertebrate eye[WP]. parietal eye uberon third eye UBERON:0004869 parietal organ cjm cjm A part of the epithalamus present in some animal species. The eye may be photoreceptive and is usually associated with the pineal gland, regulating circadian rhythmicity and hormone production for thermoregulation. The parietal eye is a part of the epithalamus, which can be divided into two major parts; the epiphysis (the pineal organ, or pineal gland if mostly endocrine) and the parietal organ (often called the parietal eye, or third eye if it is photoreceptive). It arises as an anterior evagination of the pineal organ or as a separate outgrowth of the roof of the diencephalon. In some species, it protrudes through the skull.[4] The parietal eye uses a different biochemical method of detecting light than rod cells or cone cells in a normal vertebrate eye[WP]. parietal eye third eye Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP]. check BILA AAO:0011100 BILA:0000047 FMA:295570 XAO:0000271 outer layer of lateral plate mesoderm uberon parietal mesoderm somatic mesoderm UBERON:0004871 somatic layer of lateral plate mesoderm Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP]. parietal mesoderm ISBN:9780878932504 somatic mesoderm BILA:0000047 Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 FMA:295568 XAO:0000276 inner layer of lateral plate mesoderm uberon splanchnic mesoderm UBERON:0004872 splanchnic layer of lateral plate mesoderm Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors BILA visceral mesoderm BILA:0000044 splanchnic mesoderm ISBN:9780878932504 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. TODO - check relationship to LPM EHDAA2:0001903 EHDAA:383 EMAPA:16181 FMA:295564 NCIT:C34303 UMLS:C1519472 VHOG:0000558 uberon ventral splanchnic mesoderm UBERON:0004873 splanchnopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. UMLS:C1519472 ncithesaurus:Splanchnopleure ventral splanchnic mesoderm A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/ sources differ as to whether this is part-of or develops-from the LPM EHDAA2:0001847 EHDAA:381 EMAPA:16180 FMA:295566 NCIT:C34301 UMLS:C1519423 VHOG:0000557 uberon UBERON:0004874 somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. UMLS:C1519423 ncithesaurus:Somatopleure A portion of the urogenital ridge which is the source of much of the urinary system[WP]. FMA:72168 NCIT:C34219 UMLS:C1283944 uberon chorda nephrogenica UBERON:0004875 part_of or develops_from urogenital ridge? nephrogenic cord A portion of the urogenital ridge which is the source of much of the urinary system[WP]. UMLS:C1283944 ncithesaurus:Nephrogenic_Cord chorda nephrogenica One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP] EHDAA2:0004022 EMAPA:30888 FMA:321919 urethral fold urogenital fold uberon urogenital ridge UBERON:0004876 urogenital fold EHDAA2 Wikipedia EHDAA2 One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. MP:0011835 MP:anna urethral fold EMAPA:30888 urogenital fold EHDAA2:0004022 MP:0011835 urogenital ridge MP:0011835 The central region of trunk mesoderm. This tissue forms the notochord Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 ZFA:0000091 axial chorda mesoderm chorda mesoderm dorsal mesoderm presumptive notochord uberon UBERON:0004880 chordamesoderm The central region of trunk mesoderm. This tissue forms the notochord Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 axial chorda mesoderm ZFA:0000091 dorsal mesoderm presumptive notochord ZFA:0000091 The mass of tissue made up of mesenchymal cells in the lung. EMAPA:32866 lung-associated mesenchyme mesenchyme of lung pulmonary mesenchyme uberon UBERON:0004883 lung mesenchyme The mass of tissue made up of mesenchymal cells in the lung. GO:0060484 lung-associated mesenchyme GO:0060484 mesenchyme of lung OBOL:automatic pulmonary mesenchyme GO:0060484 The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra we follow EHDAA2 in dividing the UGS into epithelium and lumen EHDAA2:0004061 EMAPA:31509 UGE epithelium of urogenital sinus uberon UBERON:0004902 urogenital sinus epithelium The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra we follow EHDAA2 in dividing the UGS into epithelium and lumen EHDAA2 UGE epithelium of urogenital sinus OBOL:automatic A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila optic nerve BTO:0000966 EV:0100351 FBbt:00001956 TADS:0000232 optic nerve (generic) uberon UBERON:0004904 for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II) neuron projection bundle connecting eye with brain A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila optic nerve BTO:0000966 Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 joint uberon UBERON:0004905 articulation Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. A portion of the gut that is derived from ectoderm. ectodermal gut gut ectoderm uberon UBERON:0004906 ectodermal part of digestive tract A portion of the gut that is derived from ectoderm. GO:0007439 gut ectoderm EMAPA:32930 The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L gut FMA:49179 NCIT:C33010 UMLS:C0226875 galen:LowerGastrointestinalTract lower GI tract lower gastrointestinal tract uberon UBERON:0004907 lower digestive tract The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 MA WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L FMA gut GO:0048565 UMLS:C0226875 ncithesaurus:Lower_Gastrointestinal_Tract The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus FMA:49177 NCIT:C33837 UMLS:C0226874 galen:UpperGastrointestinalTract upper GI tract upper gastrointestinal tract uberon UBERON:0004908 upper digestive tract The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus FMA UMLS:C0226874 ncithesaurus:Upper_Gastrointestinal_Tract An epithelium surrounding a gonad. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts EHDAA:4032 EHDAA:5931 FBbt:00004859 NCIT:C32676 UMLS:C1517534 gonad epithelium gonadal epithelium uberon gonadal sheath UBERON:0004909 epithelium of gonad An epithelium surrounding a gonad. OBOL:automatic UMLS:C1517534 ncithesaurus:Germinal_Epithelium gonad epithelium OBOL:automatic gonadal epithelium OBOL:automatic gonadal sheath FBbt:00004859 An epithelium surrounding a testis. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts BTO:0001364 EMAPA:17973 FBbt:00004955 testis epithelium testis sheath uberon UBERON:0004910 epithelium of male gonad An epithelium surrounding a testis. OBOL:automatic testis epithelium OBOL:automatic testis sheath FBbt:00004955 An epithelium surrounding an ovary. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts BTO:0003661 FBbt:00004896 ovarian epithelium ovary epithelium ovarian sheath uberon UBERON:0004911 epithelium of female gonad An epithelium surrounding an ovary. OBOL:automatic ovarian epithelium OBOL:automatic ovary epithelium OBOL:automatic ovarian sheath FBbt:00004896 EHDAA2:0000171 EMAPA:16561 EMAPA_RETIRED:16565 VHOG:0001351 uberon hepatic diverticulum UBERON:0004912 biliary bud http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png EHDAA2 EHDAA2 EHDAA2-modified hepatic diverticulum EMAPA:16561 A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct. Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO] CALOHA:TS-2348 FMA:15076 GAID:283 MESH:A03.159.183.079.300.900 NCIT:C13011 TAO:0005167 UMLS:C0042425 ZFA:0005167 galen:AmpullaOfVater Vater's ampulla ampulla biliaropancreatica ampulla of Vater ampulla of bile duct biliaropancreatic ampulla papilla Vateri uberon ampulla Vaterii ampulla hepatopancreatica papilla duodeni major UBERON:0004913 hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct. Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO] 2012-08-14 TAO:0005167 TAO ZFIN:ZDB-PUB-070212-11 ZFIN:ZDB-PUB-080414-12 UMLS:C0042425 ncithesaurus:Ampulla_of_Vater ampulla biliaropancreatica FMA:15076 FMA:TA ampulla of bile duct FMA:15076 papilla Vateri ZFA:0005167 ampulla Vaterii ampulla hepatopancreatica papilla duodeni major ZFA:0005167 One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct. EMAPA:18662 FMA:15953 MA:0003107 NCIT:C119578 papilla duodenalis papilla of duodenum uberon papilla duodeni UBERON:0004914 duodenal papilla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct. papilla duodeni muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP]. EMAPA:18663 FMA:15077 GAID:285 MESH:A03.159.183.079.300.900.600 NCIT:C13065 UMLS:C0028872 Oddi's sphincter hepatopancreatic ampullary sphincter musculus sphincter ampullae musculus sphincter ampullae hepatopancreatica sphincter of Oddi sphincter of ampulla of vater uberon UBERON:0004915 sphincter of hepatopancreatic ampulla http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP]. UMLS:C0028872 ncithesaurus:Sphincter_of_Oddi hepatopancreatic ampullary sphincter FMA:15077 musculus sphincter ampullae FMA:15077 musculus sphincter ampullae hepatopancreatica FMA:15077 FMA:TA sphincter of ampulla of vater FMA:15077 A sphincter muscle that is part of a anal region. EMAPA:36052 anal region sphincter sphincter analia uberon UBERON:0004916 anal sphincter A sphincter muscle that is part of a anal region. OBOL:automatic A sphincter muscle surrounding the urethra. EMAPA:37789 MA:0002650 sphincter muscle of urethra sphincter of urethra sphincter urethrae urethral sphincter muscle uberon UBERON:0004917 urethral sphincter A sphincter muscle surrounding the urethra. EMAPA:37789 MA:th A proximal-distal subdivision of the digestive tract. intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. FBbt:00100315 FMA:71131 uberon alimentary system subdivision intestinal tract segment of intestinal tract subdivision of alimentary system UBERON:0004921 subdivision of digestive tract A proximal-distal subdivision of the digestive tract. alimentary system subdivision FMA:71131 subdivision of alimentary system FMA:71131 A part of a wall of an organ that forms a layer. FMA:82485 uberon UBERON:0004923 organ component layer A part of a wall of an organ that forms a layer. The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 FMA:75144 pharyngeal submucosa pharynx submucosa tela submucosa pharyngea tela submucosa pharyngis uberon pharyngobasilar fascia submucous coat of pharynx submucous layer of pharynx UBERON:0004924 submucosa of pharynx The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 pharyngeal submucosa FMA:75144 pharynx submucosa OBOL:automatic tela submucosa pharyngea FMA:75144 FMA:TA tela submucosa pharyngis BTO:0002113 submucous coat of pharynx BTO:0002113 submucous layer of pharynx BTO:0002113 A submucosa that is part of a hypopharynx [Automatically generated definition]. FMA:55072 hypopharynx submucosa laryngeal pharynx submucosa laryngopharynx submucosa submucosa of hypopharynx submucosa of laryngeal pharynx tela submucosa (pars laryngea pharyngis) uberon UBERON:0004925 submucosa of laryngopharynx A submucosa that is part of a hypopharynx [Automatically generated definition]. OBOL:automatic hypopharynx submucosa OBOL:automatic laryngeal pharynx submucosa OBOL:automatic laryngopharynx submucosa OBOL:automatic submucosa of hypopharynx OBOL:automatic submucosa of laryngeal pharynx OBOL:automatic tela submucosa (pars laryngea pharyngis) FMA:55072 A submucosa that is part of a cystic duct [Automatically generated definition]. FMA:18013 cystic duct submucosa cystic ductal submucosa uberon UBERON:0004926 submucosa of cystic duct A submucosa that is part of a cystic duct [Automatically generated definition]. OBOL:automatic cystic duct submucosa OBOL:automatic cystic ductal submucosa FMA:18013 A submucosa that is part of a cecum [Automatically generated definition]. FMA:14999 caecum submucosa cecum submucosa intestinum crassum caecum submucosa submucosa of caecum submucosa of intestinum crassum caecum uberon UBERON:0004927 submucosa of cecum A submucosa that is part of a cecum [Automatically generated definition]. OBOL:automatic caecum submucosa OBOL:automatic cecum submucosa OBOL:automatic intestinum crassum caecum submucosa OBOL:automatic submucosa of caecum OBOL:automatic submucosa of intestinum crassum caecum OBOL:automatic A submucosa that is part of an appendix [Automatically generated definition]. FMA:14992 appendiceal submucosa appendix submucosa caecal appendix submucosa submucosa of caecal appendix submucosa of vermiform appendix submucosa of vermix vermiform appendix submucosa vermix submucosa uberon UBERON:0004928 submucosa of appendix A submucosa that is part of an appendix [Automatically generated definition]. OBOL:automatic appendiceal submucosa FMA:14992 appendix submucosa OBOL:automatic caecal appendix submucosa OBOL:automatic submucosa of caecal appendix OBOL:automatic submucosa of vermiform appendix OBOL:automatic submucosa of vermix OBOL:automatic vermiform appendix submucosa OBOL:automatic vermix submucosa OBOL:automatic A submucosa that is part of an ascending colon [Automatically generated definition]. FMA:15006 ascending colon submucosa uberon UBERON:0004929 submucosa of ascending colon A submucosa that is part of an ascending colon [Automatically generated definition]. OBOL:automatic ascending colon submucosa OBOL:automatic A submucosa that is part of a transverse colon [Automatically generated definition]. FMA:15013 transverse colon submucosa uberon UBERON:0004930 submucosa of transverse colon A submucosa that is part of a transverse colon [Automatically generated definition]. OBOL:automatic transverse colon submucosa OBOL:automatic A submucosa that is part of a descending colon [Automatically generated definition]. FMA:15020 descending colon submucosa uberon UBERON:0004931 submucosa of descending colon A submucosa that is part of a descending colon [Automatically generated definition]. OBOL:automatic descending colon submucosa OBOL:automatic A submucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15027 sigmoid colon submucosa uberon UBERON:0004932 submucosa of sigmoid colon A submucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic sigmoid colon submucosa OBOL:automatic A submucosa that is part of a body of stomach [Automatically generated definition]. FMA:17059 body of stomach submucosa corpus gastricum (ventriculare) submucosa gastric body submucosa stomach body submucosa submucosa of corpus gastricum (ventriculare) submucosa of gastric body submucosa of stomach body uberon UBERON:0004934 submucosa of body of stomach A submucosa that is part of a body of stomach [Automatically generated definition]. OBOL:automatic body of stomach submucosa OBOL:automatic corpus gastricum (ventriculare) submucosa OBOL:automatic gastric body submucosa OBOL:automatic stomach body submucosa OBOL:automatic submucosa of corpus gastricum (ventriculare) OBOL:automatic submucosa of gastric body OBOL:automatic submucosa of stomach body OBOL:automatic A submucosa that is part of a cardia of stomach [Automatically generated definition]. FMA:17457 cardia of stomach submucosa cardial part of stomach submucosa gastric cardia submucosa pars cardiaca (gaster) submucosa stomach cardiac region submucosa submucosa of cardial part of stomach submucosa of gastric cardia submucosa of pars cardiaca (gaster) submucosa of stomach cardiac region uberon UBERON:0004935 submucosa of cardia of stomach A submucosa that is part of a cardia of stomach [Automatically generated definition]. OBOL:automatic cardia of stomach submucosa OBOL:automatic cardial part of stomach submucosa OBOL:automatic gastric cardia submucosa OBOL:automatic pars cardiaca (gaster) submucosa OBOL:automatic stomach cardiac region submucosa OBOL:automatic submucosa of cardial part of stomach OBOL:automatic submucosa of gastric cardia OBOL:automatic submucosa of pars cardiaca (gaster) OBOL:automatic submucosa of stomach cardiac region OBOL:automatic A submucosa that is part of a pyloric antrum [Automatically generated definition]. FMA:17060 antrum of stomach submucosa pyloric antrum submucosa stomach pyloric antrum submucosa submucosa of antrum of stomach submucosa of stomach pyloric antrum uberon UBERON:0004936 submucosa of pyloric antrum A submucosa that is part of a pyloric antrum [Automatically generated definition]. OBOL:automatic antrum of stomach submucosa OBOL:automatic pyloric antrum submucosa OBOL:automatic stomach pyloric antrum submucosa OBOL:automatic submucosa of antrum of stomach OBOL:automatic submucosa of stomach pyloric antrum OBOL:automatic A submucosa that is part of a pylorus [Automatically generated definition]. EMAPA:27201 FMA:17462 pyloric part of stomach submucosa pyloric submucosa pylorus submucosa stomach pyloric region submucosa submucosa of pyloric part of stomach submucosa of stomach pyloric region uberon UBERON:0004937 submucosa of pylorus A submucosa that is part of a pylorus [Automatically generated definition]. OBOL:automatic pyloric part of stomach submucosa OBOL:automatic pylorus submucosa FMA:17462 pylorus submucosa OBOL:automatic stomach pyloric region submucosa OBOL:automatic submucosa of pyloric part of stomach OBOL:automatic submucosa of stomach pyloric region OBOL:automatic A submucosa that is part of a biliary tree [Automatically generated definition]. FMA:18009 biliary tract submucosa biliary tree submucosa submucosa of biliary tract uberon UBERON:0004938 submucosa of biliary tree A submucosa that is part of a biliary tree [Automatically generated definition]. OBOL:automatic biliary tract submucosa OBOL:automatic biliary tree submucosa OBOL:automatic submucosa of biliary tract OBOL:automatic A submucosa that is part of a common bile duct [Automatically generated definition]. FMA:18011 common bile duct submucosa common bile ductal submucosa ductus choledochus (biliaris) submucosa submucosa of ductus choledochus (biliaris) uberon UBERON:0004939 submucosa of common bile duct A submucosa that is part of a common bile duct [Automatically generated definition]. OBOL:automatic common bile duct submucosa OBOL:automatic common bile ductal submucosa FMA:18011 ductus choledochus (biliaris) submucosa OBOL:automatic submucosa of ductus choledochus (biliaris) OBOL:automatic A submucosa that is part of a common hepatic duct [Automatically generated definition]. FMA:18014 common hepatic duct submucosa common hepatic ductal submucosa hepatic duct submucosa submucosa of hepatic duct uberon UBERON:0004940 submucosa of common hepatic duct A submucosa that is part of a common hepatic duct [Automatically generated definition]. OBOL:automatic common hepatic duct submucosa OBOL:automatic common hepatic ductal submucosa FMA:18014 hepatic duct submucosa OBOL:automatic submucosa of hepatic duct OBOL:automatic A submucosa that is part of a right hepatic duct [Automatically generated definition]. FMA:18015 right hepatic duct submucosa right hepatic ductal submucosa uberon UBERON:0004941 submucosa of right hepatic duct A submucosa that is part of a right hepatic duct [Automatically generated definition]. OBOL:automatic right hepatic duct submucosa OBOL:automatic right hepatic ductal submucosa FMA:18015 A submucosa that is part of a left hepatic duct [Automatically generated definition]. FMA:18017 left hepatic duct submucosa left hepatic ductal submucosa uberon UBERON:0004942 submucosa of left hepatic duct A submucosa that is part of a left hepatic duct [Automatically generated definition]. OBOL:automatic left hepatic duct submucosa OBOL:automatic left hepatic ductal submucosa FMA:18017 The submucous layer of the wall of the urinary bladder. BTO:0002117 EMAPA:32275 FMA:15929 bladder submucosa submucosa of bladder tela submucosa (vesica urinaria) tela submucosa vesicae tela submucosa vesicae urinariae urinary bladder submucosa uberon submucous layer of urinary bladder UBERON:0004943 submucosa of urinary bladder The submucous layer of the wall of the urinary bladder. BTO:0002117 bladder submucosa OBOL:automatic submucosa of bladder OBOL:automatic tela submucosa (vesica urinaria) FMA:15929 FMA:TA tela submucosa vesicae FMA:15929 FMA:TA tela submucosa vesicae urinariae BTO:0002117 urinary bladder submucosa OBOL:automatic submucous layer of urinary bladder BTO:0002117 A submucosa that is part of a neck of urinary bladder [Automatically generated definition]. EMAPA:32276 FMA:17851 bladder neck submucosa neck of bladder submucosa neck of urinary bladder submucosa submucosa of bladder neck submucosa of neck of bladder submucosa of urinary bladder neck submucosa of vesical neck urinary bladder neck submucosa vesical neck submucosa uberon UBERON:0004945 submucosa of neck of urinary bladder A submucosa that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck submucosa OBOL:automatic neck of bladder submucosa OBOL:automatic neck of urinary bladder submucosa OBOL:automatic submucosa of bladder neck OBOL:automatic submucosa of neck of bladder OBOL:automatic submucosa of urinary bladder neck OBOL:automatic submucosa of vesical neck OBOL:automatic urinary bladder neck submucosa OBOL:automatic vesical neck submucosa OBOL:automatic A submucosa that is part of a ileum [Automatically generated definition]. FMA:14957 ileal submucosa ileum submucosa uberon UBERON:0004946 submucosa of ileum A submucosa that is part of a ileum [Automatically generated definition]. OBOL:automatic ileal submucosa FMA:14957 ileum submucosa OBOL:automatic A submucosa that is part of a bronchiole [Automatically generated definition]. FMA:62775 bronchiole submucosa lobular bronchiole submucosa submucosa of lobular bronchiole uberon UBERON:0004952 submucosa of bronchiole A submucosa that is part of a bronchiole [Automatically generated definition]. OBOL:automatic bronchiole submucosa OBOL:automatic lobular bronchiole submucosa OBOL:automatic submucosa of lobular bronchiole OBOL:automatic A mucosa that is part of a ureter [Automatically generated definition]. FMA:15894 galen:MucousMembraneOfUreter mucosa of organ of ureter mucosal layer of ureter mucous membrane of ureter organ mucosa of ureter tunica mucosa (ureter) tunica mucosa ureteris ureter mucosa ureter mucosa of organ ureter mucous membrane ureter organ mucosa ureteral mucosa ureteric mucosa uberon UBERON:0004980 mucosa of ureter A mucosa that is part of a ureter [Automatically generated definition]. OBOL:automatic mucosa of organ of ureter OBOL:automatic mucosal layer of ureter FMA:15894 mucous membrane of ureter OBOL:automatic organ mucosa of ureter OBOL:automatic tunica mucosa (ureter) FMA:15894 tunica mucosa ureteris FMA:15894 FMA:TA ureter mucosa OBOL:automatic ureter mucosa of organ OBOL:automatic ureter mucous membrane OBOL:automatic ureter organ mucosa OBOL:automatic ureteral mucosa FMA:15894 ureteric mucosa FMA:15894 A mucosa that is part of a vagina [Automatically generated definition]. BTO:0005676 FMA:19975 mucosa of organ of vagina mucous membrane of vagina organ mucosa of vagina tunica mucosa vaginae vagina mucosa vagina mucosa of organ vagina mucous membrane vagina organ mucosa vaginal mucosa uberon UBERON:0004983 mucosa of vagina A mucosa that is part of a vagina [Automatically generated definition]. OBOL:automatic mucosa of organ of vagina OBOL:automatic mucous membrane of vagina OBOL:automatic organ mucosa of vagina OBOL:automatic tunica mucosa vaginae FMA:19975 FMA:TA vagina mucosa OBOL:automatic vagina mucosa of organ OBOL:automatic vagina mucous membrane OBOL:automatic vagina organ mucosa OBOL:automatic vaginal mucosa FMA:19975 A mucosa that is part of a seminal vesicle [Automatically generated definition]. FMA:19405 mucosa of organ of seminal gland mucosa of organ of seminal vesicle mucosa of seminal gland mucous membrane of seminal gland mucous membrane of seminal vesicle organ mucosa of seminal gland organ mucosa of seminal vesicle seminal gland mucosa seminal gland mucosa of organ seminal gland mucous membrane seminal gland organ mucosa seminal vesicle mucosa seminal vesicle mucosa of organ seminal vesicle mucous membrane seminal vesicle organ mucosa tunica mucosa glandulae vesiculosae uberon UBERON:0004984 mucosa of seminal vesicle A mucosa that is part of a seminal vesicle [Automatically generated definition]. OBOL:automatic mucosa of organ of seminal gland OBOL:automatic mucosa of organ of seminal vesicle OBOL:automatic mucosa of seminal gland OBOL:automatic mucous membrane of seminal gland OBOL:automatic mucous membrane of seminal vesicle OBOL:automatic organ mucosa of seminal gland OBOL:automatic organ mucosa of seminal vesicle OBOL:automatic seminal gland mucosa OBOL:automatic seminal gland mucosa of organ OBOL:automatic seminal gland mucous membrane OBOL:automatic seminal gland organ mucosa OBOL:automatic seminal vesicle mucosa OBOL:automatic seminal vesicle mucosa of organ OBOL:automatic seminal vesicle mucous membrane OBOL:automatic seminal vesicle organ mucosa OBOL:automatic tunica mucosa glandulae vesiculosae FMA:19405 FMA:TA A mucosa that is part of a ejaculatory duct [Automatically generated definition]. FMA:19373 ejaculatory duct mucosa ejaculatory duct mucosa of organ ejaculatory duct mucous membrane ejaculatory duct organ mucosa ejaculatory ductal mucosa mucosa of organ of ejaculatory duct mucous membrane of ejaculatory duct organ mucosa of ejaculatory duct uberon UBERON:0004985 mucosa of ejaculatory duct A mucosa that is part of a ejaculatory duct [Automatically generated definition]. OBOL:automatic ejaculatory duct mucosa OBOL:automatic ejaculatory duct mucosa of organ OBOL:automatic ejaculatory duct mucous membrane OBOL:automatic ejaculatory duct organ mucosa OBOL:automatic ejaculatory ductal mucosa FMA:19373 mucosa of organ of ejaculatory duct OBOL:automatic mucous membrane of ejaculatory duct OBOL:automatic organ mucosa of ejaculatory duct OBOL:automatic A mucosa that is part of a vas deferens [Automatically generated definition]. FMA:19240 deferent duct mucosa deferent duct mucosa of organ deferent duct mucous membrane deferent duct organ mucosa deferent ductal mucosa ductus deferens mucosa ductus deferens mucosa of organ ductus deferens mucous membrane ductus deferens organ mucosa mucosa of ductus deferens mucosa of organ of deferent duct mucosa of organ of ductus deferens mucosa of organ of sperm duct mucosa of organ of vas deferen mucosa of organ of vas deferens mucosa of sperm duct mucosa of vas deferen mucosa of vas deferens mucous membrane of deferent duct mucous membrane of ductus deferens mucous membrane of sperm duct mucous membrane of vas deferen mucous membrane of vas deferens organ mucosa of deferent duct organ mucosa of ductus deferens organ mucosa of sperm duct organ mucosa of vas deferen organ mucosa of vas deferens sperm duct mucosa sperm duct mucosa of organ sperm duct mucous membrane sperm duct organ mucosa tunica mucosa (ductus deferens) tunica mucosa ductus deferentis vas deferen mucosa vas deferen mucosa of organ vas deferen mucous membrane vas deferen organ mucosa vas deferens mucosa vas deferens mucosa of organ vas deferens mucous membrane vas deferens organ mucosa uberon UBERON:0004986 mucosa of deferent duct A mucosa that is part of a vas deferens [Automatically generated definition]. OBOL:automatic deferent duct mucosa OBOL:automatic deferent duct mucosa of organ OBOL:automatic deferent duct mucous membrane OBOL:automatic deferent duct organ mucosa OBOL:automatic deferent ductal mucosa FMA:19240 ductus deferens mucosa OBOL:automatic ductus deferens mucosa of organ OBOL:automatic ductus deferens mucous membrane OBOL:automatic ductus deferens organ mucosa OBOL:automatic mucosa of ductus deferens OBOL:automatic mucosa of organ of deferent duct OBOL:automatic mucosa of organ of ductus deferens OBOL:automatic mucosa of organ of sperm duct OBOL:automatic mucosa of organ of vas deferen OBOL:automatic mucosa of organ of vas deferens OBOL:automatic mucosa of sperm duct OBOL:automatic mucosa of vas deferen OBOL:automatic mucosa of vas deferens OBOL:automatic mucous membrane of deferent duct OBOL:automatic mucous membrane of ductus deferens OBOL:automatic mucous membrane of sperm duct OBOL:automatic mucous membrane of vas deferen OBOL:automatic mucous membrane of vas deferens OBOL:automatic organ mucosa of deferent duct OBOL:automatic organ mucosa of ductus deferens OBOL:automatic organ mucosa of sperm duct OBOL:automatic organ mucosa of vas deferen OBOL:automatic organ mucosa of vas deferens OBOL:automatic sperm duct mucosa OBOL:automatic sperm duct mucosa of organ OBOL:automatic sperm duct mucous membrane OBOL:automatic sperm duct organ mucosa OBOL:automatic tunica mucosa (ductus deferens) FMA:19240 tunica mucosa ductus deferentis FMA:19240 FMA:TA vas deferen mucosa OBOL:automatic vas deferen mucosa of organ OBOL:automatic vas deferen mucous membrane OBOL:automatic vas deferen organ mucosa OBOL:automatic vas deferens mucosa OBOL:automatic vas deferens mucosa of organ OBOL:automatic vas deferens mucous membrane OBOL:automatic vas deferens organ mucosa OBOL:automatic A mucosa that is part of a hypopharynx [Automatically generated definition]. FMA:55030 hypopharynx mucosa hypopharynx mucosa of organ hypopharynx mucous membrane hypopharynx organ mucosa laryngeal pharynx mucosa laryngeal pharynx mucosa of organ laryngeal pharynx mucous membrane laryngeal pharynx organ mucosa laryngopharynx mucosa laryngopharynx mucosa of organ laryngopharynx mucous membrane laryngopharynx organ mucosa mucosa of hypopharynx mucosa of laryngeal pharynx mucosa of organ of hypopharynx mucosa of organ of laryngeal pharynx mucosa of organ of laryngopharynx mucous membrane of hypopharynx mucous membrane of laryngeal pharynx mucous membrane of laryngopharynx organ mucosa of hypopharynx organ mucosa of laryngeal pharynx organ mucosa of laryngopharynx uberon UBERON:0004987 mucosa of laryngopharynx A mucosa that is part of a hypopharynx [Automatically generated definition]. OBOL:automatic hypopharynx mucosa OBOL:automatic hypopharynx mucosa of organ OBOL:automatic hypopharynx mucous membrane OBOL:automatic hypopharynx organ mucosa OBOL:automatic laryngeal pharynx mucosa OBOL:automatic laryngeal pharynx mucosa of organ OBOL:automatic laryngeal pharynx mucous membrane OBOL:automatic laryngeal pharynx organ mucosa OBOL:automatic laryngopharynx mucosa OBOL:automatic laryngopharynx mucosa of organ OBOL:automatic laryngopharynx mucous membrane OBOL:automatic laryngopharynx organ mucosa OBOL:automatic mucosa of hypopharynx OBOL:automatic mucosa of laryngeal pharynx OBOL:automatic mucosa of organ of hypopharynx OBOL:automatic mucosa of organ of laryngeal pharynx OBOL:automatic mucosa of organ of laryngopharynx OBOL:automatic mucous membrane of hypopharynx OBOL:automatic mucous membrane of laryngeal pharynx OBOL:automatic mucous membrane of laryngopharynx OBOL:automatic organ mucosa of hypopharynx OBOL:automatic organ mucosa of laryngeal pharynx OBOL:automatic organ mucosa of laryngopharynx OBOL:automatic A mucosa that is part of a cystic duct [Automatically generated definition]. FMA:14690 cystic duct mucosa cystic duct mucosa of organ cystic duct mucous membrane cystic duct organ mucosa cystic ductal mucosa mucosa of organ of cystic duct mucous membrane of cystic duct organ mucosa of cystic duct uberon UBERON:0004988 mucosa of cystic duct A mucosa that is part of a cystic duct [Automatically generated definition]. OBOL:automatic cystic duct mucosa OBOL:automatic cystic duct mucosa of organ OBOL:automatic cystic duct mucous membrane OBOL:automatic cystic duct organ mucosa OBOL:automatic cystic ductal mucosa FMA:14690 mucosa of organ of cystic duct OBOL:automatic mucous membrane of cystic duct OBOL:automatic organ mucosa of cystic duct OBOL:automatic A mucosa that is part of an appendix [Automatically generated definition]. CALOHA:TS-2022 FMA:14991 appendiceal mucous membrane appendix mucosa appendix mucosa of organ appendix mucous membrane appendix organ mucosa caecal appendix mucosa caecal appendix mucosa of organ caecal appendix mucous membrane caecal appendix organ mucosa mucosa of caecal appendix mucosa of organ of appendix mucosa of organ of caecal appendix mucosa of organ of vermiform appendix mucosa of organ of vermix mucosa of vermiform appendix mucosa of vermix mucous membrane of appendix mucous membrane of caecal appendix mucous membrane of vermiform appendix mucous membrane of vermix organ mucosa of appendix organ mucosa of caecal appendix organ mucosa of vermiform appendix organ mucosa of vermix vermiform appendix mucosa vermiform appendix mucosa of organ vermiform appendix mucous membrane vermiform appendix organ mucosa vermix mucosa vermix mucosa of organ vermix mucous membrane vermix organ mucosa uberon UBERON:0004989 mucosa of appendix A mucosa that is part of an appendix [Automatically generated definition]. OBOL:automatic appendiceal mucous membrane FMA:14991 appendix mucosa OBOL:automatic appendix mucosa of organ OBOL:automatic appendix mucous membrane OBOL:automatic appendix organ mucosa OBOL:automatic caecal appendix mucosa OBOL:automatic caecal appendix mucosa of organ OBOL:automatic caecal appendix mucous membrane OBOL:automatic caecal appendix organ mucosa OBOL:automatic mucosa of caecal appendix OBOL:automatic mucosa of organ of appendix OBOL:automatic mucosa of organ of caecal appendix OBOL:automatic mucosa of organ of vermiform appendix OBOL:automatic mucosa of organ of vermix OBOL:automatic mucosa of vermiform appendix OBOL:automatic mucosa of vermix OBOL:automatic mucous membrane of appendix OBOL:automatic mucous membrane of caecal appendix OBOL:automatic mucous membrane of vermiform appendix OBOL:automatic mucous membrane of vermix OBOL:automatic organ mucosa of appendix OBOL:automatic organ mucosa of caecal appendix OBOL:automatic organ mucosa of vermiform appendix OBOL:automatic organ mucosa of vermix OBOL:automatic vermiform appendix mucosa OBOL:automatic vermiform appendix mucosa of organ OBOL:automatic vermiform appendix mucous membrane OBOL:automatic vermiform appendix organ mucosa OBOL:automatic vermix mucosa OBOL:automatic vermix mucosa of organ OBOL:automatic vermix mucous membrane OBOL:automatic vermix organ mucosa OBOL:automatic A mucosa that is part of an ascending colon [Automatically generated definition]. FMA:15005 ascending colon mucosa ascending colon mucosa of organ ascending colon mucous membrane ascending colon organ mucosa mucosa of organ of ascending colon mucous membrane of ascending colon organ mucosa of ascending colon uberon UBERON:0004990 mucosa of ascending colon A mucosa that is part of an ascending colon [Automatically generated definition]. OBOL:automatic ascending colon mucosa OBOL:automatic ascending colon mucosa of organ OBOL:automatic ascending colon mucous membrane OBOL:automatic ascending colon organ mucosa OBOL:automatic mucosa of organ of ascending colon OBOL:automatic mucous membrane of ascending colon OBOL:automatic organ mucosa of ascending colon OBOL:automatic A mucosa that is part of a transverse colon [Automatically generated definition]. FMA:15012 mucosa of organ of transverse colon mucous membrane of transverse colon organ mucosa of transverse colon transverse colon mucosa transverse colon mucosa of organ transverse colon mucous membrane transverse colon organ mucosa uberon UBERON:0004991 mucosa of transverse colon A mucosa that is part of a transverse colon [Automatically generated definition]. OBOL:automatic mucosa of organ of transverse colon OBOL:automatic mucous membrane of transverse colon OBOL:automatic organ mucosa of transverse colon OBOL:automatic transverse colon mucosa OBOL:automatic transverse colon mucosa of organ OBOL:automatic transverse colon mucous membrane OBOL:automatic transverse colon organ mucosa OBOL:automatic A mucosa that is part of a descending colon [Automatically generated definition]. FMA:15019 descending colon mucosa descending colon mucosa of organ descending colon mucous membrane descending colon organ mucosa mucosa of organ of descending colon mucous membrane of descending colon organ mucosa of descending colon uberon UBERON:0004992 mucosa of descending colon A mucosa that is part of a descending colon [Automatically generated definition]. OBOL:automatic descending colon mucosa OBOL:automatic descending colon mucosa of organ OBOL:automatic descending colon mucous membrane OBOL:automatic descending colon organ mucosa OBOL:automatic mucosa of organ of descending colon OBOL:automatic mucous membrane of descending colon OBOL:automatic organ mucosa of descending colon OBOL:automatic A mucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15026 mucosa of organ of sigmoid colon mucous membrane of sigmoid colon organ mucosa of sigmoid colon sigmoid colon mucosa sigmoid colon mucosa of organ sigmoid colon mucous membrane sigmoid colon organ mucosa uberon UBERON:0004993 mucosa of sigmoid colon A mucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic mucosa of organ of sigmoid colon OBOL:automatic mucous membrane of sigmoid colon OBOL:automatic organ mucosa of sigmoid colon OBOL:automatic sigmoid colon mucosa OBOL:automatic sigmoid colon mucosa of organ OBOL:automatic sigmoid colon mucous membrane OBOL:automatic sigmoid colon organ mucosa OBOL:automatic A mucosa that is part of a body of stomach [Automatically generated definition]. FMA:17054 body of stomach mucosa body of stomach mucosa of organ body of stomach mucous membrane body of stomach organ mucosa corpus gastricum (ventriculare) mucosa corpus gastricum (ventriculare) mucosa of organ corpus gastricum (ventriculare) mucous membrane corpus gastricum (ventriculare) organ mucosa gastric body mucosa gastric body mucosa of organ gastric body mucous membrane gastric body organ mucosa mucosa of corpus gastricum (ventriculare) mucosa of gastric body mucosa of organ of body of stomach mucosa of organ of corpus gastricum (ventriculare) mucosa of organ of gastric body mucosa of organ of stomach body mucosa of stomach body mucous membrane of body of stomach mucous membrane of corpus gastricum (ventriculare) mucous membrane of gastric body mucous membrane of stomach body organ mucosa of body of stomach organ mucosa of corpus gastricum (ventriculare) organ mucosa of gastric body organ mucosa of stomach body stomach body mucosa stomach body mucosa of organ stomach body mucous membrane stomach body organ mucosa uberon UBERON:0004995 mucosa of body of stomach A mucosa that is part of a body of stomach [Automatically generated definition]. OBOL:automatic body of stomach mucosa OBOL:automatic body of stomach mucosa of organ OBOL:automatic body of stomach mucous membrane OBOL:automatic body of stomach organ mucosa OBOL:automatic corpus gastricum (ventriculare) mucosa OBOL:automatic corpus gastricum (ventriculare) mucosa of organ OBOL:automatic corpus gastricum (ventriculare) mucous membrane OBOL:automatic corpus gastricum (ventriculare) organ mucosa OBOL:automatic gastric body mucosa OBOL:automatic gastric body mucosa of organ OBOL:automatic gastric body mucous membrane OBOL:automatic gastric body organ mucosa OBOL:automatic mucosa of corpus gastricum (ventriculare) OBOL:automatic mucosa of gastric body OBOL:automatic mucosa of organ of body of stomach OBOL:automatic mucosa of organ of corpus gastricum (ventriculare) OBOL:automatic mucosa of organ of gastric body OBOL:automatic mucosa of organ of stomach body OBOL:automatic mucosa of stomach body OBOL:automatic mucous membrane of body of stomach OBOL:automatic mucous membrane of corpus gastricum (ventriculare) OBOL:automatic mucous membrane of gastric body OBOL:automatic mucous membrane of stomach body OBOL:automatic organ mucosa of body of stomach OBOL:automatic organ mucosa of corpus gastricum (ventriculare) OBOL:automatic organ mucosa of gastric body OBOL:automatic organ mucosa of stomach body OBOL:automatic stomach body mucosa OBOL:automatic stomach body mucosa of organ OBOL:automatic stomach body mucous membrane OBOL:automatic stomach body organ mucosa OBOL:automatic A mucosa that is part of a cardia of stomach [Automatically generated definition]. FMA:17456 cardia of stomach mucosa cardia of stomach mucosa of organ cardia of stomach mucous membrane cardia of stomach organ mucosa cardial part of stomach mucosa cardial part of stomach mucosa of organ cardial part of stomach mucous membrane cardial part of stomach organ mucosa gastric cardia mucosa gastric cardia mucosa of organ gastric cardia mucous membrane gastric cardia organ mucosa mucosa of cardial part of stomach mucosa of gastric cardia mucosa of organ of cardia of stomach mucosa of organ of cardial part of stomach mucosa of organ of gastric cardia mucosa of organ of pars cardiaca (gaster) mucosa of organ of stomach cardiac region mucosa of pars cardiaca (gaster) mucosa of stomach cardiac region mucous membrane of cardia of stomach mucous membrane of cardial part of stomach mucous membrane of gastric cardia mucous membrane of pars cardiaca (gaster) mucous membrane of stomach cardiac region organ mucosa of cardia of stomach organ mucosa of cardial part of stomach organ mucosa of gastric cardia organ mucosa of pars cardiaca (gaster) organ mucosa of stomach cardiac region pars cardiaca (gaster) mucosa pars cardiaca (gaster) mucosa of organ pars cardiaca (gaster) mucous membrane pars cardiaca (gaster) organ mucosa stomach cardiac region mucosa stomach cardiac region mucosa of organ stomach cardiac region mucous membrane stomach cardiac region organ mucosa uberon UBERON:0004996 mucosa of cardia of stomach A mucosa that is part of a cardia of stomach [Automatically generated definition]. OBOL:automatic cardia of stomach mucosa OBOL:automatic cardia of stomach mucosa of organ OBOL:automatic cardia of stomach mucous membrane OBOL:automatic cardia of stomach organ mucosa OBOL:automatic cardial part of stomach mucosa OBOL:automatic cardial part of stomach mucosa of organ OBOL:automatic cardial part of stomach mucous membrane OBOL:automatic cardial part of stomach organ mucosa OBOL:automatic gastric cardia mucosa OBOL:automatic gastric cardia mucosa of organ OBOL:automatic gastric cardia mucous membrane OBOL:automatic gastric cardia organ mucosa OBOL:automatic mucosa of cardial part of stomach OBOL:automatic mucosa of gastric cardia OBOL:automatic mucosa of organ of cardia of stomach OBOL:automatic mucosa of organ of cardial part of stomach OBOL:automatic mucosa of organ of gastric cardia OBOL:automatic mucosa of organ of pars cardiaca (gaster) OBOL:automatic mucosa of organ of stomach cardiac region OBOL:automatic mucosa of pars cardiaca (gaster) OBOL:automatic mucosa of stomach cardiac region OBOL:automatic mucous membrane of cardia of stomach OBOL:automatic mucous membrane of cardial part of stomach OBOL:automatic mucous membrane of gastric cardia OBOL:automatic mucous membrane of pars cardiaca (gaster) OBOL:automatic mucous membrane of stomach cardiac region OBOL:automatic organ mucosa of cardia of stomach OBOL:automatic organ mucosa of cardial part of stomach OBOL:automatic organ mucosa of gastric cardia OBOL:automatic organ mucosa of pars cardiaca (gaster) OBOL:automatic organ mucosa of stomach cardiac region OBOL:automatic pars cardiaca (gaster) mucosa OBOL:automatic pars cardiaca (gaster) mucosa of organ OBOL:automatic pars cardiaca (gaster) mucous membrane OBOL:automatic pars cardiaca (gaster) organ mucosa OBOL:automatic stomach cardiac region mucosa OBOL:automatic stomach cardiac region mucosa of organ OBOL:automatic stomach cardiac region mucous membrane OBOL:automatic stomach cardiac region organ mucosa OBOL:automatic A mucosa that is part of a pyloric antrum [Automatically generated definition]. BTO:0004107 FMA:17055 antral mucosa antrum of stomach mucosa antrum of stomach mucosa of organ antrum of stomach mucous membrane antrum of stomach organ mucosa mucosa of antrum of stomach mucosa of organ of antrum of stomach mucosa of organ of pyloric antrum mucosa of organ of stomach pyloric antrum mucosa of stomach pyloric antrum mucous membrane of antrum of stomach mucous membrane of pyloric antrum mucous membrane of stomach pyloric antrum organ mucosa of antrum of stomach organ mucosa of pyloric antrum organ mucosa of stomach pyloric antrum pyloric antrum mucosa pyloric antrum mucosa of organ pyloric antrum mucous membrane pyloric antrum organ mucosa stomach pyloric antrum mucosa stomach pyloric antrum mucosa of organ stomach pyloric antrum mucous membrane stomach pyloric antrum organ mucosa uberon gastric antrum mucosa UBERON:0004997 mucosa of pyloric antrum A mucosa that is part of a pyloric antrum [Automatically generated definition]. OBOL:automatic antral mucosa BTO:0004107 antrum of stomach mucosa OBOL:automatic antrum of stomach mucosa of organ OBOL:automatic antrum of stomach mucous membrane OBOL:automatic antrum of stomach organ mucosa OBOL:automatic mucosa of antrum of stomach OBOL:automatic mucosa of organ of antrum of stomach OBOL:automatic mucosa of organ of pyloric antrum OBOL:automatic mucosa of organ of stomach pyloric antrum OBOL:automatic mucosa of stomach pyloric antrum OBOL:automatic mucous membrane of antrum of stomach OBOL:automatic mucous membrane of pyloric antrum OBOL:automatic mucous membrane of stomach pyloric antrum OBOL:automatic organ mucosa of antrum of stomach OBOL:automatic organ mucosa of pyloric antrum OBOL:automatic organ mucosa of stomach pyloric antrum OBOL:automatic pyloric antrum mucosa OBOL:automatic pyloric antrum mucosa of organ OBOL:automatic pyloric antrum mucous membrane OBOL:automatic pyloric antrum organ mucosa OBOL:automatic stomach pyloric antrum mucosa OBOL:automatic stomach pyloric antrum mucosa of organ OBOL:automatic stomach pyloric antrum mucous membrane OBOL:automatic stomach pyloric antrum organ mucosa OBOL:automatic gastric antrum mucosa BTO:0004107 A mucosa that is part of a pylorus [Automatically generated definition]. BTO:0004110 EMAPA:27199 FMA:17461 mucosa of organ of pyloric part of stomach mucosa of organ of pylorus mucosa of organ of stomach pyloric region mucosa of pyloric part of stomach mucosa of stomach pyloric region mucous membrane of pyloric part of stomach mucous membrane of pylorus mucous membrane of stomach pyloric region organ mucosa of pyloric part of stomach organ mucosa of pylorus organ mucosa of stomach pyloric region pyloric part of stomach mucosa pyloric part of stomach mucosa of organ pyloric part of stomach mucous membrane pyloric part of stomach organ mucosa pylorus mucosa pylorus mucosa of organ pylorus mucous membrane pylorus organ mucosa stomach pyloric region mucosa stomach pyloric region mucosa of organ stomach pyloric region mucous membrane stomach pyloric region organ mucosa uberon antropyloric mucosa UBERON:0004998 mucosa of pylorus A mucosa that is part of a pylorus [Automatically generated definition]. OBOL:automatic mucosa of organ of pyloric part of stomach OBOL:automatic mucosa of organ of pylorus OBOL:automatic mucosa of organ of stomach pyloric region OBOL:automatic mucosa of pyloric part of stomach OBOL:automatic mucosa of stomach pyloric region OBOL:automatic mucous membrane of pyloric part of stomach OBOL:automatic mucous membrane of pylorus OBOL:automatic mucous membrane of stomach pyloric region OBOL:automatic organ mucosa of pyloric part of stomach OBOL:automatic organ mucosa of pylorus OBOL:automatic organ mucosa of stomach pyloric region OBOL:automatic pyloric part of stomach mucosa OBOL:automatic pyloric part of stomach mucosa of organ OBOL:automatic pyloric part of stomach mucous membrane OBOL:automatic pyloric part of stomach organ mucosa OBOL:automatic pylorus mucosa OBOL:automatic pylorus mucosa of organ OBOL:automatic pylorus mucous membrane OBOL:automatic pylorus organ mucosa OBOL:automatic stomach pyloric region mucosa OBOL:automatic stomach pyloric region mucosa of organ OBOL:automatic stomach pyloric region mucous membrane OBOL:automatic stomach pyloric region organ mucosa OBOL:automatic antropyloric mucosa BTO:0002984 A mucosa that is part of a biliary tree [Automatically generated definition]. FMA:14695 biliary tract mucosa biliary tract mucosa of organ biliary tract mucous membrane biliary tract organ mucosa biliary tree mucosa biliary tree mucosa of organ biliary tree mucous membrane biliary tree organ mucosa mucosa of biliary tract mucosa of organ of biliary tract mucosa of organ of biliary tree mucous membrane of biliary tract mucous membrane of biliary tree organ mucosa of biliary tract organ mucosa of biliary tree uberon UBERON:0004999 mucosa of biliary tree A mucosa that is part of a biliary tree [Automatically generated definition]. OBOL:automatic biliary tract mucosa OBOL:automatic biliary tract mucosa of organ OBOL:automatic biliary tract mucous membrane OBOL:automatic biliary tract organ mucosa OBOL:automatic biliary tree mucosa OBOL:automatic biliary tree mucosa of organ OBOL:automatic biliary tree mucous membrane OBOL:automatic biliary tree organ mucosa OBOL:automatic mucosa of biliary tract OBOL:automatic mucosa of organ of biliary tract OBOL:automatic mucosa of organ of biliary tree OBOL:automatic mucous membrane of biliary tract OBOL:automatic mucous membrane of biliary tree OBOL:automatic organ mucosa of biliary tract OBOL:automatic organ mucosa of biliary tree OBOL:automatic A mucosa that is part of a common bile duct [Automatically generated definition]. FMA:14688 common bile duct mucosa common bile duct mucosa of organ common bile duct mucous membrane common bile duct organ mucosa common bile ductal mucosa ductus choledochus (biliaris) mucosa ductus choledochus (biliaris) mucosa of organ ductus choledochus (biliaris) mucous membrane ductus choledochus (biliaris) organ mucosa mucosa of ductus choledochus (biliaris) mucosa of organ of common bile duct mucosa of organ of ductus choledochus (biliaris) mucous membrane of common bile duct mucous membrane of ductus choledochus (biliaris) organ mucosa of common bile duct organ mucosa of ductus choledochus (biliaris) uberon UBERON:0005000 mucosa of common bile duct A mucosa that is part of a common bile duct [Automatically generated definition]. OBOL:automatic common bile duct mucosa OBOL:automatic common bile duct mucosa of organ OBOL:automatic common bile duct mucous membrane OBOL:automatic common bile duct organ mucosa OBOL:automatic common bile ductal mucosa FMA:14688 ductus choledochus (biliaris) mucosa OBOL:automatic ductus choledochus (biliaris) mucosa of organ OBOL:automatic ductus choledochus (biliaris) mucous membrane OBOL:automatic ductus choledochus (biliaris) organ mucosa OBOL:automatic mucosa of ductus choledochus (biliaris) OBOL:automatic mucosa of organ of common bile duct OBOL:automatic mucosa of organ of ductus choledochus (biliaris) OBOL:automatic mucous membrane of common bile duct OBOL:automatic mucous membrane of ductus choledochus (biliaris) OBOL:automatic organ mucosa of common bile duct OBOL:automatic organ mucosa of ductus choledochus (biliaris) OBOL:automatic A mucosa that is part of a common hepatic duct [Automatically generated definition]. FMA:14691 common hepatic duct mucosa common hepatic duct mucosa of organ common hepatic duct mucous membrane common hepatic duct organ mucosa common hepatic ductal mucosa hepatic duct mucosa hepatic duct mucosa of organ hepatic duct mucous membrane hepatic duct organ mucosa mucosa of hepatic duct mucosa of organ of common hepatic duct mucosa of organ of hepatic duct mucous membrane of common hepatic duct mucous membrane of hepatic duct organ mucosa of common hepatic duct organ mucosa of hepatic duct uberon UBERON:0005001 mucosa of common hepatic duct A mucosa that is part of a common hepatic duct [Automatically generated definition]. OBOL:automatic common hepatic duct mucosa OBOL:automatic common hepatic duct mucosa of organ OBOL:automatic common hepatic duct mucous membrane OBOL:automatic common hepatic duct organ mucosa OBOL:automatic common hepatic ductal mucosa FMA:14691 hepatic duct mucosa OBOL:automatic hepatic duct mucosa of organ OBOL:automatic hepatic duct mucous membrane OBOL:automatic hepatic duct organ mucosa OBOL:automatic mucosa of hepatic duct OBOL:automatic mucosa of organ of common hepatic duct OBOL:automatic mucosa of organ of hepatic duct OBOL:automatic mucous membrane of common hepatic duct OBOL:automatic mucous membrane of hepatic duct OBOL:automatic organ mucosa of common hepatic duct OBOL:automatic organ mucosa of hepatic duct OBOL:automatic A mucosa that is part of a right hepatic duct [Automatically generated definition]. FMA:14692 mucosa of organ of right hepatic duct mucous membrane of right hepatic duct organ mucosa of right hepatic duct right hepatic duct mucosa right hepatic duct mucosa of organ right hepatic duct mucous membrane right hepatic duct organ mucosa right hepatic ductal mucosa uberon UBERON:0005002 mucosa of right hepatic duct A mucosa that is part of a right hepatic duct [Automatically generated definition]. OBOL:automatic mucosa of organ of right hepatic duct OBOL:automatic mucous membrane of right hepatic duct OBOL:automatic organ mucosa of right hepatic duct OBOL:automatic right hepatic duct mucosa OBOL:automatic right hepatic duct mucosa of organ OBOL:automatic right hepatic duct mucous membrane OBOL:automatic right hepatic duct organ mucosa OBOL:automatic right hepatic ductal mucosa FMA:14692 A mucosa that is part of a left hepatic duct [Automatically generated definition]. FMA:14693 left hepatic duct mucosa left hepatic duct mucosa of organ left hepatic duct mucous membrane left hepatic duct organ mucosa left hepatic ductal mucosa mucosa of organ of left hepatic duct mucous membrane of left hepatic duct organ mucosa of left hepatic duct uberon UBERON:0005003 mucosa of left hepatic duct A mucosa that is part of a left hepatic duct [Automatically generated definition]. OBOL:automatic left hepatic duct mucosa OBOL:automatic left hepatic duct mucosa of organ OBOL:automatic left hepatic duct mucous membrane OBOL:automatic left hepatic duct organ mucosa OBOL:automatic left hepatic ductal mucosa FMA:14693 mucosa of organ of left hepatic duct OBOL:automatic mucous membrane of left hepatic duct OBOL:automatic organ mucosa of left hepatic duct OBOL:automatic A mucosa that is part of a right ureter [Automatically generated definition]. FMA:17806 mucosa of organ of right ureter mucous membrane of right ureter organ mucosa of right ureter right ureter mucosa right ureter mucosa of organ right ureter mucous membrane right ureter organ mucosa right ureteral mucosa uberon UBERON:0005004 mucosa of right ureter A mucosa that is part of a right ureter [Automatically generated definition]. OBOL:automatic mucosa of organ of right ureter OBOL:automatic mucous membrane of right ureter OBOL:automatic organ mucosa of right ureter OBOL:automatic right ureter mucosa OBOL:automatic right ureter mucosa of organ OBOL:automatic right ureter mucous membrane OBOL:automatic right ureter organ mucosa OBOL:automatic right ureteral mucosa FMA:17806 A mucosa that is part of a left ureter [Automatically generated definition]. FMA:17807 left ureter mucosa left ureter mucosa of organ left ureter mucous membrane left ureter organ mucosa left ureteral mucosa mucosa of organ of left ureter mucous membrane of left ureter organ mucosa of left ureter uberon UBERON:0005005 mucosa of left ureter A mucosa that is part of a left ureter [Automatically generated definition]. OBOL:automatic left ureter mucosa OBOL:automatic left ureter mucosa of organ OBOL:automatic left ureter mucous membrane OBOL:automatic left ureter organ mucosa OBOL:automatic left ureteral mucosa FMA:17807 mucosa of organ of left ureter OBOL:automatic mucous membrane of left ureter OBOL:automatic organ mucosa of left ureter OBOL:automatic A mucosa that is part of a renal pelvis [Automatically generated definition]. FMA:17931 kidney pelvis mucosa kidney pelvis mucosa of organ kidney pelvis mucous membrane kidney pelvis organ mucosa mucosa of kidney pelvis mucosa of organ of kidney pelvis mucosa of organ of pelvis of ureter mucosa of organ of renal pelvis mucosa of pelvis of ureter mucous membrane of kidney pelvis mucous membrane of pelvis of ureter mucous membrane of renal pelvis organ mucosa of kidney pelvis organ mucosa of pelvis of ureter organ mucosa of renal pelvis pelvis of ureter mucosa pelvis of ureter mucosa of organ pelvis of ureter mucous membrane pelvis of ureter organ mucosa renal pelvic mucosa renal pelvis mucosa renal pelvis mucosa of organ renal pelvis mucous membrane renal pelvis organ mucosa tunica mucosa pelvis renalis uberon UBERON:0005006 mucosa of renal pelvis A mucosa that is part of a renal pelvis [Automatically generated definition]. OBOL:automatic kidney pelvis mucosa OBOL:automatic kidney pelvis mucosa of organ OBOL:automatic kidney pelvis mucous membrane OBOL:automatic kidney pelvis organ mucosa OBOL:automatic mucosa of kidney pelvis OBOL:automatic mucosa of organ of kidney pelvis OBOL:automatic mucosa of organ of pelvis of ureter OBOL:automatic mucosa of organ of renal pelvis OBOL:automatic mucosa of pelvis of ureter OBOL:automatic mucous membrane of kidney pelvis OBOL:automatic mucous membrane of pelvis of ureter OBOL:automatic mucous membrane of renal pelvis OBOL:automatic organ mucosa of kidney pelvis OBOL:automatic organ mucosa of pelvis of ureter OBOL:automatic organ mucosa of renal pelvis OBOL:automatic pelvis of ureter mucosa OBOL:automatic pelvis of ureter mucosa of organ OBOL:automatic pelvis of ureter mucous membrane OBOL:automatic pelvis of ureter organ mucosa OBOL:automatic renal pelvic mucosa FMA:17931 renal pelvis mucosa OBOL:automatic renal pelvis mucosa of organ OBOL:automatic renal pelvis mucous membrane OBOL:automatic renal pelvis organ mucosa OBOL:automatic tunica mucosa pelvis renalis FMA:17931 FMA:TA A mucosa that is part of a neck of urinary bladder [Automatically generated definition]. FMA:17846 bladder neck mucosa bladder neck mucosa of organ bladder neck mucous membrane bladder neck organ mucosa mucosa of bladder neck mucosa of neck of bladder mucosa of organ of bladder neck mucosa of organ of neck of bladder mucosa of organ of neck of urinary bladder mucosa of organ of urinary bladder neck mucosa of organ of vesical neck mucosa of urinary bladder neck mucosa of vesical neck mucous membrane of bladder neck mucous membrane of neck of bladder mucous membrane of neck of urinary bladder mucous membrane of urinary bladder neck mucous membrane of vesical neck neck of bladder mucosa neck of bladder mucosa of organ neck of bladder mucous membrane neck of bladder organ mucosa neck of urinary bladder mucosa neck of urinary bladder mucosa of organ neck of urinary bladder mucous membrane neck of urinary bladder organ mucosa organ mucosa of bladder neck organ mucosa of neck of bladder organ mucosa of neck of urinary bladder organ mucosa of urinary bladder neck organ mucosa of vesical neck urinary bladder neck mucosa urinary bladder neck mucosa of organ urinary bladder neck mucous membrane vesical neck mucosa vesical neck mucosa of organ vesical neck mucous membrane vesical neck organ mucosa uberon UBERON:0005010 mucosa of neck of urinary bladder A mucosa that is part of a neck of urinary bladder [Automatically generated definition]. OBOL:automatic bladder neck mucosa OBOL:automatic bladder neck mucosa of organ OBOL:automatic bladder neck mucous membrane OBOL:automatic bladder neck organ mucosa OBOL:automatic mucosa of bladder neck OBOL:automatic mucosa of neck of bladder OBOL:automatic mucosa of organ of bladder neck OBOL:automatic mucosa of organ of neck of bladder OBOL:automatic mucosa of organ of neck of urinary bladder OBOL:automatic mucosa of organ of urinary bladder neck OBOL:automatic mucosa of organ of vesical neck OBOL:automatic mucosa of urinary bladder neck OBOL:automatic mucosa of vesical neck OBOL:automatic mucous membrane of bladder neck OBOL:automatic mucous membrane of neck of bladder OBOL:automatic mucous membrane of neck of urinary bladder OBOL:automatic mucous membrane of urinary bladder neck OBOL:automatic mucous membrane of vesical neck OBOL:automatic neck of bladder mucosa OBOL:automatic neck of bladder mucosa of organ OBOL:automatic neck of bladder mucous membrane OBOL:automatic neck of bladder organ mucosa OBOL:automatic neck of urinary bladder mucosa OBOL:automatic neck of urinary bladder mucosa of organ OBOL:automatic neck of urinary bladder mucous membrane OBOL:automatic neck of urinary bladder organ mucosa OBOL:automatic organ mucosa of bladder neck OBOL:automatic organ mucosa of neck of bladder OBOL:automatic organ mucosa of neck of urinary bladder OBOL:automatic organ mucosa of urinary bladder neck OBOL:automatic organ mucosa of vesical neck OBOL:automatic urinary bladder neck mucosa OBOL:automatic urinary bladder neck mucosa of organ OBOL:automatic urinary bladder neck mucous membrane OBOL:automatic vesical neck mucosa OBOL:automatic vesical neck mucosa of organ OBOL:automatic vesical neck mucous membrane OBOL:automatic vesical neck organ mucosa OBOL:automatic A mucosa that is part of a right uterine tube [Automatically generated definition]. FMA:18452 mucosa of organ of right fallopian tube mucosa of organ of right oviduct mucosa of organ of right uterine tube mucosa of right fallopian tube mucosa of right oviduct mucous membrane of right fallopian tube mucous membrane of right oviduct mucous membrane of right uterine tube organ mucosa of right fallopian tube organ mucosa of right oviduct organ mucosa of right uterine tube right fallopian tube mucosa right fallopian tube mucosa of organ right fallopian tube mucous membrane right fallopian tube organ mucosa right oviduct mucosa right oviduct mucosa of organ right oviduct mucous membrane right oviduct organ mucosa right uterine tube mucosa right uterine tube mucosa of organ right uterine tube mucous membrane right uterine tube organ mucosa uberon UBERON:0005011 mucosa of right uterine tube A mucosa that is part of a right uterine tube [Automatically generated definition]. OBOL:automatic mucosa of organ of right fallopian tube OBOL:automatic mucosa of organ of right oviduct OBOL:automatic mucosa of organ of right uterine tube OBOL:automatic mucosa of right fallopian tube OBOL:automatic mucosa of right oviduct OBOL:automatic mucous membrane of right fallopian tube OBOL:automatic mucous membrane of right oviduct OBOL:automatic mucous membrane of right uterine tube OBOL:automatic organ mucosa of right fallopian tube OBOL:automatic organ mucosa of right oviduct OBOL:automatic organ mucosa of right uterine tube OBOL:automatic right fallopian tube mucosa OBOL:automatic right fallopian tube mucosa of organ OBOL:automatic right fallopian tube mucous membrane OBOL:automatic right fallopian tube organ mucosa OBOL:automatic right oviduct mucosa OBOL:automatic right oviduct mucosa of organ OBOL:automatic right oviduct mucous membrane OBOL:automatic right oviduct organ mucosa OBOL:automatic right uterine tube mucosa OBOL:automatic right uterine tube mucosa of organ OBOL:automatic right uterine tube mucous membrane OBOL:automatic right uterine tube organ mucosa OBOL:automatic A mucosa that is part of a left uterine tube [Automatically generated definition]. FMA:18453 left fallopian tube mucosa left fallopian tube mucosa of organ left fallopian tube mucous membrane left fallopian tube organ mucosa left oviduct mucosa left oviduct mucosa of organ left oviduct mucous membrane left oviduct organ mucosa left uterine tube mucosa left uterine tube mucosa of organ left uterine tube mucous membrane left uterine tube organ mucosa mucosa of left fallopian tube mucosa of left oviduct mucosa of organ of left fallopian tube mucosa of organ of left oviduct mucosa of organ of left uterine tube mucous membrane of left fallopian tube mucous membrane of left oviduct mucous membrane of left uterine tube organ mucosa of left fallopian tube organ mucosa of left oviduct organ mucosa of left uterine tube uberon UBERON:0005012 mucosa of left uterine tube A mucosa that is part of a left uterine tube [Automatically generated definition]. OBOL:automatic left fallopian tube mucosa OBOL:automatic left fallopian tube mucosa of organ OBOL:automatic left fallopian tube mucous membrane OBOL:automatic left fallopian tube organ mucosa OBOL:automatic left oviduct mucosa OBOL:automatic left oviduct mucosa of organ OBOL:automatic left oviduct mucous membrane OBOL:automatic left oviduct organ mucosa OBOL:automatic left uterine tube mucosa OBOL:automatic left uterine tube mucosa of organ OBOL:automatic left uterine tube mucous membrane OBOL:automatic left uterine tube organ mucosa OBOL:automatic mucosa of left fallopian tube OBOL:automatic mucosa of left oviduct OBOL:automatic mucosa of organ of left fallopian tube OBOL:automatic mucosa of organ of left oviduct OBOL:automatic mucosa of organ of left uterine tube OBOL:automatic mucous membrane of left fallopian tube OBOL:automatic mucous membrane of left oviduct OBOL:automatic mucous membrane of left uterine tube OBOL:automatic organ mucosa of left fallopian tube OBOL:automatic organ mucosa of left oviduct OBOL:automatic organ mucosa of left uterine tube OBOL:automatic A mucosa that is part of a male urethra [Automatically generated definition]. FMA:239937 male urethra mucosa male urethra mucosa of organ male urethra mucous membrane male urethra organ mucosa mucosa of organ of male urethra mucous membrane of male urethra organ mucosa of male urethra uberon UBERON:0005013 mucosa of male urethra A mucosa that is part of a male urethra [Automatically generated definition]. OBOL:automatic male urethra mucosa OBOL:automatic male urethra mucosa of organ OBOL:automatic male urethra mucous membrane OBOL:automatic male urethra organ mucosa OBOL:automatic mucosa of organ of male urethra OBOL:automatic mucous membrane of male urethra OBOL:automatic organ mucosa of male urethra OBOL:automatic A mucosa that is part of a female urethra [Automatically generated definition]. FMA:239940 female urethra mucosa female urethra mucosa of organ female urethra mucous membrane female urethra organ mucosa mucosa of organ of female urethra mucous membrane of female urethra organ mucosa of female urethra uberon UBERON:0005014 mucosa of female urethra A mucosa that is part of a female urethra [Automatically generated definition]. OBOL:automatic female urethra mucosa OBOL:automatic female urethra mucosa of organ OBOL:automatic female urethra mucous membrane OBOL:automatic female urethra organ mucosa OBOL:automatic mucosa of organ of female urethra OBOL:automatic mucous membrane of female urethra OBOL:automatic organ mucosa of female urethra OBOL:automatic A mucosa that is part of a lacrimal sac [Automatically generated definition]. FMA:72061 lacrimal sac mucosa lacrimal sac mucosa of organ lacrimal sac mucous membrane lacrimal sac organ mucosa mucosa of organ of lacrimal sac mucous membrane of lacrimal sac organ mucosa of lacrimal sac uberon UBERON:0005017 mucosa of lacrimal sac A mucosa that is part of a lacrimal sac [Automatically generated definition]. OBOL:automatic lacrimal sac mucosa OBOL:automatic lacrimal sac mucosa of organ OBOL:automatic lacrimal sac mucous membrane OBOL:automatic lacrimal sac organ mucosa OBOL:automatic mucosa of organ of lacrimal sac OBOL:automatic mucous membrane of lacrimal sac OBOL:automatic organ mucosa of lacrimal sac OBOL:automatic A mucosa that is part of a tongue [Automatically generated definition]. EFO:0002553 FMA:54807 lingual mucosa mucosa of organ of tongue mucous membrane of tongue organ mucosa of tongue tongue mucosa tongue mucosa of organ tongue mucous membrane tongue organ mucosa tunica mucosa linguae uberon UBERON:0005020 mucosa of tongue A mucosa that is part of a tongue [Automatically generated definition]. OBOL:automatic lingual mucosa FMA:54807 mucosa of organ of tongue OBOL:automatic mucous membrane of tongue OBOL:automatic organ mucosa of tongue OBOL:automatic tongue mucosa OBOL:automatic tongue mucosa of organ OBOL:automatic tongue mucous membrane OBOL:automatic tongue organ mucosa OBOL:automatic tunica mucosa linguae FMA:54807 FMA:TA A mucosa that is part of a nasopharynx [Automatically generated definition]. FMA:54971 mucosa of nasal part of pharynx mucosa of organ of nasal part of pharynx mucosa of organ of nasopharynx mucosa of organ of rhinopharynx mucosa of rhinopharynx mucous membrane of nasal part of pharynx mucous membrane of nasopharynx mucous membrane of rhinopharynx nasal part of pharynx mucosa nasal part of pharynx mucosa of organ nasal part of pharynx mucous membrane nasal part of pharynx organ mucosa nasopharynx mucosa nasopharynx mucosa of organ nasopharynx mucous membrane nasopharynx organ mucosa organ mucosa of nasal part of pharynx organ mucosa of nasopharynx organ mucosa of rhinopharynx rhinopharynx mucosa rhinopharynx mucosa of organ rhinopharynx mucous membrane rhinopharynx organ mucosa uberon UBERON:0005022 mucosa of nasopharynx A mucosa that is part of a nasopharynx [Automatically generated definition]. OBOL:automatic mucosa of nasal part of pharynx OBOL:automatic mucosa of organ of nasal part of pharynx OBOL:automatic mucosa of organ of nasopharynx OBOL:automatic mucosa of organ of rhinopharynx OBOL:automatic mucosa of rhinopharynx OBOL:automatic mucous membrane of nasal part of pharynx OBOL:automatic mucous membrane of nasopharynx OBOL:automatic mucous membrane of rhinopharynx OBOL:automatic nasal part of pharynx mucosa OBOL:automatic nasal part of pharynx mucosa of organ OBOL:automatic nasal part of pharynx mucous membrane OBOL:automatic nasal part of pharynx organ mucosa OBOL:automatic nasopharynx mucosa OBOL:automatic nasopharynx mucosa of organ OBOL:automatic nasopharynx mucous membrane OBOL:automatic nasopharynx organ mucosa OBOL:automatic organ mucosa of nasal part of pharynx OBOL:automatic organ mucosa of nasopharynx OBOL:automatic organ mucosa of rhinopharynx OBOL:automatic rhinopharynx mucosa OBOL:automatic rhinopharynx mucosa of organ OBOL:automatic rhinopharynx mucous membrane OBOL:automatic rhinopharynx organ mucosa OBOL:automatic A mucosa that is part of a oropharynx [Automatically generated definition]. FMA:54933 mucosa of oral part of pharynx mucosa of organ of oral part of pharynx mucosa of organ of oropharynx mucous membrane of oral part of pharynx mucous membrane of oropharynx oral part of pharynx mucosa oral part of pharynx mucosa of organ oral part of pharynx mucous membrane oral part of pharynx organ mucosa organ mucosa of oral part of pharynx organ mucosa of oropharynx oropharynx mucosa oropharynx mucosa of organ oropharynx mucous membrane oropharynx organ mucosa uberon UBERON:0005023 mucosa of oropharynx A mucosa that is part of a oropharynx [Automatically generated definition]. OBOL:automatic mucosa of oral part of pharynx OBOL:automatic mucosa of organ of oral part of pharynx OBOL:automatic mucosa of organ of oropharynx OBOL:automatic mucous membrane of oral part of pharynx OBOL:automatic mucous membrane of oropharynx OBOL:automatic oral part of pharynx mucosa OBOL:automatic oral part of pharynx mucosa of organ OBOL:automatic oral part of pharynx mucous membrane OBOL:automatic oral part of pharynx organ mucosa OBOL:automatic organ mucosa of oral part of pharynx OBOL:automatic organ mucosa of oropharynx OBOL:automatic oropharynx mucosa OBOL:automatic oropharynx mucosa of organ OBOL:automatic oropharynx mucous membrane OBOL:automatic oropharynx organ mucosa OBOL:automatic A mucosa that is part of a middle ear [Automatically generated definition]. CALOHA:TS-0631 FMA:59663 middle ear mucosa middle ear mucosa of organ middle ear mucous membrane middle ear organ mucosa mucosa of organ of middle ear mucosa of tympanic cavity mucous membrane of middle ear organ mucosa of middle ear tunica mucosa cavitatis tympanicae uberon UBERON:0005026 mucosa of middle ear A mucosa that is part of a middle ear [Automatically generated definition]. OBOL:automatic middle ear mucosa OBOL:automatic middle ear mucosa of organ OBOL:automatic middle ear mucous membrane OBOL:automatic middle ear organ mucosa OBOL:automatic mucosa of organ of middle ear OBOL:automatic mucosa of tympanic cavity FMA:59663 mucous membrane of middle ear OBOL:automatic organ mucosa of middle ear OBOL:automatic tunica mucosa cavitatis tympanicae FMA:59663 FMA:TA A mucosa that is part of a lower lip [Automatically generated definition]. FMA:59833 NCIT:C12225 UMLS:C0226939 lower labial mucosa lower lip mucosa lower lip mucosa of organ lower lip mucous membrane lower lip organ mucosa mucosa of organ of lower lip mucous membrane of lower lip organ mucosa of lower lip uberon UBERON:0005032 mucosa of lower lip A mucosa that is part of a lower lip [Automatically generated definition]. OBOL:automatic UMLS:C0226939 ncithesaurus:Mucosa_of_the_Lower_Lip lower labial mucosa UBERON:cjm lower lip mucosa OBOL:automatic lower lip mucosa of organ OBOL:automatic lower lip mucous membrane OBOL:automatic lower lip organ mucosa OBOL:automatic mucosa of organ of lower lip OBOL:automatic mucous membrane of lower lip OBOL:automatic organ mucosa of lower lip OBOL:automatic A mucosa that is part of a gallbladder [Automatically generated definition]. FMA:14662 gall bladder mucosa gall bladder mucosa of organ gall bladder mucous membrane gall bladder organ mucosa gallbladder mucosa gallbladder mucosa of organ gallbladder mucous membrane gallbladder organ mucosa mucosa of gall bladder mucosa of organ of gall bladder mucosa of organ of gallbladder mucous membrane of gall bladder mucous membrane of gallbladder organ mucosa of gall bladder organ mucosa of gallbladder tunica mucosa (vesica biliaris) tunica mucosa vesicae biliaris uberon UBERON:0005033 mucosa of gallbladder A mucosa that is part of a gallbladder [Automatically generated definition]. OBOL:automatic gall bladder mucosa OBOL:automatic gall bladder mucosa of organ OBOL:automatic gall bladder mucous membrane OBOL:automatic gall bladder organ mucosa OBOL:automatic gallbladder mucosa OBOL:automatic gallbladder mucosa of organ OBOL:automatic gallbladder mucous membrane OBOL:automatic gallbladder organ mucosa OBOL:automatic mucosa of gall bladder OBOL:automatic mucosa of organ of gall bladder OBOL:automatic mucosa of organ of gallbladder OBOL:automatic mucous membrane of gall bladder OBOL:automatic mucous membrane of gallbladder OBOL:automatic organ mucosa of gall bladder OBOL:automatic organ mucosa of gallbladder OBOL:automatic tunica mucosa (vesica biliaris) FMA:14662 tunica mucosa vesicae biliaris FMA:14662 FMA:TA A mucosa that is part of a bronchiole [Automatically generated definition]. FMA:263230 FMA:62774 bronchiole mucosa bronchiole mucosa of organ bronchiole mucous membrane bronchiole organ mucosa lobular bronchiole mucosa lobular bronchiole mucosa of organ lobular bronchiole mucous membrane lobular bronchiole organ mucosa mucosa of lobular bronchiole mucosa of organ of bronchiole mucosa of organ of lobular bronchiole mucous membrane of bronchiole mucous membrane of lobular bronchiole organ mucosa of bronchiole organ mucosa of lobular bronchiole uberon UBERON:0005039 mucosa of bronchiole A mucosa that is part of a bronchiole [Automatically generated definition]. OBOL:automatic bronchiole mucosa OBOL:automatic bronchiole mucosa of organ OBOL:automatic bronchiole mucous membrane OBOL:automatic bronchiole organ mucosa OBOL:automatic lobular bronchiole mucosa OBOL:automatic lobular bronchiole mucosa of organ OBOL:automatic lobular bronchiole mucous membrane OBOL:automatic lobular bronchiole organ mucosa OBOL:automatic mucosa of lobular bronchiole OBOL:automatic mucosa of organ of bronchiole OBOL:automatic mucosa of organ of lobular bronchiole OBOL:automatic mucous membrane of bronchiole OBOL:automatic mucous membrane of lobular bronchiole OBOL:automatic organ mucosa of bronchiole OBOL:automatic organ mucosa of lobular bronchiole OBOL:automatic A mucosa that is part of a terminal bronchiole [Automatically generated definition]. FMA:263232 bronchiolus terminalis mucosa bronchiolus terminalis mucosa of organ bronchiolus terminalis mucous membrane bronchiolus terminalis organ mucosa mucosa of bronchiolus terminalis mucosa of organ of bronchiolus terminalis mucosa of organ of terminal bronchiole mucous membrane of bronchiolus terminalis mucous membrane of terminal bronchiole organ mucosa of bronchiolus terminalis organ mucosa of terminal bronchiole terminal bronchiole mucosa terminal bronchiole mucosa of organ terminal bronchiole mucous membrane terminal bronchiole organ mucosa uberon UBERON:0005040 mucosa of terminal bronchiole A mucosa that is part of a terminal bronchiole [Automatically generated definition]. OBOL:automatic bronchiolus terminalis mucosa OBOL:automatic bronchiolus terminalis mucosa of organ OBOL:automatic bronchiolus terminalis mucous membrane OBOL:automatic bronchiolus terminalis organ mucosa OBOL:automatic mucosa of bronchiolus terminalis OBOL:automatic mucosa of organ of bronchiolus terminalis OBOL:automatic mucosa of organ of terminal bronchiole OBOL:automatic mucous membrane of bronchiolus terminalis OBOL:automatic mucous membrane of terminal bronchiole OBOL:automatic organ mucosa of bronchiolus terminalis OBOL:automatic organ mucosa of terminal bronchiole OBOL:automatic terminal bronchiole mucosa OBOL:automatic terminal bronchiole mucosa of organ OBOL:automatic terminal bronchiole mucous membrane OBOL:automatic terminal bronchiole organ mucosa OBOL:automatic A portion of the tympanic cavity epithelium which makes up the outer (cuticular) layer of the tympanic membrane in FMA this is classified as a mucosa FMA:56844 mucosa of tympanic membrane mucous layer of tympanic membrane mucous stratum of tympanic membrane tympanic membrane external middle ear cavity epithelial component tympanic membrane mucosa uberon UBERON:0005042 inner epithelial layer of tympanic membrane A portion of the tympanic cavity epithelium which makes up the outer (cuticular) layer of the tympanic membrane in FMA this is classified as a mucosa FMA mucosa of tympanic membrane FMA:56844 mucous layer of tympanic membrane FMA:56844 mucous stratum of tympanic membrane FMA:56844 tympanic membrane external middle ear cavity epithelial component tympanic membrane mucosa FMA:56844 A mucosa that is part of a nasolacrimal duct [Automatically generated definition]. FMA:59664 mucosa of organ of nasolacrimal duct mucous membrane of nasolacrimal duct nasolacrimal duct mucosa nasolacrimal duct mucosa of organ nasolacrimal duct mucous membrane nasolacrimal duct organ mucosa nasolacrimal ductal mucosa organ mucosa of nasolacrimal duct uberon UBERON:0005043 mucosa of nasolacrimal duct A mucosa that is part of a nasolacrimal duct [Automatically generated definition]. OBOL:automatic mucosa of organ of nasolacrimal duct OBOL:automatic mucous membrane of nasolacrimal duct OBOL:automatic nasolacrimal duct mucosa OBOL:automatic nasolacrimal duct mucosa of organ OBOL:automatic nasolacrimal duct mucous membrane OBOL:automatic nasolacrimal duct organ mucosa OBOL:automatic nasolacrimal ductal mucosa FMA:59664 organ mucosa of nasolacrimal duct OBOL:automatic A mucosa that is part of a fallopian tube [Automatically generated definition]. FMA:18319 fallopian tube mucosa fallopian tube mucosa of organ fallopian tube mucous membrane fallopian tube organ mucosa mucosa of fallopian tube mucosa of organ of fallopian tube mucosa of organ of uterine tube mucosa of oviduct mucous membrane of fallopian tube mucous membrane of uterine tube organ mucosa of fallopian tube organ mucosa of uterine tube tunica mucosa tubae uterinae uterine tubal mucosa uterine tube mucosa uterine tube mucosa of organ uterine tube mucous membrane uterine tube organ mucosa uberon UBERON:0005048 mucosa of uterine tube A mucosa that is part of a fallopian tube [Automatically generated definition]. OBOL:automatic fallopian tube mucosa OBOL:automatic fallopian tube mucosa of organ OBOL:automatic fallopian tube mucous membrane OBOL:automatic fallopian tube organ mucosa OBOL:automatic mucosa of fallopian tube OBOL:automatic mucosa of organ of fallopian tube OBOL:automatic mucosa of organ of uterine tube OBOL:automatic mucosa of oviduct FMA:18319 mucous membrane of fallopian tube OBOL:automatic mucous membrane of uterine tube OBOL:automatic organ mucosa of fallopian tube OBOL:automatic organ mucosa of uterine tube OBOL:automatic tunica mucosa tubae uterinae FMA:18319 FMA:TA uterine tubal mucosa FMA:18319 uterine tube mucosa OBOL:automatic uterine tube mucosa of organ OBOL:automatic uterine tube mucous membrane OBOL:automatic uterine tube organ mucosa OBOL:automatic A mucosa that is part of a uterine tube infundibulum [Automatically generated definition]. FMA:18357 mucosa of infundibulum of fallopian tube mucosa of infundibulum of oviduct mucosa of organ of uterine tube infundibulum mucosa of uterine tube infundibulum mucous membrane of uterine tube infundibulum organ mucosa of uterine tube infundibulum uterine tube infundibulum mucosa uterine tube infundibulum mucosa of organ uterine tube infundibulum mucous membrane uterine tube infundibulum organ mucosa uberon UBERON:0005049 mucosa of infundibulum of uterine tube A mucosa that is part of a uterine tube infundibulum [Automatically generated definition]. OBOL:automatic mucosa of infundibulum of fallopian tube FMA:18357 mucosa of infundibulum of oviduct FMA:18357 mucosa of organ of uterine tube infundibulum OBOL:automatic mucosa of uterine tube infundibulum OBOL:automatic mucous membrane of uterine tube infundibulum OBOL:automatic organ mucosa of uterine tube infundibulum OBOL:automatic uterine tube infundibulum mucosa OBOL:automatic uterine tube infundibulum mucosa of organ OBOL:automatic uterine tube infundibulum mucous membrane OBOL:automatic uterine tube infundibulum organ mucosa OBOL:automatic The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP] EMAPA:18331 FMA:19812 MA:0003240 body of highmore hilum of testicle mediastinum of testis testis mediastinum uberon UBERON:0005051 mediastinum testis http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP] body of highmore FMA:19812 mediastinum of testis FMA:19812 testis mediastinum FMA:19812 An organ part that is part of a long bone [Automatically generated definition]. FMA:24008 long bone zone uberon UBERON:0005055 zone of long bone An organ part that is part of a long bone [Automatically generated definition]. OBOL:automatic An external genitalia that is part of a female reproductive system [Automatically generated definition]. in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126] BTO:0003100 EMAPA:30984 FMA:45649 galen:FemaleExternalGenitalia external female genital organ external genitalia of female reproductive system female external genitalia uberon organa genitalia feminina externa UBERON:0005056 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 external female genitalia An external genitalia that is part of a female reproductive system [Automatically generated definition]. OBOL:automatic external female genital organ BTO:0003100 external genitalia of female reproductive system OBOL:automatic female external genitalia FMA:45649 organa genitalia feminina externa BTO:0003100 An organ that is part of a immune system [Automatically generated definition]. immune system organ uberon UBERON:0005057 immune organ An organ that is part of a immune system [Automatically generated definition]. OBOL:automatic A gland that is part of a hemolymphoid system [Automatically generated definition]. hemopoietic or lymphoid organ EMAPA:18766 MA:0002962 hemopoietic or lymphoid gland uberon haemolymphoid system gland UBERON:0005058 hemolymphoid system gland A gland that is part of a hemolymphoid system [Automatically generated definition]. OBOL:automatic hemopoietic or lymphoid organ GO:0048534 hemopoietic or lymphoid gland haemolymphoid system gland EMAPA:18766 The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 NCIT:C34224 UMLS:C0814992 XAO:0000248 uberon UBERON:0005061 neural groove The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. GO:0001842 The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. UMLS:C0814992 ncithesaurus:Neural_Groove One of the two elevated edges of the neural groove[GO,MP]. In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 UMLS:C0814993 XAO:0004087 medullary fold uberon UBERON:0005062 neural fold One of the two elevated edges of the neural groove[GO,MP]. GO:0001842 MP:0011256 In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. UMLS:C0814993 ncithesaurus:Neural_Fold medullary fold MP:0011256 . uberon UBERON:0005064 left ventricular trabecular myocardium GO . GO:0003225 . uberon UBERON:0005066 right ventricular trabecular myocardium GO . GO:0003227 A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 uberon neural tube rod UBERON:0005068 neural rod A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. GO:0014024 ZFA:0000133 An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000133 TAO ZFIN:curator neural tube rod GO:0014027 An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain. The boundary between the diencephalon and the mesencephalon.[TAO] relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO] EMAPA:36449 TAO:0001367 ZFA:0001367 diencephalic-mesencephalic boundary forebrain midbrain boundary forebrain-midbrain boundary region uberon UBERON:0005075 forebrain-midbrain boundary definitional An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain. OBOL:automatic The boundary between the diencephalon and the mesencephalon.[TAO] 2012-08-14 TAO:0001367 TAO ZFIN:curator relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO] 2012-08-14 TAO:0001367 TAO diencephalic-mesencephalic boundary ZFA:0001367 forebrain midbrain boundary ZFA:0001367 forebrain-midbrain boundary region EMAPA:36449 An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. hindbrain-spinal cord boundary region uberon UBERON:0005076 hindbrain-spinal cord boundary An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. OBOL:automatic A product of the somatic follicle cell epithelium and a structure that supports the egg in a hostile environment, minimizing water loss whilst allowing gas exchanges essential for embryonic respiration[GO]. egg shell http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0278 shell (egg) LanguaL term definition: The covering of a bird or reptile egg. eggshell The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. uberon UBERON:0005080 metanephric ureteric bud The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. GO:0035502 The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. uberon UBERON:0005081 ureter ureteric bud The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. GO:0035503 A hole in a tube[GO]. AEO:0000078 EHDAA2:0004618 RETIRED_EHDAA2:0003078 uberon UBERON:0005082 tube lumen A hole in a tube[GO]. GO:0060609 An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO] consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures AEO:0000218 uberon epithelial placode UBERON:0005085 ectodermal placode An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO] GO:0060788 in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures GO epithelial placode AEO:0000112 A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]. EMAPA:36479 hair placode vibrissa placode uberon hair gem hair germ hair peg UBERON:0005086 hair follicle placode Wikipathways:WP2062 A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]. GO:0060789 hair placode hair gem ISBN:9780878932504 hair germ hair peg ISBN:9780878932504 An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO]. Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO] In mammals this may be located in the alveolar ridges, but note that some species such as zebrafish have ceratobranchial teeth. Sharks have dermal denticles that share developmental origins. Currently we don't include location information due to this diversity, but in future we may include specific subclasses and/or taxon GCIs. BTO:0001511 TAO:0001153 ZFA:0001153 dental anlage dental placode dental primordium odontogenic placode tooth anlage tooth primordium uberon tooth germ UBERON:0005087 tooth placode NCBIBook:NBK53175 check for other species An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO]. GO:0060790 Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO] 2012-08-14 TAO:0001153 TAO ZFIN:curator dental placode OBOL:automatic dental primordium ZFA:0001153 odontogenic placode OBOL:automatic tooth anlage MP:0000117 tooth primordium MP:0000117 tooth germ ZFA:0001153 A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO]. TODO - add bud uberon UBERON:0005088 sebaceous gland placode NCBIBook:NBK53175 Wikipathways:WP2062 A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO]. GO:0060791 An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud[GO]. TODO - add bud uberon UBERON:0005089 sweat gland placode NCBIBook:NBK53175 Wikipathways:WP2062 An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud[GO]. GO:0060793 Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila EMAPA:32715 FBbt:00005073 FMA:30316 musculus uberon muscle muscle element UBERON:0005090 muscle structure Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. GO:0061061 musculus FMA:30316 Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG] EHDAA2:0001841 EHDAA:484 EMAPA:16239 FMA:70318 VHOG:0000489 sinus venosus right horn uberon UBERON:0005092 right horn of sinus venosus FMA Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG] 2012-09-17 VHOG:0000489 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003 sinus venosus right horn VHOG:0000489 . class added for consistency with GO - consider merging with kidney mesenchyme. uberon kidney anlage UBERON:0005095 kidney rudiment GO . GO:0072003 kidney anlage GOC:mtg_kidney_jan10 An epithelium that is part of a mesonephros [Automatically generated definition]. uberon UBERON:0005103 mesonephric epithelium An epithelium that is part of a mesonephros [Automatically generated definition]. OBOL:automatic A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] VHOG:0001526 uberon UBERON:0005106 metanephric tubule A metanephric tubule is an epithelial tube that is part of the metanephros[GO]. GO:0072173 The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] 2012-09-17 VHOG:0001526 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. uberon UBERON:0005108 metanephric epithelium An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]. GO:0072207 Any smooth muscle tissue that is part of a metanephros. uberon UBERON:0005109 metanephric smooth muscle tissue Any smooth muscle tissue that is part of a metanephros. GO:0072208 A metanephric nephron is the functional unit of the metanephros[GO]. The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG] UBERON:0005142 VHOG:0000719 uberon UBERON:0005110 metanephric nephron Wikipedia Bgee:AN A metanephric nephron is the functional unit of the metanephros[GO]. GO:0072273 The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG] 2012-09-17 VHOG:0000719 VHOG DOI:10.1093/icb/34.4.542 Ruppert EE, Evolutionary Origin of the Vertebrate Nephron. Integrative and Comparative Biology (1994) Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO]. uberon UBERON:0005111 metanephric pyramid Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO]. GO:0072211 EHDAA2:0001140 uberon UBERON:0005113 metanephric cortex mesenchyme EHDAA2 The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO]. uberon UBERON:0005115 metanephric cortical collecting duct true true The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO]. GO:0072219 The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO]. uberon UBERON:0005134 metanephric nephron epithelium true The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO]. GO:0072243 The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. UBERON:0005112 uberon UBERON:0005137 metanephric capsule The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]. GO:0072213 A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO]. UBERON:0005128 UBERON:0005152 uberon UBERON:0005146 metanephric nephron tubule ISBN:9780878932504 A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO]. GO:0072282 The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. EHDAA2:0001245 EHDAA:9346 EMAPA:27678 metanephric vesicle uberon UBERON:0005147 metanephric renal vesicle EHDAA2 The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. GO:0072283 A bud is a protrusion that forms from an epithelial sheet by localized folding. BTO:0001639 uberon UBERON:0005153 epithelial bud A bud is a protrusion that forms from an epithelial sheet by localized folding. GO:0060572 A cord of epithelial cells without a lumen and usually several cells thick. AEO:0000216 EHDAA2:0004052 uberon UBERON:0005154 epithelial cord AEO A cord of epithelial cells without a lumen and usually several cells thick. AEO:0000216 Any anatomical structure that is part of the reproductive system. reproductive system element reproductive system structure uberon UBERON:0005156 reproductive structure Any anatomical structure that is part of the reproductive system. An epithelial sheet bent on a linear axis. uberon UBERON:0005157 epithelial fold An epithelial sheet bent on a linear axis. GO:0060571 The functional tissue of the central nervous system consisting of neurons and glial cells. CNS parenchyma central nervous system parenchyma parenchyma of CNS parenchyma of central nervous system uberon UBERON:0005158 parenchyma of central nervous system The functional tissue of the central nervous system consisting of neurons and glial cells. CL:tm CNS parenchyma OBOL:automatic central nervous system parenchyma OBOL:automatic parenchyma of CNS OBOL:automatic A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' AAO:0011000 CARO:0001000 FBbt:00007060 FMA:83115 multi-cell-component structure multi-cell-part structure uberon cell part cluster UBERON:0005162 multi cell part structure FMA A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. CARO:0001000 we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' CARO FMA multi-cell-component structure CARO:0001000 multi-cell-part structure CARO:0001000 cell part cluster FMA:83115 Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion). TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same A duct that carries bile from the liver to the small intestine.[TAO] The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG] The hepatic duct is the duct that leads from the liver to the bile duct[GO]. EHDAA2:0000741 EHDAA:3049 EMAPA:16843 FMA:71891 MA:0000357 NCIT:C32730 OpenCyc:Mx4rvWo8WJwpEbGdrcN5Y29ycA UMLS:C0917710 VHOG:0000219 galen:HepaticDuct uberon UBERON:0005171 hepatic duct Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion). A duct that carries bile from the liver to the small intestine.[TAO] 2012-08-14 TAO:0001100 TAO ZFIN:curator The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG] 2012-09-17 VHOG:0000219 VHOG The hepatic duct is the duct that leads from the liver to the bile duct[GO]. GO:0061011 UMLS:C0917710 ncithesaurus:Hepatic_Duct An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. MA:0000522 abdomen organ uberon UBERON:0005172 abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. abdomen organ MA:0000522 An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. EMAPA:37062 MA:0000529 abdominal segment organ uberon UBERON:0005173 abdominal segment element An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. EMAPA:37062 MA:th abdominal segment organ MA:0000529 An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. EMAPA:37274 MA:0001901 back organ dorsal region organ uberon UBERON:0005174 dorsal region element An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. EMAPA:37274 MA:th back organ MA:0001901 An organ that is part of a chest [Automatically generated definition]. EMAPA:37272 MA:0000552 uberon UBERON:0005175 chest organ An organ that is part of a chest [Automatically generated definition]. OBOL:automatic EMAPA:37272 MA:th A circumscribed mass of ectodermal cells which bud off from the dental lamina; it becomes cup-shaped and develops on its internal face the ameloblast layer of cells that produces the enamel cap of a developing tooth. A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO] NOT develops_from NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation BTO:0001722 CALOHA:TS-0271 EMAPA:32888 FMA:312389 MA:0001604 MESH:A14.254.900.720.265 TAO:0005138 ZFA:0005138 dental organ enamel organ uberon odontogenic organ organum enameleum UBERON:0005176 . Alternate definition: A cellular aggregation seen in histologic sections of a developing tooth. It lies above a condensation of ectomesenchymal cells called the odontogenic papilla. tooth enamel organ A circumscribed mass of ectodermal cells which bud off from the dental lamina; it becomes cup-shaped and develops on its internal face the ameloblast layer of cells that produces the enamel cap of a developing tooth. ISBN:0-683-40008-8 MP:0010747 A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO] 2012-08-14 TAO:0005138 TAO ZFIN:curator dental organ ZFA:0005138 enamel organ MP:0010747 organum enameleum An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. EMAPA:37270 MA:0000516 trunk organ uberon UBERON:0005177 trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. EMAPA:37270 MA:th trunk organ MA:0000516 An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. EMAPA:37273 MA:0000557 thoracic cavity organ uberon UBERON:0005178 thoracic cavity element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. EMAPA:37273 MA:th thoracic cavity organ MA:0000557 An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. EMAPA:37275 MA:0000543 pelvic element pelvis organ pelvis region organ uberon UBERON:0005179 pelvic region element An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. EMAPA:37275 MA:th pelvis organ MA:0000543 An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. EMAPA:37271 MA:0000563 uberon upper body organ UBERON:0005181 thoracic segment organ An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. EMAPA:37271 MA:th upper body organ MA:0000563 Innermost layer of the hair shaft. BTO:0004671 EMAPA:35389 MA:0000158 uberon medulla of hair shaft UBERON:0005184 hair medulla Innermost layer of the hair shaft. medulla of hair shaft BTO:0004671 The portion of the collecting duct that resides in the renal medulla BTO:0004536 EMAPA:28061 EMAPA:35459 MA:0002935 kidney medulla collecting duct medullary collecting duct uberon UBERON:0005185 renal medulla collecting duct The portion of the collecting duct that resides in the renal medulla kidney medulla collecting duct MA:0002935 medullary collecting duct EMAPA:28061 An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP]. EMAPA:37513 FMA:18930 MA:0001940 arteria ductus deferentis artery of ductus deferens ductus deferens artery vas deferens artery uberon UBERON:0005192 deferent duct artery FMA Wikipedia An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP]. EMAPA:37513 MA:th arteria ductus deferentis artery of ductus deferens FMA:18930 ductus deferens artery FMA:18930 A vein that is part of a thorax [Automatically generated definition]. EMAPA:37197 MA:0002235 NCIT:C53142 UMLS:C0226629 uberon UBERON:0005194 thoracic vein A vein that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37197 MA:th UMLS:C0226629 ncithesaurus:Thoracic_Vein A vein that is part of a vas deferens [Automatically generated definition]. EMAPA:37514 MA:0002100 uberon UBERON:0005195 deferent duct vein A vein that is part of a vas deferens [Automatically generated definition]. OBOL:automatic EMAPA:37514 MA:th A gland that is part of a larynx submucosa [Automatically generated definition]. EMAPA:35475 MA:0002729 uberon laryngeal submucosa gland UBERON:0005204 larynx submucosa gland A gland that is part of a larynx submucosa [Automatically generated definition]. OBOL:automatic laryngeal submucosa gland EMAPA:35475 EMAPA:35902 FMA:19979 MA:0002737 uberon vagina stroma UBERON:0005205 lamina propria of vagina vagina stroma MA:0002737 Stromal matrix surrounding blood vessels within the choroid plexus. EMAPA:36609 MA:0000825 choroid plexus stromal matrix uberon UBERON:0005206 choroid plexus stroma Stromal matrix surrounding blood vessels within the choroid plexus. PMCID:PMC3496674 choroid plexus stromal matrix PMCID:PMC3496674 A capsule that is part of a tonsil [Automatically generated definition]. FMA:294647 MA:0000776 uberon UBERON:0005207 tonsil capsule A capsule that is part of a tonsil [Automatically generated definition]. OBOL:automatic A valve that is part of a right atrium [Automatically generated definition]. EHDAA2:0000302 EMAPA:17327 MA:0001871 valve of right atrium uberon right atrium valves superior vena cava valve UBERON:0005208 right atrium valve A valve that is part of a right atrium [Automatically generated definition]. OBOL:automatic valve of right atrium EMAPA:17327 right atrium valves EHDAA2:0000302 superior vena cava valve EMAPA:17327 An external ectoderm that is part of a optic eminence [Automatically generated definition]. EMAPA:16539 RETIRED_EHDAA2:0001311 VHOG:0000520 uberon UBERON:0005216 optic eminence surface ectoderm true An external ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic A subarachnoid space that is part of a midbrain [Automatically generated definition]. Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG] EMAPA:19055 VHOG:0001304 subarachnoid space midbrain uberon subarachnoid space mesencephalon UBERON:0005217 midbrain subarachnoid space A subarachnoid space that is part of a midbrain [Automatically generated definition]. OBOL:automatic Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0001304 VHOG subarachnoid space midbrain VHOG:0001304 subarachnoid space mesencephalon VHOG:0001304 A subarachnoid space that is part of a diencephalon [Automatically generated definition]. Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG] EMAPA:19053 VHOG:0001302 subarachnoid space diencephalon uberon UBERON:0005218 diencephalon subarachnoid space A subarachnoid space that is part of a diencephalon [Automatically generated definition]. OBOL:automatic Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG] 2012-09-17 VHOG:0001302 VHOG subarachnoid space diencephalon VHOG:0001302 A subarachnoid space that is part of a hindbrain [Automatically generated definition]. Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG] EMAPA:18211 VHOG:0001303 subarachnoid space hindbrain uberon subarachnoid space rhombencephalon UBERON:0005219 hindbrain subarachnoid space A subarachnoid space that is part of a hindbrain [Automatically generated definition]. OBOL:automatic Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG] 2012-09-17 VHOG:0001303 VHOG subarachnoid space hindbrain VHOG:0001303 subarachnoid space rhombencephalon VHOG:0001303 A parenchyma that is part of a right lobe of liver [Automatically generated definition]. EHDAA2:0001010 EMAPA:18317 FMA:71657 VHOG:0000840 parenchyma of right lobe of liver uberon UBERON:0005221 liver right lobe parenchyma A parenchyma that is part of a right lobe of liver [Automatically generated definition]. OBOL:automatic parenchyma of right lobe of liver FMA:71657 A parenchyma that is part of a left lobe of liver [Automatically generated definition]. EHDAA2:0001002 EMAPA:18310 FMA:71658 VHOG:0000839 parenchyma of left lobe of liver uberon UBERON:0005222 liver left lobe parenchyma A parenchyma that is part of a left lobe of liver [Automatically generated definition]. OBOL:automatic parenchyma of left lobe of liver FMA:71658 An epithelium that is part of a hindlimb stylopod [Automatically generated definition]. EHDAA2:0002131 EMAPA:17500 VHOG:0001041 uberon UBERON:0005225 upper leg epithelium EHDAA2 An epithelium that is part of a hindlimb stylopod [Automatically generated definition]. OBOL:automatic An epithelium that is part of a toe [Automatically generated definition]. EMAPA:32946 VHOG:0001031 hind limb digit epithelium toe epithelium foot digit epithelium uberon UBERON:0005226 pedal digit epithelium EHDAA2 EHDAA2 An epithelium that is part of a toe [Automatically generated definition]. OBOL:automatic hind limb digit epithelium OBOL:accepted foot digit epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a finger [Automatically generated definition]. EHDAA2:0000406 EMAPA:32647 VHOG:0001032 finger epithelium fore limb digit epithelium hand digit epithelium uberon UBERON:0005227 manual digit epithelium EHDAA2 An epithelium that is part of a finger [Automatically generated definition]. OBOL:automatic fore limb digit epithelium OBOL:accepted hand digit epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a forelimb stylopod [Automatically generated definition]. EHDAA2:0002113 EMAPA:17425 VHOG:0000990 uberon UBERON:0005228 upper arm epithelium EHDAA2 An epithelium that is part of a forelimb stylopod [Automatically generated definition]. OBOL:automatic An epithelium that is part of a lower leg [Automatically generated definition]. EHDAA2:0001031 EMAPA:17497 VHOG:0001050 uberon UBERON:0005229 lower leg epithelium EHDAA2 An epithelium that is part of a lower leg [Automatically generated definition]. OBOL:automatic An ectoderm that is part of a optic eminence [Automatically generated definition]. EHDAA:940 EMAPA:16539 RETIRED_EHDAA2:0001309 VHOG:0001105 uberon UBERON:0005234 optic eminence ectoderm An ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] EHDAA2:0001154 EMAPA:17078 VHOG:0000320 metencephalon basal plate uberon UBERON:0005239 basal plate metencephalon The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] 2012-09-17 VHOG:0000320 VHOG metencephalon basal plate EHDAA2:0001154 An endocardium that is part of a interventricular septum [Automatically generated definition]. TODO - split? EHDAA2:0000886 EHDAA2:0000887 FMA:83584 VHOG:0000615 endocardium of interventricular septum uberon interventricular septum endocardial tissue UBERON:0005243 interventricular septum endocardium An endocardium that is part of a interventricular septum [Automatically generated definition]. OBOL:automatic endocardium of interventricular septum FMA:83584 interventricular septum endocardial tissue VHOG:0000615 A myocardium that is part of a bulbus cordis [Automatically generated definition]. EMAPA:36488 VHOG:0000609 uberon bulbus cordis cardiac muscle UBERON:0005248 bulbus cordis myocardium A myocardium that is part of a bulbus cordis [Automatically generated definition]. OBOL:automatic bulbus cordis cardiac muscle VHOG:0000609 A renal pelvis that is part of a metanephros. The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG] VHOG:0000945 metanephros pelvis uberon UBERON:0005249 metanephric renal pelvis A renal pelvis that is part of a metanephros. OBOL:automatic The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG] 2012-09-17 VHOG:0000945 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 metanephros pelvis VHOG:0000945 A gland that is part of a stomodeum. check this VHOG:0000658 stomatodaeum gland uberon UBERON:0005250 stomatodeum gland A gland that is part of a stomodeum. OBOL:automatic stomatodaeum gland VHOG:0000658 An anatomical cavity that is part of a yolk sac [Automatically generated definition]. In mammals, the yolk sac cavity contains fluid rather than platelets in EHDAA2, there are separate primary and secondary yolk sac cavities EMAPA:16055 FMA:63942 VHOG:0000843 cavity of yolk sac yolk sac lumen uberon yolk sac space UBERON:0005251 yolk sac cavity An anatomical cavity that is part of a yolk sac [Automatically generated definition]. OBOL:automatic In mammals, the yolk sac cavity contains fluid rather than platelets ISBN:0073040584 in EHDAA2, there are separate primary and secondary yolk sac cavities EHDAA2 cavity of yolk sac FMA:63942 yolk sac space FMA:63942 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 EHDAA2:0000732 EHDAA:179 EMAPA:16098 EMAPA_RETIRED:16269 FMA:76622 TAO:0000113 VHOG:0000332 ZFA:0000113 cephalic mesenchyme uberon cranial mesenchyme desmocranium UBERON:0005253 head mesenchyme EHDAA2 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. ISBN:0683400088 MP:0011260 Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000113 TAO ZFIN:curator cephalic mesenchyme MP:0011260 cranial mesenchyme MGI:anna desmocranium FMA:76622 Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition]. EHDAA2:0002132 EMAPA:17501 VHOG:0000506 uberon UBERON:0005254 upper leg mesenchyme Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition]. OBOL:automatic Mesenchyme that is part of a developing toe [Automatically generated definition]. EMAPA:32947 VHOG:0000463 hind limb digit mesenchyme toe mesenchyme foot digit mesenchyme uberon finger ray mesenchyme pedal digital ray mesenchyme UBERON:0005255 pedal digit mesenchyme EHDAA2 Mesenchyme that is part of a developing toe [Automatically generated definition]. OBOL:automatic hind limb digit mesenchyme OBOL:accepted foot digit mesenchyme NCBITaxon:9606 OBOL:accepted finger ray mesenchyme pedal digital ray mesenchyme Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 EHDAA:377 EMAPA:16177 TAO:0000081 VHOG:0000281 ZFA:0000081 uberon trunk and cervical mesenchyme UBERON:0005256 trunk mesenchyme EHDAA2 Mesenchyme that is part of a developing trunk. OBOL:automatic trunk and cervical mesenchyme EHDAA2:0002092 Mesenchyme that is part of a developing finger [Automatically generated definition]. In EHDAA2, the metacarpal cartilage condensation is considered part of the digits - it might be better to call the whole structure digital ray mesenchyme/condensation EHDAA2:0000407 EMAPA:32645 VHOG:0001416 finger mesenchyme fore limb digit mesenchyme hand digit mesenchyme uberon anterior limb digital ray mesenchyme finger ray mesenchyme manual digital ray mesenchyme UBERON:0005257 manual digit mesenchyme Mesenchyme that is part of a developing finger [Automatically generated definition]. OBOL:automatic fore limb digit mesenchyme OBOL:accepted hand digit mesenchyme NCBITaxon:9606 OBOL:accepted anterior limb digital ray mesenchyme finger ray mesenchyme manual digital ray mesenchyme Mesenchyme that is part of a developing forelimb stylopod [Automatically generated definition]. EHDAA2:0002114 EMAPA:17426 VHOG:0000505 uberon UBERON:0005258 upper arm mesenchyme Mesenchyme that is part of a developing forelimb stylopod [Automatically generated definition]. OBOL:automatic Mesenchyme that is part of a developing lower leg [Automatically generated definition]. EHDAA2:0001032 EMAPA:17498 VHOG:0000752 uberon UBERON:0005259 lower leg mesenchyme Mesenchyme that is part of a developing lower leg [Automatically generated definition]. OBOL:automatic An artery that supplies the renal cortex. EMAPA:28147 MA:0002582 kidney cortex artery renal cortex artery uberon renal cortex arterial system UBERON:0005268 renal cortex artery MA An artery that supplies the renal cortex. kidney cortex artery MP:0011314 renal cortex artery MA:0002582 renal cortex arterial system MA:0002582 Artery that receives blood from the renal cortex[MP, modified] EMAPA:28152 MA:0002592 uberon kidney cortex vein renal cortex venous system UBERON:0005269 renal cortex vein MA Artery that receives blood from the renal cortex[MP, modified] MGI:csmith kidney cortex vein MP:0011322 renal cortex venous system MA:0002592 A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP]. TODO - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity' EFO:0003650 EHDAA2:0004362 EV:0100306 FMA:242675 MBA:73 TAO:0001261 ZFA:0001261 CNS ventricular system ventricular system ventricular system of neuraxis uberon ventricle system ventriculi cerebri UBERON:0005281 ventricular system of central nervous system http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png ZFA A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP]. CNS ventricular system EHDAA2:0004362 ventricular system ZFA:0001261 ventricular system of neuraxis FMA:242675 ventricle system ventriculi cerebri The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] CALOHA:TS-1295 EMAPA:37447 FMA:242787 VHOG:0000005 brain ventricular system uberon UBERON:0005282 ventricular system of brain The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000005 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 EMAPA:37447 MA:th brain ventricular system VHOG:0000005 A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm]. Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]. Vascularized tela choroidea is choroid plexus. Note that the structure in ZFA may be different FMA:242849 TAO:0000447 ZFA:0000447 uberon tela chorioidea UBERON:0005283 tela choroidea FMA A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm]. ISBN:0471888893 Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]. ZFA:0000447 Note that the structure in ZFA may be different ZFA tela chorioidea FMA:242849 Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP]. Tela chorioidea that lines the fourth ventricle.[TAO] tela choroidea BAMS:tc4v FMA:78493 TAO:0005158 ZFA:0005158 choroid membrane choroid membrane of fourth ventricle tela chorioidea fourth ventricle tela choroidea fourth ventricle tela choroidea of fourth ventricle tela choroidea ventriculi quarti uberon tela choroidea ventriculi quarti UBERON:0005287 tela choroidea of fourth ventricle Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP]. ZFIN:curator Tela chorioidea that lines the fourth ventricle.[TAO] 2012-08-14 TAO:0005158 TAO ZFIN:curator tela choroidea FMA:78493 FMA:TA choroid membrane FMA:78493 choroid membrane of fourth ventricle FMA:78493 tela choroidea ventriculi quarti FMA:78493 FMA:TA tela choroidea ventriculi quarti Tela chorioidea that lines the telencephalic ventricle. BAMS:tclv FMA:83712 TAO:0005160 ZFA:0005160 tela chorioidea of lateral ventricle tela chorioidea of telencephalic ventricle tela chorioidea telencephalic ventricle tela choroidea (ventriculi lateralis) tela choroidea of lateral ventricle tela choroidea telencephalic ventricle uberon UBERON:0005289 tela choroidea of telencephalic ventricle Tela chorioidea that lines the telencephalic ventricle. ZFIN:curator tela chorioidea telencephalic ventricle ZFA:0005160 tela choroidea (ventriculi lateralis) FMA:83712 FMA:TA tela choroidea of lateral ventricle FMA:83712 The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes BTO:0000758 CALOHA:TS-0607 CALOHA:TS-2365 DHBA:10662 EHDAA2:0001207 EHDAA:5526 EMAPA:17082 HBA:9512 MA:0000205 VHOG:0000456 uberon myelencephalon (medulla oblongata) UBERON:0005290 myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. BTO:0000758 The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] 2012-09-17 VHOG:0000456 VHOG The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000456 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 myelencephalon (medulla oblongata) DHBA:10662 A portion of tissue that is part of an embryo. CALOHA:TS-2100 portion of embryonic tissue uberon developing tissue UBERON:0005291 embryonic tissue A portion of tissue that is part of an embryo. OBOL:automatic portion of embryonic tissue OBOL:automatic Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. BTO:0003360 CALOHA:TS-2119 EFO:0001406 MAT:0000061 MIAA:0000061 extra-embryonic tissue uberon UBERON:0005292 extraembryonic tissue Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. the elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary TODO - check developmental relationships. merge with urogenital ridge? in eutherians, SRY transforms the indifferent gonad into testes AAO:0011047 BTO:0001402 EFO:0001414 EHDAA2:0004044 EMAPA:35899 FMA:321917 NCIT:C34184 NCIT:C34321 UMLS:C0231047 UMLS:C1512243 XAO:0000018 genital ridge gonadal ridge indifferent gonadal ridge uberon crista gonadalis genital cord UBERON:0005294 gonadal ridge http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1106.png the elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary MGI:anna MP:0011411 UMLS:C0231047 ncithesaurus:Urogenital_Ridge UMLS:C1512243 ncithesaurus:Gonadal_Ridge genital ridge MP:0011411 gonadal ridge indifferent gonadal ridge crista gonadalis genital cord MP:0011411 Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female. EHDAA2:0004051 NCIT:C34183 RETIRED_EHDAA2:0001523 UMLS:C1512242 uberon genital cord gonad cord gonadal cord primitive sex cord UBERON:0005295 sex cord EHDAA2 Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female. UMLS:C1512242 ncithesaurus:Gonadal_Cord structures that develop from sex cords in the female. After further development they become the ovarian follicles. TODO check secondary vs cortical vs ovary EHDAA2:0001363 EHDAA:8130 EMAPA:31058 NCIT:C34134 UMLS:C1511527 VHOG:0001339 ovigerous cord ovigerous cords uberon cortical cord cortical sex cord ovary primitive sex cord secondary cord UBERON:0005296 ovary sex cord structures that develop from sex cords in the female. After further development they become the ovarian follicles. UMLS:C1511527 ncithesaurus:Cortical_Cord ovigerous cords VHOG:0001339 The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP]. TODO - check primary vs testis EHDAA2:0002011 EHDAA:8152 EMAPA:29098 VHOG:0001321 testis cord testis primary sex cords uberon primary sex cord testis primitive sex cord UBERON:0005297 testis sex cord Bgee:AN The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP]. testis cord MP:0006424 testis primary sex cords EHDAA2:0002011 A zone of skin that is part of a clitoris [Automatically generated definition]. FMA:20168 clitoris skin uberon UBERON:0005298 skin of clitoris A zone of skin that is part of a clitoris [Automatically generated definition]. OBOL:automatic A retractable double-layered fold of skin and mucous membrane that covers the clitoral glans. FMA has FMA:27886 skin of prepuce of clitoris EMAPA:30699 FMA:20169 NCIT:C32590 UMLS:C0227771 clitoral hood clitoral prepuce clitoris prepuce prepuce of female prepuce of the clitoris preputium clitoridis uberon UBERON:0005299 prepuce of clitoris http://upload.wikimedia.org/wikipedia/commons/b/bd/Clitoris_outer_anatomy.gif A retractable double-layered fold of skin and mucous membrane that covers the clitoral glans. UMLS:C0227771 ncithesaurus:Female_Prepuce clitoral hood prepuce of female EMAPA:30699 preputium clitoridis A pronephric nephron is the functional unit of the pronephros[GO]. The structure that is the basic functional unit of the pronephros.[AAO] AAO:0011091 XAO:0000285 uberon UBERON:0005309 pronephric nephron A pronephric nephron is the functional unit of the pronephros[GO]. GO:0039019 The structure that is the basic functional unit of the pronephros.[AAO] 2012-06-20 AAO:0011091 AAO UBERON:0005309 The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO]. Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO] TAO:0001558 XAO:0004105 ZFA:0001558 pronephric tubule uberon ciliated neck segment UBERON:0005310 pronephric nephron tubule GO The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO]. GO:0039020 ISBN:0073040584 Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO] 2012-08-14 TAO:0001558 TAO ZFIN:curator pronephric tubule ZFA:0001558 ciliated neck segment ZFA:0001558 The endothelial lining of the endocardium. FMA:83596 endocardium endothelium endothelium of endocardium uberon UBERON:0005316 endocardial endothelium The endothelial lining of the endocardium. UBERON:cjm endocardium endothelium FMA:83596 endothelium of endocardium FMA:83596 An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. BTO:0000137 pulmonary artery endothelial tube uberon UBERON:0005317 pulmonary artery endothelium An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. GO:0061155 pulmonary artery endothelial tube GO:0061155 The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO]. AAO:0010390 XAO:0000151 uberon UBERON:0005319 mesonephric collecting duct true The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO]. GO:0061211 . uberon UBERON:0005321 mesonephric smooth muscle tissue . GO:0061214 A nephron that is part of a mesonephros. The structure that is the basic functional unit of the kidney.[AAO] AAO:0010387 XAO:0000292 ZFA:0005592 nephron of mesonephros uberon stage IV nephron UBERON:0005322 mesonephric nephron XAO A nephron that is part of a mesonephros. The structure that is the basic functional unit of the kidney.[AAO] 2012-06-20 AAO:0010387 AAO stage IV nephron ZFA:0005592 Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. AAO:0011062 EHDAA2:0001132 EMAPA:16745 XAO:0000291 uberon UBERON:0005323 mesonephric mesenchyme Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]. GO:0061219 The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO]. uberon UBERON:0005330 mesonephric nephron epithelium true The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO]. GO:0061241 The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. ZFA:0005586 mesonephric vesicle uberon UBERON:0005331 mesonephric renal vesicle ZFA The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]. GO:0061243 A lamina propria that is part of a mucosa of oral region. EMAPA:26947 lamina propria of oral mucosa uberon UBERON:0005334 oral lamina propria A lamina propria that is part of a mucosa of oral region. OBOL:automatic A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. FMA:13225 XAO:0004140 heart ventricle outflow tract outflow part of ventricle ventricular outflow tract uberon UBERON:0005337 outflow tract of ventricle A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. heart ventricle outflow tract MP:0010224 ventricular outflow tract An outflow tract that is part of a aorta. merge with LVOT? EHDAA2:0001353 EMAPA:17329 MA:0000101 VHOG:0001394 uberon UBERON:0005338 outflow tract aortic component An outflow tract that is part of a aorta. OBOL:automatic merge with RVOT? EHDAA2:0001359 EHDAA:4401 EMAPA:17330 MA:0000102 VHOG:0001395 uberon UBERON:0005339 outflow tract pulmonary component The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]. A single stem cell in the ventricular layer can give rise to neurons (and glial cells) in any of the cortical layers (Walsh and Cepko 1988)[NCBIBook:NBK10047] in humans develops into cortical layers II-VI CP CxP BAMS:CTXpl DHBA:10515 EMAPA:32711 MBA:695 PBA:294021914 cerebral cortex cortical plate future cortical layers II-VI neocortex cortical plate uberon future neocortex UBERON:0005343 cortical plate NCBIBook:NBK10047 The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]. MP:0008439 CP BRAINSPAN:BRAINSPAN CxP future cortical layers II-VI future neocortex The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP]. FMA:19937 GAID:395 MESH:D013085 NCIT:C12329 UMLS:C0037855 uberon funiculus spermaticus spermatic chord UBERON:0005352 spermatic cord Male:anatomy.png The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP]. MP:0010145 UMLS:C0037855 ncithesaurus:Spermatic_Cord funiculus spermaticus A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord. EMAPA:35209 FMA:242770 ventricular layer uberon region of wall of ventricular system of neuraxis UBERON:0005358 ventricle of nervous system A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord. ventricular layer EMAPA:35209 region of wall of ventricular system of neuraxis FMA:242770 the group of sensory neuron cell bodies associated with the vagus nerve gX EMAPA:16798 FMA:53472 MA:0001081 TAO:0007067 VHOG:0000684 ZFA:0007067 ganglion of vagus nerve right glossopharyngeal ganglion vagal ganglion vagus ganglion vagus neural ganglion uberon vagus X UBERON:0005362 vagus X ganglion ZFA the group of sensory neuron cell bodies associated with the vagus nerve ISBN:0-683-40008-8 MP:0001100 gX ZFA:0007067 ganglion of vagus nerve FMA:53472 right glossopharyngeal ganglion FMA:53472 vagal ganglion ZFA:0007067 vagus neural ganglion FMA:53472 vagus X EMAPA:16798 An epithelium that lines the nasal cavity. this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism CALOHA:TS-0656 EHDAA2:0001227 EHDAA:6803 EMAPA:17605 FMA:63140 MA:0001324 NCIT:C49261 UMLS:C1709151 VHOG:0000501 nasal epithelium uberon nasal mucosa UBERON:0005384 nasal cavity epithelium An epithelium that lines the nasal cavity. UMLS:C1709151 ncithesaurus:Nasal_Cavity_Epithelium nasal epithelium FMA:63140 nasal mucosa MA:0001324 An array of photoreceptors and any supporting cells found in an eye. FBbt:00004200 light-sensitive tissue uberon UBERON:0005388 photoreceptor array An array of photoreceptors and any supporting cells found in an eye. A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. directing or focusing light onto light receptors lens uberon UBERON:0005389 transparent eye structure A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. One of: the common carotid artery, or its branches, the external and internal carotid arteries. This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] AAO:0010217 BTO:0000168 CALOHA:TS-0116 EFO:0000818 EHDAA:6385 EMAPA:18609 EV:0100379 FMA:70504 GAID:478 MA:0001925 MAT:0000501 MESH:D002339 NCIT:C12687 OpenCyc:Mx4rvg7rcJwpEbGdrcN5Y29ycA TAO:0000097 UMLS:C0007272 VHOG:0000266 ZFA:0000097 galen:CarotidArtery carotid carotid artery subdivision of common carotid artery uberon common carotid arterial subdivision UBERON:0005396 carotid artery segment FMA One of: the common carotid artery, or its branches, the external and internal carotid arteries. Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000097 TAO ZFIN:curator UMLS:C0007272 ncithesaurus:Carotid_Artery carotid AAO:0010217 carotid artery MA:0001925 subdivision of common carotid artery FMA:70504 common carotid arterial subdivision FMA:70504 An arachnoid mater that surrounds a brain. The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] EMAPA:32661 FMA:83981 MA:0000814 NCIT:C49331 VHOG:0000230 arachnoidea mater cranialis arachnoidea mater encephali brain arachnoid matter cranial arachnoid mater uberon UBERON:0005397 brain arachnoid mater An arachnoid mater that surrounds a brain. OBOL:automatic The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000230 VHOG In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] 2012-09-17 VHOG:0000230 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639 arachnoidea mater cranialis FMA:83981 FMA:TA arachnoidea mater encephali FMA:83981 FMA:TA brain arachnoid matter MA:0000814 cranial arachnoid mater FMA:83981 A sex gland that is part of a female reproductive system. BTO:0000254 MA:0000383 uberon UBERON:0005398 female reproductive gland A sex gland that is part of a female reproductive system. OBOL:automatic A sex gland that is part of a male reproductive system. BTO:0000080 EMAPA:19285 MA:0000399 uberon accessory sex gland UBERON:0005399 male reproductive gland A sex gland that is part of a male reproductive system. OBOL:automatic accessory sex gland EMAPA:19285 An arachnoid mater that is part of a telencephalon. EMAPA:17775 MA:0000980 telencephalon arachnoid matter uberon UBERON:0005400 telencephalon arachnoid mater An arachnoid mater that is part of a telencephalon. OBOL:automatic telencephalon arachnoid matter MA:0000980 A gray matter that is part of a cerebral hemisphere. BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon BTO:0000823 CALOHA:TS-2361 EMAPA:37477 FMA:61821 MA:0000944 cerebral gray matter cerebral grey matter cerebral hemisphere grey matter uberon UBERON:0005401 cerebral hemisphere gray matter A gray matter that is part of a cerebral hemisphere. OBOL:automatic BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon BTO EMAPA:37477 MA:th cerebral gray matter BTO:0000823 cerebral grey matter MA:0000944 Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow. All vertebrates possess at least 4 circumventricular organs (including the hypothalamus) which can monitor the contents of the cerebrospinal fluid and secrete additional substances into it. (Butler, 1996, p. 330) CVOs contain neural tissue and are an integral part of neuroendocrine function; all of the CVOs, besides the subcommissural organ, contain extensive vasculature and fenestrated capillaries which leads to a leaky BBB at the site of the organs; the lack of a BBB allows CVOs to act as an alternative route for peptides and hormones in the neural tissue to the peripheral blood stream, while still protecting it from toxic substances EMAPA:35243 FMA:84081 MA:0002942 NLXANAT:20090312 CVO circumventricular organ circumventricular organ of neuraxis uberon UBERON:0005408 circumventricular organ http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow. MP:0013562 CVO NLXANAT:20090312 circumventricular organ NLXANAT:20090312 circumventricular organ of neuraxis FMA:84081 The part of the digestive system that excludes the hepatobiliary system. the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. BTO:0000058 CALOHA:TS-0407 EHDAA2:0000110 EHDAA:514 EMAPA:16246 EV:0100056 FMA:71132 GAID:294 MA:0000323 MESH:A03.492 NCIT:C12378 UMLS:C0012240 VHOG:0000412 galen:GastrointestinalTract uberon GI tract alimentary system alimentary tract gastro-intestinal system gastroenterological system gastrointestinal (GI) tract gastrointestinal system gastrointestinal tract UBERON:0005409 alimentary part of gastrointestinal system The part of the digestive system that excludes the hepatobiliary system. The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. ncithesaurus:Gastrointestinal_System All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] 2012-09-17 VHOG:0000412 VHOG ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3 that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. MA UMLS:C0012240 ncithesaurus:Gastrointestinal_System GI tract GAID:294 alimentary system MA:0000323 alimentary tract MA:0000323 gastro-intestinal system FMA:71132 gastroenterological system UBERON:cjm gastrointestinal (GI) tract GAID:294 gastrointestinal system FMA:71132 gastrointestinal tract FMA:71132 A limb bud that develops into a forelimb. AAO:0010381 BTO:0001645 EHDAA:1699 EMAPA:16406 FMA:296782 MIAA:0000065 RETIRED_EHDAA2:0003198 XAO:0003065 anterior limb bud limb bud - forelimb upper limb bud wing bud uberon arm bud UBERON:0005417 Genes: Tbx5 specifies forelimbs. Wnt2b restricts Fgf10 in chick // In tetrapods, the position of the forelimb is associated with the anterior expression border of Hoxc6 in the paraxial mesoderm (Burke et al., 1995) forelimb bud lexical A limb bud that develops into a forelimb. limb bud - forelimb MIAA:0000065 upper limb bud RETIRED_EHDAA2:0003198 wing bud NCBITaxon:8782 OBOL:automatic A limb bud that develops into a hindlimb. The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO] AAO:0010382 EHDAA:2358 EMAPA:16779 MIAA:0000256 RETIRED_EHDAA2:0003197 XAO:0003066 hind limb bud posterior limb bud uberon leg bud limb bud - hindlimb UBERON:0005418 Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick. hindlimb bud lexical A limb bud that develops into a hindlimb. The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO] 2012-06-20 AAO:0010382 AAO XAO:curator hind limb bud XAO:0003066 A limb bud that develops into a forelimb or pectoral fin. Fin bud that develops into the pectoral fin.[TAO] While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] EFO:0003430 TAO:0000141 VHOG:0001754 VHOG_RETIRED:0001259 ZFA:0000141 forelimb - pectoral fin bud uberon pectoral fin bud pectoral fin buds UBERON:0005419 at this time we have no need to name a more specific 'pectoral fin bud' class, but we may in future pectoral appendage bud A limb bud that develops into a forelimb or pectoral fin. OBOL:automatic Fin bud that develops into the pectoral fin.[TAO] 2012-08-14 TAO:0000141 TAO ZFIN:curator While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG] 2012-09-17 VHOG:0001754 VHOG DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004) forelimb - pectoral fin bud VHOG:0001754 pectoral fin bud TAO:0000141 pectoral fin buds TAO:0000141 A limb bud that develops into a hindlimb or pelvic fin. Fin bud that develops into the pelvic fin.[TAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] EFO:0003469 TAO:0001384 VHOG:0001260 ZFA:0001384 hindlimb/pelvic fin bud uberon pelvic fin bud pelvic fin buds UBERON:0005420 at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future pelvic appendage bud A limb bud that develops into a hindlimb or pelvic fin. OBOL:automatic Fin bud that develops into the pelvic fin.[TAO] 2012-08-14 TAO:0001384 TAO ZFIN:curator Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001260 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 hindlimb/pelvic fin bud VHOG:0001260 pelvic fin bud TAO:0001384 pelvic fin buds ZFA:0001384 An apical ectodermal ridge that is part of a pectoral appendage bud. An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] EFO:0003487 EHDAA2:0000138 EMAPA:16778 TAO:0000085 TAO:0000736 VHOG:0001064 ZFA:0000085 AER forelimb apical ectodermal ridge forelimb apical ectodermal ridge pectoral fin bud upper limb bud apical ectodermal ridge wing AER wing apical ectodermal ridge uberon aer pectoral fin apical ectodermal ridge pectoral fin apical fold pectoral fin UBERON:0005421 pectoral appendage apical ectodermal ridge EHDAA2 An apical ectodermal ridge that is part of a pectoral appendage bud. OBOL:automatic An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG] 2012-09-17 VHOG:0001064 VHOG Apical ectodermal ridge that is part of the pectoral fin bud.[TAO] 2012-08-14 TAO:0000085 TAO ZFIN:curator Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] 2012-09-17 VHOG:0001064 VHOG AER forelimb VHOG:0001064 apical ectodermal ridge forelimb VHOG:0001064 apical ectodermal ridge pectoral fin bud ZFA:0000085 upper limb bud apical ectodermal ridge EHDAA2:0000138 wing AER Giesha:syn wing apical ectodermal ridge aer pectoral fin TAO:0000085 apical ectodermal ridge pectoral fin TAO:0000085 apical fold pectoral fin TAO:0000085 An apical ectodermal ridge that is part of a pelvic appendage bud. An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] EFO:0003681 EHDAA2:0003194 EMAPA:16892 TAO:0001385 VHOG:0001066 ZFA:0001385 apical ectodermal ridge hind limb apical ectodermal ridge hindlimb lower lmb bud apical ectodermal ridge uberon AER hindlimb apical ectodermal ridge pelvic fin bud leg AER UBERON:0005422 pelvic appendage apical ectodermal ridge EHDAA2 An apical ectodermal ridge that is part of a pelvic appendage bud. OBOL:automatic An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] 2012-09-17 VHOG:0001066 VHOG Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] 2012-08-14 TAO:0001385 TAO ZIFIN:curator Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] 2012-09-17 VHOG:0001066 VHOG apical ectodermal ridge hind limb VHOG:0001066 apical ectodermal ridge hindlimb VHOG:0001066 lower lmb bud apical ectodermal ridge EHDAA2:0003194 AER hindlimb VHOG:0001066 apical ectodermal ridge pelvic fin bud TAO:0001385 AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 uberon developing structure developmental structure developmental tissue UBERON:0005423 developing anatomical structure developmental tissue MIAA:0000019 Portion of tissue that is the inner layer of the optic cup and will become the neural retina. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001304 EMAPA:16675 TAO:0001071 VHOG:0000490 ZFA:0001071 future neural retina future retinal neural layer inner layer optic cup optic cup inner layer presumptive retinas uberon future NR future neural epithelium future neural layer presumptive retina UBERON:0005425 presumptive neural retina Portion of tissue that is the inner layer of the optic cup and will become the neural retina. ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000490 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 inner layer optic cup ZFA:0001071 optic cup inner layer EHDAA2:0001304 presumptive retinas ZFA:0001071 future neural epithelium EMAPA:16675 future neural layer EMAPA:16675 presumptive retina TAO:0001071 Portion of tissue that gives rise to the lens. A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals EHDAA2:0000983 EHDAA:4737 EMAPA:17163 TAO:0002205 VHOG:0001163 ZFA:0001679 hollow lens vesicle solid lens vesicle uberon immature lens lens mass presumptive lens UBERON:0005426 lens vesicle Portion of tissue that gives rise to the lens. ZFIN:curator A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] 2012-09-17 VHOG:0001163 VHOG (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0001163 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals ZFA hollow lens vesicle solid lens vesicle ZFA:0001679 immature lens ZFA:0001679 lens mass ZFA:0001679 ZFIN:ZDB-PUB-091023-49 presumptive lens ZFA:0001679 Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 uberon UBERON:0005427 corneal primordium ZFA Obol ZFA Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. ZFIN:ZDB-PUB-061010-3 Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) EHDAA2:0002156 EHDAA:669 TAO:0000818 VHOG:0001208 XAO:0004191 ZFA:0000818 VNC uberon enteric neural crest post-otic neural crest UBERON:0005428 vagal neural crest Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. ZFIN:curator Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] 2012-08-14 TAO:0000818 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001208 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) filemaps.com VNC XAO:0004191 post-otic neural crest ZFA:0000818 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. EHDAA2:0004145 EHDAA:9826 EMAPA:36461 FMA:71008 RETIRED_EHDAA2:0000133 saccus aorticus uberon UBERON:0005432 aortic sac EHDAA2 EHDAA2 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates MP:0012510 the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. saccus aorticus FMA:24219 cervical region neck subdivision region of neck subdivision of neck uberon UBERON:0005434 cervical region cervical region FMA:24219 neck subdivision FMA:24219 region of neck FMA:24219 subdivision of neck FMA:24219 the short trunk that recieves most of the cardiac veins carrying the blood from the myocardium and delivers it to the right atrium, with the sinoatrial connection occurring between the inferior vena cava and the atrioventricular orifice The sinus, before entering the auricle, is considerably dilated - nearly to the size of the end of the little finger. Its wall is partly muscular, and at its junction with the great coronary vein is somewhat constricted and furnished with a valve consisting of two unequal segments EHDAA2:0000320 EHDAA:9884 EMAPA:37836 FMA:4706 NCIT:C32378 UMLS:C0456944 sinus coronarius uberon sinus coronarius UBERON:0005438 coronary sinus http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray491.png the short trunk that recieves most of the cardiac veins carrying the blood from the myocardium and delivers it to the right atrium, with the sinoatrial connection occurring between the inferior vena cava and the atrioventricular orifice ISBN:0-683-40008-8 MP:0010436 The sinus, before entering the auricle, is considerably dilated - nearly to the size of the end of the little finger. Its wall is partly muscular, and at its junction with the great coronary vein is somewhat constricted and furnished with a valve consisting of two unequal segments WP EMAPA:37836 MA:th UMLS:C0456944 ncithesaurus:Coronary_Sinus sinus coronarius A segment of autopod that is part of a pes. foot region FMA:24993 foot subdivision regio pedis segment of foot subdivision of foot uberon UBERON:0005445 segment of pes A segment of autopod that is part of a pes. OBOL:automatic foot region FMA:24993 foot subdivision FMA:24993 regio pedis FMA:24993 FMA:TA segment of foot FMA:24993 subdivision of foot FMA:24993 A segment of autopod that is part of a manus. hand region FMA:24945 hand subdivision regio manus segment of hand subdivision of hand uberon UBERON:0005451 segment of manus A segment of autopod that is part of a manus. OBOL:automatic hand region FMA:24945 hand subdivision FMA:24945 regio manus segment of hand FMA:24945 subdivision of hand FMA:24945 The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] AAO:0000249 EHDAA2:0000893 EHDAA:10631 EMAPA:18713 FMA:56432 NCIT:C12496 UMLS:C0222712 VHOG:0001113 Posterior lacerate foramen uberon foramen jugulare UBERON:0005456 jugular foramen http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] 2012-06-20 AAO:0000249 AAO AAO:LAP One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] 2012-09-17 VHOG:0001113 VHOG relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] 2012-06-20 AAO:0000249 AAO UMLS:C0222712 ncithesaurus:Jugular_Foramen Posterior lacerate foramen FMA:56432 foramen jugulare A thymus lobe that is in the left side of a thymus. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:71195 RETIRED_EHDAA2:0000964 left lobe of thymus left thymic lobe uberon UBERON:0005457 left thymus lobe A thymus lobe that is in the left side of a thymus. OBOL:automatic left lobe of thymus FMA:71195 left thymic lobe FMA:71195 A vitelline vein that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000971 EMAPA:16380 EMAPA:16698 FMA:70307 uberon UBERON:0005460 left vitelline vein A vitelline vein that is in the left side of a multicellular organism. OBOL:automatic An axial muscle that originates in the cervical vertebraae inserts on the scapula. AAO:0010689 EHDAA2:0000992 EHDAA:8309 FMA:32519 levator scapulae uberon levator scapula levator scapulae muscle levator scapulæ musculus levator scapulae UBERON:0005461 Axial muscle group[Kardong] levator scapulae muscle Levator:scapulae.png EHDAA2 cervical nerve and dorsal scapular nerve dbpedia EHDAA2 Posterior tubercles of transverse processes of C1 - C4 vertebrae dbpedia Superior part of medial border of scapula dbpedia An axial muscle that originates in the cervical vertebraae inserts on the scapula. levator scapulae FMA:32519 levator scapula levator scapulae muscle levator scapulæ musculus levator scapulae Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA]. lumbar lumbar region BTO:0001505 EMAPA:36623 FMA:61681 MA:0000027 NCIT:C34004 UMLS:C0024090 abdominal back back of abdomen dorsum of abdomen lower back lumbar part of back lumbar region of back posterior part of abdomen regio lumbalis uberon loin lombus lumbos UBERON:0005462 overlaps with region sometimes called 'loin' lower back MA Subdivision of abdominal segment of trunk which in humans is demarcated from the front of the abdomen by the posterior surface of the anterior layer of the thoracolumbar fascia and the anterior surface of the lumbar vertebral column; together with the front of the abdomen, it constitutes the abdomen[Modified from FMA]. FMA:61681 lumbar region FMA:61681 UMLS:C0024090 ncithesaurus:Lumbar_Region abdominal back FMA:61681 back of abdomen FMA:61681 dorsum of abdomen FMA:61681 lower back MA:0000027 lumbar part of back FMA:61681 lumbar region of back posterior part of abdomen FMA:61681 regio lumbalis FMA:61681 FMA:TA loin BTO:0001505 A space between the capsule and the cortex which allows the free movement of lymphatic fluid and so contains a sparsity of lymphocytes. It is continuous with the similar lymph sinuses that flank the trabeculae. marginal sinus EMAPA:37662 FMA:312355 MA:0003027 NCIT:C33033 NCIT:C33642 UMLS:C1518051 UMLS:C1518052 lymph node subcortical sinus uberon lymph path lymph sinus marginal sinus of lymph node subcapsular sinus UBERON:0005463 subcapsular sinus of lymph node http://upload.wikimedia.org/wikipedia/commons/6/68/Gray597.png A space between the capsule and the cortex which allows the free movement of lymphatic fluid and so contains a sparsity of lymphocytes. It is continuous with the similar lymph sinuses that flank the trabeculae. marginal sinus EMAPA:37662 MA:th UMLS:C1518051 ncithesaurus:Lymph_Node_Sinus UMLS:C1518052 ncithesaurus:Lymph_Node_Subcapsular_Sinus lymph node subcortical sinus MA:0003027 lymph path lymph sinus marginal sinus of lymph node subcapsular sinus A thymus lobe that is in the right side of a thymus. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:71194 RETIRED_EHDAA2:0001758 right lobe of thymus right thymic lobe uberon UBERON:0005469 right thymus lobe A thymus lobe that is in the right side of a thymus. OBOL:automatic right lobe of thymus FMA:71194 right thymic lobe FMA:71194 A vitelline vein that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001766 EMAPA:16381 EMAPA:16699 FMA:70306 uberon UBERON:0005472 right vitelline vein A vitelline vein that is in the right side of a multicellular organism. OBOL:automatic trunk part of spinal nerve, where dorsal and ventral roots meet to form the spinal nerve, before branching off to dorsal and ventral rami. EHDAA2:0001900 FMA:5929 spinal nerve (trunk) spinal neural trunk trunk of spinal nerve uberon UBERON:0005476 spinal nerve trunk trunk part of spinal nerve, where dorsal and ventral roots meet to form the spinal nerve, before branching off to dorsal and ventral rami. spinal nerve (trunk) FMA:5929 spinal neural trunk FMA:5929 trunk of spinal nerve FMA:5929 A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. sulcus limitans BAMS:slim BAMS:slm neural tube lateral wall sulcus limitans uberon UBERON:0005478 sulcus limitans of neural tube EHDAA2 A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. neural tube lateral wall sulcus limitans EHDAA2:0001265 Either of the two lateral lobes that constitute the thymus. each lobe of the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. Each lobe is composed of numerous lobules held together by delicate areolar tissue; the entire organ being enclosed in an investing capsule of a similar but denser structure. The primary lobules vary in size from that of a pin's head to that of a small pea, and are made up of a number of small nodules or follicles.[WP] FMA:71193 RETIRED_EHDAA2:0002021 lateral lobe of thymus lobe of thymus uberon UBERON:0005483 thymus lobe FMA-abduced-lr Either of the two lateral lobes that constitute the thymus. lateral lobe of thymus lobe of thymus FMA:71193 the paired veins that carry blood from the yolk sac back to the embryo One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO] Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG] check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO EMAPA:36021 FMA:70305 NCIT:C34329 RETIRED_EHDAA2:0002209 UMLS:C0231091 VHOG:0000401 XAO:0000376 XAO:0004147 embryonic vitelline vein vascular vitelline network vena vitellina uberon omphalomesenteric vein vein of omphalomesenteric system vitelline veins UBERON:0005487 vitelline vein http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png the paired veins that carry blood from the yolk sac back to the embryo MGI:csmith MP:0010666 One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO] XAO XAO:0004147 Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG] 2012-09-17 VHOG:0000401 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO XAO UMLS:C0231091 ncithesaurus:Vitelline_Vein embryonic vitelline vein VHOG:0000401 vascular vitelline network XAO:0004147 vena vitellina omphalomesenteric vein EMAPA:16244 vitelline veins XAO:0004147 Cranial neural crest which gives rise to the glossopharyngeal ganglion. EHDAA2:0000714 EHDAA:660 TAO:0007066 ZFA:0007066 uberon UBERON:0005491 glossopharyngeal neural crest Cranial neural crest which gives rise to the glossopharyngeal ganglion. ZFA:0007066 Portion of tissue on the side of the lumen of the neural tube. EHDAA2:0001257 EHDAA:2873 EHDAA:912 EMAPA:16166 TAO:0001435 VHOG:0000513 ZFA:0001435 lateral wall neural tube uberon UBERON:0005496 neural tube lateral wall Portion of tissue on the side of the lumen of the neural tube. ZFA:0001435 lateral wall neural tube ZFA:0001435 todo - epidermis? todo - track down EHDAA2 class in new release In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm. EFO:0003643 EHDAA:257 EMAPA:16074 RETIRED_EHDAA2:0001273 TAO:0001178 VHOG:0001372 XAO:0004091 ZFA:0001178 non neural ectoderm epidermal ectoderm epithelial ectoderm uberon surface ectoderm ventral ectoderm UBERON:0005497 Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). non-neural ectoderm ZFA In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] 2012-09-17 VHOG:0001372 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) non neural ectoderm ZFA:0001178 epidermal ectoderm epithelial ectoderm surface ectoderm ventral ectoderm ZFA:0001178 Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 EHDAA:436 EMAPA:16215 FMA:321916 TAO:0000149 ZFA:0000149 primitive heart tube early primitive heart tube uberon UBERON:0005498 primitive heart tube ZFA Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 primitive heart tube EMAPA:16215 early primitive heart tube EMAPA:16208 A neural tube lateral wall that is part of a rhombomere. EMAPA:32819 EMAPA:35364 uberon future hindbrain lateral wall UBERON:0005501 rhombomere lateral wall A neural tube lateral wall that is part of a rhombomere. OBOL:automatic future hindbrain lateral wall EMAPA:35364 A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]. we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO] variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals EFO:0003622 EHDAA2:0002023 EHDAA:2969 EMAPA:17523 TAO:0001077 ZFA:0001077 thymic primordium thymic rudiment uberon UBERON:0005562 thymus primordium ZFA EHDAA2 mesenchymal ZFA A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]. ZFA:0001077 we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution. ISBN:0781714125 A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO] 2012-08-14 TAO:0001077 TAO ZFIN:curator variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals ISBN:0781714125 thymic primordium OBOL:automatic thymic rudiment ZFA:0001077 Cranial neural crest which gives rise to the trigeminal ganglion. todo - compare ZFA and EHDAA2 representation We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003484 EHDAA2:0002083 EHDAA:667 EMAPA:16170 TAO:0000080 VHOG:0000269 ZFA:0000080 uberon UBERON:0005563 trigeminal neural crest ZFA EHDAA2 Cranial neural crest which gives rise to the trigeminal ganglion. ZFA:0000080 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000269 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 Portion of tissue that gives rise to the immature gonad. Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] this is a very broad grouping class EFO:0003651 EHDAA:5927 EMAPA:17204 RETIRED_EHDAA2:0002148 TAO:0001262 WBbt:0008366 ZFA:0001262 future gonad gonadal primordium primitive gonad undifferentiated gonad uberon immature gonad UBERON:0005564 gonad primordium Obol ZFA Portion of tissue that gives rise to the immature gonad. ZFA:0001262 Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] 2012-08-14 TAO:0001262 TAO ZFIN:curator future gonad gonadal primordium ZFA:0001262 primitive gonad undifferentiated gonad ZFA:0001262 immature gonad Cranial neural crest that gives rise to the facio-acoustic ganglion. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0000492 EHDAA:658 EMAPA:16312 TAO:0000762 VHOG:0000268 ZFA:0000762 facio acoustic neural crest uberon UBERON:0005565 facio-acoustic neural crest EHDAA2 EHDAA2 Cranial neural crest that gives rise to the facio-acoustic ganglion. ZFA:0000762 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000268 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 facio acoustic neural crest ZFA:0000762 Somite located in the head region, caudal to the otic vesicle in humans this includes somites 1-4 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2:0003437 EMAPA:16172 XAO:0000313 occipital somite uberon cranial somite UBERON:0005594 head somite EHDAA2 EHDAA2 Somite located in the head region, caudal to the otic vesicle They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2 occipital somite XAO:0000313 cranial somite XAO:0000313 A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. UBERON:3010717 AAO:0011059 EFO:0002578 EMAPA:36007 XAO:0001002 uberon lateral diverticula lung diverticulum lung endoderm UBERON:0005597 lung primordium XAO XAO A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. XAO:0001002 lateral diverticula XAO:0001002 lung diverticulum AAO:3010717 lung endoderm EFO:0002578 A somite that is part of a trunk. AAO:0010385 EHDAA2:0003438 EMAPA:16184 XAO:0000314 uberon UBERON:0005598 trunk somite A somite that is part of a trunk. OBOL:automatic The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum. The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG] EHDAA2:0000416 EHDAA:3001 EMAPA:17025 MA:0001618 NCIT:C34142 UMLS:C1512038 VHOG:0000352 uberon dorsal mesentery UBERON:0005602 dorsal mesogastrium MA EHDAA2 The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum. The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG] 2012-09-17 VHOG:0000352 VHOG UMLS:C1512038 ncithesaurus:Dorsal_Mesogastrium dorsal mesentery EMAPA:16844 MA:0001636 VHOG:0000215 extrahepatic part of the hepatic duct hepatic duct extrahepatic part uberon UBERON:0005604 extrahepatic part of hepatic duct MA MA extrahepatic part of the hepatic duct VHOG:0000215 hepatic duct extrahepatic part MA:0001636 A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa] EHDAA2:0000789 EHDAA:4733 EMAPA:17302 FMA:312291 MA:0000272 VHOG:0001477 uberon UBERON:0005606 hyaloid cavity A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa] 2012-09-17 VHOG:0001477 VHOG Any of the arteries that arise from a bifurcation of the aorta supplying the pelvic or abdomen. Examples: Common iliac artery, External iliac artery, Internal iliac artery this is an extremely loose and flexible grouping class that is the superclass of the mammalian common iliac and its main brahces, together with analagous structures in other tetrapods we place the XAO structure here for now. In terms of analagy, it is more closely related to common iliac, but the relationships currently attached to this class are mammal specific BTO:0004665 EHDAA:2551 EMAPA:17309 MA:0001971 MESH:D007083 NCIT:C12733 RETIRED_EHDAA2:0000807 UMLS:C0020887 XAO:0000361 galen:IliacArtery uberon UBERON:0005609 iliac artery Any of the arteries that arise from a bifurcation of the aorta supplying the pelvic or abdomen. Examples: Common iliac artery, External iliac artery, Internal iliac artery we place the XAO structure here for now. In terms of analagy, it is more closely related to common iliac, but the relationships currently attached to this class are mammal specific XAO UMLS:C0020887 ncithesaurus:Iliac_Artery Any of the three veins including the common, external and internal iliac veins. EHDAA2:0000811 EMAPA:37151 MA:0002142 MESH:D007084 NCIT:C12734 UMLS:C0020888 uberon pelvic vein UBERON:0005610 iliac vein Any of the three veins including the common, external and internal iliac veins. ncithesaurus:Iliac_Vein EMAPA:37151 MA:th UMLS:C0020888 ncithesaurus:Iliac_Vein A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Contributes to the arch of aorta in humans EHDAA2:0000936 EHDAA:404 EMAPA:16205 MA:0000478 VHOG:0000484 uberon UBERON:0005613 left dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000484 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 Contributes to the arch of aorta in humans A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm lens epithelium EHDAA2:0000984 EHDAA:9059 EMAPA:17304 EMAPA:17839 FMA:70612 MA:0001302 NCIT:C33641 RETIRED_EHDAA2:0000976 UMLS:C1182652 VHOG:0001425 lens subcapsular epithelium subcapsular lens epithelium uberon anterior epithelium of lens vesicle anterior surface of lens UBERON:0005614 lens anterior epithelium A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. UMLS:C1182652 ncithesaurus:Subcapsular_Epithelium_of_the_Lens lens subcapsular epithelium subcapsular lens epithelium FMA:70612 anterior epithelium of lens vesicle EMAPA:17304 anterior surface of lens FMA:58889 Arteries which arise from the abdominal aorta and distribute to most of the intestines. includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries BTO:0000779 EHDAA2:0001123 EHDAA:4343 EMAPA:17312 MA:0002003 MESH:D008638 NCIT:C52975 UMLS:C0025465 VHOG:0001117 XAO:0000370 uberon UBERON:0005616 mesenteric artery Arteries which arise from the abdominal aorta and distribute to most of the intestines. MESH:A07.231.114.565 UMLS:C0025465 ncithesaurus:Mesenteric_Artery A vein that returns blood from the intestines. In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein BTO:0002781 EHDAA:4442 EMAPA:17348 MA:0002177 MESH:D008642 NCIT:C53055 RETIRED_EHDAA2:0001125 UMLS:C0025473 uberon intestinal vein UBERON:0005617 mesenteric vein A vein that returns blood from the intestines. MESH:A07.231.908.670.385 UMLS:C0025473 ncithesaurus:Mesenteric_Vein intestinal vein A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Normally regresses in humans EHDAA2:0001720 EHDAA:406 EMAPA:16206 MA:0000479 VHOG:0000485 uberon UBERON:0005622 right dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000485 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 Normally regresses in humans Artery that supplies blood to the adrenal glands. EHDAA2:0001965 EHDAA:8596 EMAPA:37124 MA:0001914 NCIT:C33708 ncithesaurus:Adrenal_Artery uberon adrenal artery UBERON:0005624 suprarenal artery Artery that supplies blood to the adrenal glands. EMAPA:37124 MA:th adrenal artery MA:0001914 The cavity formed by the tubotympanic recess epithelium. EHDAA2:0002095 FMA:312393 cavity of tubotympanic recess tubotympanic recess cavity tubotympanic recess space uberon tubotympanic recess UBERON:0005625 tubotympanic recess lumen ISBN:0073040584 The cavity formed by the tubotympanic recess epithelium. tubotympanic recess EHDAA2:0002095 Portion of ventral mesentery closest to the stomach. The mesentery that originates from the ventral side of the peritoneal cavity.[TAO] The ventral sheet of the primitive mesentery that encloses the stomach. The lesser omentum develops from the ventral mesogastrium. [TFD][VHOG] EHDAA2:0002176 EHDAA:3005 EMAPA:17026 MA:0001621 NCIT:C34327 TAO:0005133 UMLS:C1519967 VHOG:0000351 ZFA:0005133 uberon foregut ventral mesentery UBERON:0005626 "The primitive gut is enveloped by a mesentery that has a dorsal and a ventral aspect. The ventral mesentery degenerates during development with the exception of the foregut ventral mesentery, which develops into specialized structures (see foregut embryology)" [http://sprojects.mmi.mcgill.ca/embryology/gi/pgm.htm]. todo - check ventral mesogastrium http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray984.png EHDAA2 Portion of ventral mesentery closest to the stomach. The mesentery that originates from the ventral side of the peritoneal cavity.[TAO] 2012-08-14 TAO:0005133 TAO ZFIN:curator The ventral sheet of the primitive mesentery that encloses the stomach. The lesser omentum develops from the ventral mesogastrium. [TFD][VHOG] 2012-09-17 VHOG:0000351 VHOG UMLS:C1519967 ncithesaurus:Ventral_Mesogastrium foregut ventral mesentery A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part. In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]. AEO:0000219 EHDAA2:0004112 EMAPA:35904 FMA:5900 XAO:0004143 plexus vasculosus uberon UBERON:0005629 vascular plexus A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part. In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]. plexus vasculosus Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)] EHDAA2 is a mereological sum. EHDAA2:0004714 FMA:305915 uberon UBERON:0005631 extraembryonic membrane https://github.com/obophenotype/uberon/wiki/Modeling-extraembryonic-membranes Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. ISBN:0073040584 EHDAA2 is a mereological sum. EHDAA2 An epithelium that is part of a caecum. EHDAA2:0000209 uberon UBERON:0005636 caecum epithelium An epithelium that is part of a caecum. OBOL:automatic An epithelium that is part of a pylorus. EHDAA2:0001582 EMAPA:17633 RETIRED_EHDAA2:0001927 uberon UBERON:0005637 pyloric region epithelium An epithelium that is part of a pylorus. OBOL:automatic An epithelium that is part of a anterior chamber of eyeball. EHDAA2:0000130 uberon UBERON:0005638 anterior chamber epithelium An epithelium that is part of a anterior chamber of eyeball. OBOL:automatic An epithelium that is part of a manual digit 5. EHDAA2:0000536 EMAPA:17442 fore limb digit 5 epithelium manual digit V epithelium hand digit 5 epithelium uberon UBERON:0005648 manual digit 5 epithelium An epithelium that is part of a manual digit 5. OBOL:automatic fore limb digit 5 epithelium OBOL:accepted manual digit V epithelium hand digit 5 epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a pedal digit 5. EHDAA2:0002058 EMAPA:17473 hind limb digit 5 epithelium pedal digit V epithelium foot digit 5 epithelium uberon UBERON:0005652 pedal digit 5 epithelium An epithelium that is part of a pedal digit 5. OBOL:automatic hind limb digit 5 epithelium OBOL:accepted pedal digit V epithelium foot digit 5 epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a lens vesicle. EHDAA2:0000987 EMAPA:17165 VHOG:0000532 uberon UBERON:0005656 lens vesicle epithelium An epithelium that is part of a lens vesicle. OBOL:automatic An ectoderm that is part of a pharyngeal arch 2. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000055 EMAPA:16277 EMAPA:16397 EMAPA:16398 RETIRED_EHDAA2:0000064 VHOG:0001062 2nd pharyngeal arch ectoderm uberon UBERON:0005660 2nd arch ectoderm An ectoderm that is part of a pharyngeal arch 2. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001062 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 2nd pharyngeal arch ectoderm VHOG:0001062 An ectoderm that is part of a pharyngeal arch 3. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000072 EMAPA:16400 EMAPA:16582 EMAPA:16584 RETIRED_EHDAA2:0000079 VHOG:0000946 3rd pharyngeal arch ectoderm uberon UBERON:0005661 3rd arch ectoderm An ectoderm that is part of a pharyngeal arch 3. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000946 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 3rd pharyngeal arch ectoderm VHOG:0000946 An ectoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004032 EMAPA:16762 EMAPA:16764 EMAPA:16768 RETIRED_EHDAA2:0000094 VHOG:0001095 4th pharyngeal arch ectoderm uberon UBERON:0005662 4th arch ectoderm An ectoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001095 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 4th pharyngeal arch ectoderm VHOG:0001095 An endoderm that is part of a pharyngeal arch 2. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000061 EMAPA:16274 EMAPA:16276 EMAPA:16278 RETIRED_EHDAA2:0000065 VHOG:0001108 2nd pharyngeal arch endoderm uberon UBERON:0005664 2nd arch endoderm An endoderm that is part of a pharyngeal arch 2. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001108 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 2nd pharyngeal arch endoderm VHOG:0001108 An endoderm that is part of a pharyngeal arch 3. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000075 EMAPA:16401 EMAPA:16585 EMAPA:16587 RETIRED_EHDAA2:0000080 VHOG:0001081 3rd pharyngeal arch endoderm uberon UBERON:0005665 3rd arch endoderm An endoderm that is part of a pharyngeal arch 3. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001081 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 3rd pharyngeal arch endoderm VHOG:0001081 An endoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004033 EMAPA:16765 EMAPA:16767 EMAPA:16769 RETIRED_EHDAA2:0000095 VHOG:0001092 4th pharyngeal arch endoderm uberon UBERON:0005666 4th arch endoderm An endoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001092 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 4th pharyngeal arch endoderm VHOG:0001092 EHDAA2:0000314 uberon UBERON:0005667 connecting stalk mesoderm EHDAA2 EHDAA2 A mesothelium that is part of a peritoneal cavity. we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood peritoneum BTO:0003156 EHDAA2:0001447 EMAPA:16139 FMA:18147 mesothelium of peritoneal component mesothelium of peritoneum peritoneal mesothelium peritoneum mesothelium uberon UBERON:0005669 peritoneal cavity mesothelium A mesothelium that is part of a peritoneal cavity. OBOL:automatic we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood EMAPA peritoneum EMAPA:16139 mesothelium of peritoneal component EMAPA:16139 mesothelium of peritoneum FMA:18147 peritoneal mesothelium BTO:0003156 peritoneal mesothelium EMAPA:16139 peritoneum mesothelium FMA:18147 An endothelium that is part of a right lung. EHDAA2:0001755 uberon UBERON:0005672 right lung endothelium An endothelium that is part of a right lung. OBOL:automatic An endothelium that is part of a left lung. EHDAA2:0000961 uberon UBERON:0005673 left lung endothelium An endothelium that is part of a left lung. OBOL:automatic A mesentery that is part of a caecum. RETIRED_EHDAA2:0000210 uberon UBERON:0005677 caecum mesentery A mesentery that is part of a caecum. OBOL:automatic A dorsal mesentery that is part of a midgut. EMAPA:16722 EMAPA:17040 EMAPA:18671 RETIRED_EHDAA2:0001187 uberon UBERON:0005685 midgut dorsal mesentery A dorsal mesentery that is part of a midgut. OBOL:automatic A dorsal mesentery that is part of a caecum. RETIRED_EHDAA2:0000208 uberon UBERON:0005686 caecum dorsal mesentery A dorsal mesentery that is part of a caecum. OBOL:automatic An anatomical cavity that is part of a lens vesicle. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] cavity of lens lens cavity EHDAA2:0000986 EMAPA:17164 VHOG:0000531 cavity of lens vesicle uberon UBERON:0005688 lens vesicle cavity An anatomical cavity that is part of a lens vesicle. OBOL:automatic (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000531 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 lens cavity EHDAA2:0000986 cavity of lens vesicle EMAPA:17164 Mesenchyme that is part of a pharyngeal arch 2. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000066 EHDAA:625 EMAPA:16279 FMA:295698 VHOG:0001102 2nd pharyngeal arch mesenchyme uberon 2nd branchial arch mesenchyme pharyngeal arch 2 mesenchyme UBERON:0005689 2nd arch mesenchyme Mesenchyme that is part of a pharyngeal arch 2. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001102 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 2nd pharyngeal arch mesenchyme VHOG:0001102 Mesenchyme that is part of a pharyngeal arch 3. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000081 EHDAA:1094 EMAPA:16402 FMA:295700 VHOG:0001083 3rd pharyngeal arch mesenchyme uberon 3rd branchial arch mesenchyme pharyngeal arch 3 mesenchyme UBERON:0005690 3rd arch mesenchyme Mesenchyme that is part of a pharyngeal arch 3. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001083 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 3rd pharyngeal arch mesenchyme VHOG:0001083 Mesenchyme that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000096 EHDAA:1677 EMAPA:16770 FMA:295702 VHOG:0001052 4th pharyngeal arch mesenchyme uberon 4th branchial arch mesenchyme pharyngeal arch 4 mesenchyme UBERON:0005691 4th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001052 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 4th pharyngeal arch mesenchyme VHOG:0001052 Mesenchyme that is part of a developing manual digit 5. EHDAA2:0000537 EMAPA:17443 fore limb digit 5 mesenchyme manual digit V mesenchyme hand digit 5 mesenchyme uberon UBERON:0005695 manual digit 5 mesenchyme Mesenchyme that is part of a developing manual digit 5. OBOL:automatic fore limb digit 5 mesenchyme OBOL:accepted manual digit V mesenchyme hand digit 5 mesenchyme NCBITaxon:9606 OBOL:accepted Mesenchyme that is part of a developing pedal digit 5. EHDAA2:0002059 EMAPA:17474 hind limb digit 5 mesenchyme pedal digit V mesenchyme foot digit 5 mesenchyme uberon UBERON:0005699 pedal digit 5 mesenchyme Mesenchyme that is part of a developing pedal digit 5. OBOL:automatic hind limb digit 5 mesenchyme OBOL:accepted pedal digit V mesenchyme foot digit 5 mesenchyme NCBITaxon:9606 OBOL:accepted Mesenchyme that is part of a optic eminence. EHDAA:942 EMAPA:16324 RETIRED_EHDAA2:0001310 VHOG:0001073 uberon UBERON:0005702 optic eminence mesenchyme Mesenchyme that is part of a optic eminence. OBOL:automatic A mesentery of duodenum that is part of a foregut. EHDAA2:0000564 uberon UBERON:0005711 foregut duodenum mesentery A mesentery of duodenum that is part of a foregut. OBOL:automatic A mesentery of duodenum that is part of a midgut. EHDAA2:0001193 uberon UBERON:0005712 midgut duodenum mesentery A mesentery of duodenum that is part of a midgut. OBOL:automatic An apical ectodermal ridge that is part of a footplate. EHDAA2:0000547 EMAPA:17251 uberon UBERON:0005719 footplate apical ectodermal ridge true An apical ectodermal ridge that is part of a footplate. OBOL:automatic A venous system that is part of a hindbrain. EHDAA2:0000776 EMAPA:18632 VHOG:0001322 uberon rhombencephalon venous system UBERON:0005720 hindbrain venous system A venous system that is part of a hindbrain. OBOL:automatic rhombencephalon venous system VHOG:0001322 A mesoderm that has the potential to develop into a pronephros. Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] AAO:0011090 EFO:0003479 TAO:0000067 VHOG:0001239 XAO:0000264 ZFA:0000067 uberon pronephric anlage pronephric bulge pronephric mesenchyme pronephric primordium UBERON:0005721 the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm ZFA Bgee:AN A mesoderm that has the potential to develop into a pronephros. OBOL:automatic Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] 2012-06-20 AAO:0011090 AAO XAO:curator pronephric anlage XAO:0000264 pronephric bulge XAO:0000264 pronephric mesenchyme XAO:0000264 pronephric primordium XAO:0000264 A sensory system that is capable of olfacttion (the sensory perception of smell). consider splitting into main and accessory. See also: vomeronasal organ we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system]. The sensory system used for olfaction (the sense of smell).[AAO] In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP]. AAO:0000334 AAO:0000978 BILA:0000144 EFO:0001973 EMAPA:36004 FMA:7190 MA:0002445 NCIT:C94501 NLXANAT:090806 OpenCyc:Mx4rvViw75wpEbGdrcN5Y29ycA TAO:0001149 UMLS:C0228065 XAO:0003196 ZFA:0001149 uberon UBERON:0005725 olfactory system A sensory system that is capable of olfacttion (the sensory perception of smell). The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system]. The sensory system used for olfaction (the sense of smell).[AAO] 2012-06-20 AAO:0000978 AAO AAO:EJS UMLS:C0228065 ncithesaurus:Olfactory_System BILA:0000139 uberon UBERON:0005726 chemosensory system . EHDAA2:0000474 EMAPA:31862 EMAPA:31863 FMA:296719 VHOG:0000616 extra-embryonic mesoderm extraembryonic mesenchyme uberon UBERON:0005728 extraembryonic mesoderm EHDAA2 EHDAA2 . A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme. Embryonic region that develops into the pectoral fin bud.[TAO] TAO:0001453 ZFA:0001453 pectoral appendage field of lateral plate mesoderm pectoral fin field uberon UBERON:0005729 pectoral appendage field A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme. OBOL:automatic Embryonic region that develops into the pectoral fin bud.[TAO] 2012-08-14 TAO:0001453 TAO ZFIN:curator pectoral fin field ZFA:0001453 A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. Embryonic region that develops into the pelvic fin bud.[TAO] TAO:0001454 ZFA:0001454 pelvic appendage field of lateral plate mesoderm pelvic fin field uberon UBERON:0005730 pelvic appendage field A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. OBOL:automatic Embryonic region that develops into the pelvic fin bud.[TAO] 2012-08-14 TAO:0001454 TAO ZFIN:curator pelvic fin field ZFA:0001454 A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this. limb/fin field of lateral plate mesoderm paired limb/fin field uberon UBERON:0005732 paired limb/fin field ISBN:9780878932504 ZFA-inferred A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. ISBN:9780878932504 A ring of cells capable of forming a limb. limb field of lateral plate mesoderm uberon UBERON:0005733 the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995) limb field A ring of cells capable of forming a limb. ISBN:9780878932504 The outermost layer of a blood vessel, composed mainly of fibrous tissue. TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]. BTO:0002010 EMAPA:36299 NCIT:C33818 UMLS:C0225342 adventitia externa tunica adventitia tunica adventitia of vessel uberon external coat tunica adventitia vasorum tunica externa vasorum UBERON:0005734 tunica adventitia of blood vessel Illu:artery.jpg cjm The outermost layer of a blood vessel, composed mainly of fibrous tissue. ISBN:0073040584 The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]. UMLS:C0225342 ncithesaurus:Tunica_Adventitia adventitia externa tunica adventitia tunica adventitia of vessel external coat tunica adventitia vasorum tunica externa vasorum A tunica intima that is part of a artery. EMAPA:36293 EV:0100028 FMA:14272 galen:IntimaOfArtery arterial intima tunica interna (intima)(arteriae) uberon UBERON:0005740 tunica intima of artery A tunica intima that is part of a artery. OBOL:automatic arterial intima EV:0100028 tunica interna (intima)(arteriae) FMA:14272 An outermost connective tissue covering of an organ, vessel, or other structure[WP]. BTO:0002010 FMA:45635 tunica advetitia tunica externa uberon UBERON:0005742 adventitia http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg An outermost connective tissue covering of an organ, vessel, or other structure[WP]. tunica advetitia tunica externa FMA:45635 Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). foramen AAO:0010438 TAO:0001736 VHOG:0001760 ZFA:0005386 foramens@fr foramina@fr uberon UBERON:0005744 bone foramen http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. TAO:curator in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). FMA foramen ZFA:0005386 foramens@fr TAO:0001736 foramina@fr TAO:0001736 The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. caudal portion of nephrogenic cord caudal region of nephrogenic cord rear part of nephrogenic cord rear portion of nephrogenic cord uberon UBERON:0005753 caudal part of nephrogenic cord The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. caudal portion of nephrogenic cord OBOL:automatic caudal region of nephrogenic cord OBOL:automatic rear part of nephrogenic cord OBOL:automatic rear portion of nephrogenic cord The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. uberon UBERON:0005754 rostral part of nephrogenic cord The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. A acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 uberon UBERON:0005764 acellular membrane A acellular anatomical structure that is the bounding layer of a anatomical structure. OBOL:automatic An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 GAID:915 NCIT:C13191 UMLS:C0004799 basement membrane of connective tissue membrana basalis uberon basement membrane UBERON:0005769 basement membrane of epithelium FMA An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. UMLS:C0004799 ncithesaurus:Basement_Membrane basement membrane of connective tissue FMA:63872 membrana basalis basement membrane FMA:63872 Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. TODO - check ridge vs cord vs nephrogenic cord vs blastema EHDAA2:0001242 EHDAA:1015 EMAPA:16368 VHOG:0001240 uberon nephric cord UBERON:0005792 nephric ridge Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. nephric cord VHOG:0001240 FMA:72173 fetal uterus uberon UBERON:0005795 embryonic uterus fetal uterus FMA:72173 Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. FMA:13087 NCIT:C34027 UMLS:C0506947 aortic section uberon aortic segment portion of aorta segment of aorta UBERON:0005800 section of aorta Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. ncithesaurus:Aortic_Segment UMLS:C0506947 ncithesaurus:Aortic_Segment aortic segment FMA:13087 segment of aorta FMA:13087 The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch relationship loss: part_of axial vasculature (TAO:0001073)[TAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] AAO:0011029 BTO:0004673 EHDAA:402 EMAPA:18606 TAO:0000014 VHOG:0000264 XAO:0000051 ZFA:0000014 DA aorta dorsalis uberon aortae dorsales dorsal aorta root dorsal aortae dorsal aortic root dorsal aortæ UBERON:0005805 dorsal aorta http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. GO:0035907 Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000014 TAO ZFIN:curator The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch BTO:0004673 relationship loss: part_of axial vasculature (TAO:0001073)[TAO] 2012-08-14 TAO:0000014 TAO When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000264 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 DA ZFA:0000014 aorta dorsalis XAO:0000051 aortae dorsales dorsal aorta root VHOG:0000264 dorsal aortae dorsal aortic root VHOG:0000264 dorsal aortæ In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]. FMA:45628 MESH:D011168 NCIT:C33344 UMLS:C0226727 portal venous system uberon UBERON:0005806 portal system In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]. UMLS:C0226727 ncithesaurus:Portal_Venous_System portal venous system FMA:45628 A bone tissue that is part of a long bone. FMA:83117 uberon osseous tissue of long bone UBERON:0005808 bone tissue of long bone A bone tissue that is part of a long bone. OBOL:automatic osseous tissue of long bone FMA:83117 This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term BIRNLEX:2665 FMA:62420 MA:0003080 axial part of spinal cord axial regional part of spinal cord segment of spinal cord uberon spinal neuromeres UBERON:0005844 spinal cord segment axial part of spinal cord BIRNLEX:2665 axial regional part of spinal cord BIRNLEX:2665 segment of spinal cord FMA:62420 spinal neuromeres TAO:0001332 A spinal cord segment that adjacent_to a caudal region. FMA:256635 MA:0003084 coccygeal segment of spinal cord coccygeal segments of spinal cord [1-3] pars coccygea medullae spinalis segmenta coccygea medullae spinalis [1-3] uberon segmenta coccygea UBERON:0005845 for spinal cord segments, we treat coccygeal/caudal as synonyms - we only differentiate where bone is concerned caudal segment of spinal cord A spinal cord segment that adjacent_to a caudal region. OBOL:automatic coccygeal segment of spinal cord FMA:256635 coccygeal segments of spinal cord [1-3] FMA:256635 pars coccygea medullae spinalis FMA:256635 FMA:TA segmenta coccygea medullae spinalis [1-3] FMA:256635 FMA:TA segmenta coccygea NeuroNames:1656 A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 EHDAA:8979 mesenchyme condensation uberon UBERON:0005856 developing mesenchymal condensation AEO cjm A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 mesenchyme condensation EMAPA:25351 Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. isa cell condensation in VSAO; has_part chondroblast in AEO AEO:0000147 EHDAA2_RETIRED:0003147 EMAPA:32731 VSAO:0000092 XAO:0004022 cartilage condensation cartilagenous condensation chondrogenic condensation uberon UBERON:0005863 cartilaginous condensation AEO AEO Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. GO:curator isa cell condensation in VSAO; has_part chondroblast in AEO VSAO cartilage condensation EMAPA:25353 cartilagenous condensation EHDAA2:0003147 chondrogenic condensation VSAO:0000092 UBERON:0008714 AEO:0000149 EHDAA2_RETIRED:0003149 pre muscle mass premuscle mass uberon UBERON:0005865 pre-muscle condensation A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. AEO:0000150 EHDAA2:0003150 EMAPA:32736 pre-chondrogenic condensation precartilage condensation precartilagenous condensation prechondrogenic condensation uberon UBERON:0005866 pre-cartilage condensation AEO AEO A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. AEO:0000150 AEO:JB A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip check develops_from EHDAA2:0001061 EHDAA:5871 EMAPA:17355 FMA:293051 NCIT:C34204 UMLS:C1512982 uberon mandibular process mandibular swelling prominentia mandibularis UBERON:0005867 mandibular prominence the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip ISBN:0-683-40008-8 MP:0010939 UMLS:C1512982 ncithesaurus:Mandibular_Prominence mandibular process mandibular swelling prominentia mandibularis the paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw EHDAA2:0001070 EHDAA:5877 EMAPA:17359 FMA:293049 NCIT:C34206 UMLS:C1513037 embryonic maxillary process maxillary process maxillary process of embryo uberon prominentia maxilaris UBERON:0005868 maxillary prominence http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png the paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw ISBN:0-683-40008-8 MP:0010940 UMLS:C1513037 ncithesaurus:Maxillary_Prominence maxillary process EHDAA2:0001070 prominentia maxilaris An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]. we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]. AAO:0011068 EFO:0003496 EHDAA2:0001295 EHDAA:4772 EMAPA:16800 FMA:295840 XAO:0000275 XAO:0004073 nasal pit uberon UBERON:0005870 olfactory pit EHDAA2 EMAPA EHDAA2 XAO:0000275 nasal pit An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]. GO:0060166 By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]. nasal pit XAO:0000275 A groove that is situated between the 1st and 2nd pharyngeal arch. In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] EHDAA2:0000009 EHDAA:575 EMAPA:16119 VHOG:0000554 VHOG:0000969 1st arch branchial groove 1st arch groove ectoderm 1st pharyngeal groove 1st pharyngeal groove ectoderm branchial groove of 1st arch uberon 1st branchial cleft 1st pharyngeal cleft UBERON:0005872 1st arch pharyngeal cleft A groove that is situated between the 1st and 2nd pharyngeal arch. ISBN:0124020607 VHOG:OG In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] 2012-09-17 VHOG:0000969 VHOG DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010) 1st arch branchial groove EHDAA2:0000008 1st arch groove ectoderm EHDAA2:0000009 1st pharyngeal groove VHOG:0000969 1st pharyngeal groove ectoderm VHOG:0000554 branchial groove of 1st arch EMAPA:16119 1st branchial cleft EMAPA:16119 1st pharyngeal cleft VHOG:0000969 A groove that is situated between the 2nd and 3rd pharyngeal arch. EHDAA2:0000057 EHDAA:613 EMAPA:16396 VHOG:0000568 VHOG:0000972 2nd arch branchial groove 2nd arch groove ectoderm 2nd pharyngeal groove 2nd pharyngeal groove ectoderm branchial groove of 2nd arch uberon 2nd branchial cleft 2nd pharyngeal cleft UBERON:0005873 2nd arch pharyngeal cleft A groove that is situated between the 2nd and 3rd pharyngeal arch. ISBN:0124020607 VHOG:OG 2nd arch branchial groove EHDAA2:0000054 2nd arch groove ectoderm EHDAA2:0000057 2nd pharyngeal groove VHOG:0000972 2nd pharyngeal groove ectoderm VHOG:0000568 branchial groove of 2nd arch EMAPA:16396 2nd branchial cleft EMAPA:16396 2nd pharyngeal cleft VHOG:0000972 A groove that is situated between the 3rd and 4th pharyngeal arch. EHDAA2:0000074 EHDAA:1082 EMAPA:16581 VHOG:0000572 VHOG:0000973 3rd arch branchial groove 3rd arch groove ectoderm 3rd pharyngeal groove 3rd pharyngeal groove ectoderm branchial groove of 3rd arch uberon 3rd branchial cleft 3rd pharyngeal cleft UBERON:0005874 3rd arch pharyngeal cleft A groove that is situated between the 3rd and 4th pharyngeal arch. ISBN:0124020607 VHOG:OG 3rd arch branchial groove EHDAA2:0000071 3rd arch groove ectoderm EHDAA2:0000074 3rd pharyngeal groove VHOG:0000973 3rd pharyngeal groove ectoderm VHOG:0000572 branchial groove of 3rd arch EMAPA:16581 3rd branchial cleft EMAPA:16581 3rd pharyngeal cleft VHOG:0000973 the embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG] embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP] In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG] All amniotes studied to date initiate external genital development with the formation of paired genital swellings. In mammals, archosaurs, and turtles, these swellings merge to form a single genital tubercle, the precursor of the penis and clitoris[PMID:24960313] GT development is indistinguishable in male and female mouse embryos until approximately E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP:0011771] todo - add taxon constraints we assume the EMAPA class is the undifferentiated form based on TS timings EHDAA2:0000705 EHDAA:5925 EMAPA:17382 FMA:302888 VHOG:0000583 undifferentiated genital tubercle uberon genital tubercle phallic tubercle tuberculum genitale tuberculum phallicum UBERON:0005876 undifferentiated genital tubercle http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png EHDAA2 the embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin MGI:anna MP:0011771 The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG] 2012-09-17 VHOG:0000583 VHOG embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP] MP In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG] 2012-09-17 VHOG:0000583 VHOG DOI:10.1242/dev.036830 Seifert AW, Yamaguchi T, Cohn MJ, Functional and phylogenetic analysis shows that Fgf8 is a marker of genital induction in mammals but is not required for external genital development. Development (2009) we assume the EMAPA class is the undifferentiated form based on TS timings EMAPA undifferentiated genital tubercle VHOG:0000583 genital tubercle EMAPA:17382 tuberculum genitale tuberculum phallicum An external pocketing of pharyngeal ectoderm that contacts a region of endoderm (a pharyngeal pouch) and interdigitates in the anterior and posterior directions by the pharyngeal arches. Note we use overlaps as the relationship to the arches EMAPA distinguishes between the groove ectoderm and epithelium, with the latter arising after the former pharyngeal groove AAO:0010623 EMAPA:32750 FMA:295672 NCIT:C34250 UMLS:C1280559 pharyngeal groove ectoderm gill cleft uberon Kiemenspalten branchial cleft branchial groove pharyngeal ectodermal cleft pharyngeal slit sulcus pharyngei UBERON:0005879 pharyngeal cleft http://upload.wikimedia.org/wikipedia/commons/2/20/Kiemenbogen.jpg EHDAA2 An external pocketing of pharyngeal ectoderm that contacts a region of endoderm (a pharyngeal pouch) and interdigitates in the anterior and posterior directions by the pharyngeal arches. EMAPA distinguishes between the groove ectoderm and epithelium, with the latter arising after the former EMAPA pharyngeal groove UMLS:C1280559 ncithesaurus:Pharyngeal_Groove pharyngeal groove ectoderm branchial cleft branchial groove AAO:0010623 pharyngeal slit sulcus pharyngei A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis. uberon digit or predigit limb outgrowth UBERON:0005881 encompasses digits and prepollex. requires review autopodial extension A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis. A subdivision of skeleton that supports pharyngeal arch 2. it's not clear where AAO:'hyobranchial skeleton' belongs AAO:0000665 AAO:0010370 TAO:0001276 XAO:0003177 ZFA:0001276 hyal@fr hyocïde@fr hyoid arch skeleton pharyngeal arch 2 skeleton hyoid bars uberon hyoid arch visceral arch 2 UBERON:0005884 hyoid arch skeleton ZFA cjm A subdivision of skeleton that supports pharyngeal arch 2. OBOL:automatic it's not clear where AAO:'hyobranchial skeleton' belongs AAO hyal@fr TAO:0001276 hyocïde@fr TAO:0001276 hyoid arch skeleton ZFA:0001276 pharyngeal arch 2 skeleton ZFA:0001276 hyoid bars TAO:0001276 hyoid arch TAO:0001276 visceral arch 2 TAO:0001276 The epithelial lining of the surface of the coelom. EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium' XAO:0000329 celomic epithelium germinal epithelium of Waldeyer uberon UBERON:0005891 coelomic epithelium XAO XAO The epithelial lining of the surface of the coelom. XAO:0000329 EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium' EHDAA2 germinal epithelium of Waldeyer A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx EMAPA:37304 MA:0000670 MESH:A02.835.232.500 uberon UBERON:0005893 leg bone A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx EMAPA:37304 MA:th A bone that is part of the manus skeleton. Note that this includes the carpal bones. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:35391 MA:0000619 bone of hand bone of hand skeleton bone of manus bone of pectoral limb autopod bone of pectoral limb autopodium forelimb autopod bone forelimb autopodium bone hand bone uberon UBERON:0005897 manus bone A bone that is part of the manus skeleton. Note that this includes the carpal bones. hand bone MA:0000619 A bone that is part of the pes skeleton https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:35354 GAID:192 MA:0000643 MESH:A02.835.232.300 NCIT:C13068 OpenCyc:Mx4rv5ridZwpEbGdrcN5Y29ycA UMLS:C0016505 bone of foor proper or tarsal skeleton bone of foot bone of pedal skeleton bone of pes foot bone uberon UBERON:0005899 pes bone A bone that is part of the pes skeleton UMLS:C0016505 ncithesaurus:Foot_Bone foot bone MA:0000643 Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TODO - check An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] AAO:0010199 BTO:0004675 FMA:49187 TAO:0001414 XAO:0003173 ZFA:0001414 basicranial region occipital part of head occipital region of head uberon back of head UBERON:0005902 occipital region Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TAO:0001414 UBERONREF:0000007 An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] 2012-06-20 AAO:0010199 AAO AAO:EJS Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] 2012-08-14 TAO:0001414 TAO TAO:MAH basicranial region ZFA:0001414 occipital part of head FMA:49187 occipital region of head FMA:49187 back of head FMA:49187 Each seminal vesicle consists of a single tube, coiled upon itself, and giving off several irregular cecal diverticula; the separate coils, as well as the diverticula, are connected together by fibrous tissue. When uncoiled, the tube is about the diameter of a quill, and varies in length from 10 to 15 cm.; it ends posteriorly in a cul-de-sac; its anterior extremity becomes constricted into a narrow straight duct called the excretory duct of seminal gland (or duct of the seminal vesicle), which joins with the corresponding ductus deferens to form the ejaculatory duct[WP]. EMAPA:29282 FMA:19473 ductus excretorius (vesicula seminalis) ductus excretorius glandulae vesiculosae excretory duct of seminal gland seminal vesicle duct uberon ductus excretorius glandulae vesiculosae UBERON:0005903 duct of seminal vesicle http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1160.png Each seminal vesicle consists of a single tube, coiled upon itself, and giving off several irregular cecal diverticula; the separate coils, as well as the diverticula, are connected together by fibrous tissue. When uncoiled, the tube is about the diameter of a quill, and varies in length from 10 to 15 cm.; it ends posteriorly in a cul-de-sac; its anterior extremity becomes constricted into a narrow straight duct called the excretory duct of seminal gland (or duct of the seminal vesicle), which joins with the corresponding ductus deferens to form the ejaculatory duct[WP]. ductus excretorius (vesicula seminalis) FMA:19473 ductus excretorius glandulae vesiculosae FMA:19473 FMA:TA excretory duct of seminal gland FMA:19473 seminal vesicle duct FMA:19473 ductus excretorius glandulae vesiculosae Any of the ducts that are part of a male reproductive system. this class groups the individual ducts in a variety of species uberon UBERON:0005904 duct of male reproductive system Any of the ducts that are part of a male reproductive system. Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] EMAPA:16060 FMA:9689 MA:0000005 uberon UBERON:0005906 See notes for serous membrane serous sac Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] FMA:9689 Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] FMA:69065 endoderm-derived epithelium endoepithelium uberon UBERON:0005911 endo-epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] FMA:69065 FMA:10483 bone organ zone uberon UBERON:0005913 zone of bone organ FMA bone organ zone FMA:10483 A naris that provides one of the small external openings of the head that give passage to air for breathing. Hole on the nasal capsule that connects the nasal cavity with the exterior.[AAO] relationship loss: subclass nasal opening (AAO:0000316)[AAO] In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...).[well established][VHOG] Fish have two pairs of external nostrils. naris AAO:0000024 AAO:0000983 AAO:0010358 EHDAA2:0001275 EHDAA:9085 EMAPA:17848 FMA:59645 MA:0001320 NCIT:C33178 OpenCyc:Mx4rvViCLpwpEbGdrcN5Y29ycA TAO:0000550 UMLS:C0595944 VHOG:0000544 XAO:0003033 ZFA:0000550 external nares nostril blowhole uberon anterior nares anterior naris UBERON:0005928 external naris ZFA A naris that provides one of the small external openings of the head that give passage to air for breathing. Hole on the nasal capsule that connects the nasal cavity with the exterior.[AAO] 2012-06-20 AAO:0000024 AAO AAO:LAP relationship loss: subclass nasal opening (AAO:0000316)[AAO] 2012-06-20 AAO:0000024 AAO In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...).[well established][VHOG] 2012-09-17 VHOG:0000544 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27 naris ZFA:0000550 UMLS:C0595944 ncithesaurus:Nostril external nares nostril FMA:59645 XAO:0003033 blowhole anterior nares VHOG:0000544 anterior naris ZFA:0001427 Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 EMAPA:18043 MA:0000308 NCIT:C32172 UMLS:C0222645 VSAO:0000056 XAO:0004011 uberon skeleton axiale UBERON:0005944 axial skeleton plus cranial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. FMA:71221 VSAO:0000056 Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000056 VSAO PSPUB:0000170 UMLS:C0222645 ncithesaurus:Axial_Skeleton skeleton axiale trabecula trabecular cartilage EFO:0003677 TAO:0001321 ZFA:0001321 neurocranial trabeculae uberon UBERON:0005945 neurocranial trabecula ZFA ZFA trabecula ZFA:0001321 trabecular cartilage ZFA:0001321 neurocranial trabeculae ZFA:0001321 An outflow tract that is part of a cardiac atrium. FMA:14141 outflow part of atrium uberon UBERON:0005946 outflow tract of atrium An outflow tract that is part of a cardiac atrium. OBOL:automatic outflow part of atrium FMA:14141 Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk infundibulum EMAPA:37926 FMA:7216 NCIT:C61368 UMLS:C1881209 RVOT conus arteriosus (infundibulum) infundibulum of right ventricle outflow tract of right ventricle pulmonary conus right ventricle pulmonary outflow tract right ventricular outflow tract uberon arterial cone conus arteriosus pulmonary cone pulmonary conus UBERON:0005953 outflow part of right ventricle Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk MP:0010428 infundibulum EMAPA:37926 MA:th UMLS:C1881209 ncithesaurus:Infundibulum RVOT MP:0010428 conus arteriosus (infundibulum) FMA:7216 infundibulum of right ventricle FMA:7216 infundibulum of right ventricle MP:0010428 outflow tract of right ventricle FMA:7216 pulmonary conus FMA:7216 right ventricle pulmonary outflow tract MP:0010428 right ventricular outflow tract MP:0010428 arterial cone MP:0010428 conus arteriosus MP:0010428 pulmonary cone MP:0010428 pulmonary conus MP:0010428 Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. EMAPA:37925 FMA:9473 LVOT Sibson vestibule aortic vestibule heart left ventricle outflow tract left ventricular outflow left ventricular outflow tract outflow tract of left ventricle vestibulum aortae uberon UBERON:0005956 outflow part of left ventricle Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. MP:0010429 EMAPA:37925 MA:th LVOT MP:0010429 Sibson vestibule MP:0010429 aortic vestibule FMA:9473 aortic vestibule MP:0010429 heart left ventricle outflow tract MP:0010429 left ventricular outflow FMA:9473 left ventricular outflow tract HP:0011103 outflow tract of left ventricle FMA:9473 vestibulum aortae FMA:9473 FMA:TA Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA] FMA:9550 main part of right atrium outflow tract of right atrium uberon UBERON:0005965 outflow part of right atrium Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA] FMA:9550 FMA:FMA main part of right atrium FMA:9550 outflow tract of right atrium FMA:9550 An outflow tract of atrium that is part of a left atrium. FMA:9551 main part of left atrium outflow tract of left atrium uberon UBERON:0005966 outflow part of left atrium An outflow tract of atrium that is part of a left atrium. OBOL:automatic main part of left atrium FMA:9551 outflow tract of left atrium FMA:9551 A pore-like structure surrounding the entire circumference of the anterior chamber of the eye through which aqueous humor circulates[MP]. TODO check syns - ligaments UBERON:0004028 BTO:0001605 CALOHA:TS-1058 EFO:0003077 EV:0100352 FMA:77660 GAID:897 MA:0003086 MESH:D014129 NCIT:C12803 UMLS:C0040573 eye trabecular meshwork reticulum trabeculare trabecular meshwork of the eye uberon Hueck's ligament cribiform ligament iridis ligamentum peactin-tum iridis ligamentum pectinatum ligamentum pectinatum anguli iridocornealis ligamentum pectinatum iridis pectinate ligament pectinate ligament of iris reticulum trabeculare sclerae scleral trabeculae scleral trabecular scleral trabecule scribiform ligament trabecular mesh trabecular meshwork UBERON:0005969 eye trabecular meshwork http://upload.wikimedia.org/wikipedia/commons/2/22/Gray870.png A pore-like structure surrounding the entire circumference of the anterior chamber of the eye through which aqueous humor circulates[MP]. MP:0005203 UMLS:C0040573 ncithesaurus:Trabecular_Meshwork eye trabecular meshwork MA:0003086 reticulum trabeculare BTO:0001605 trabecular meshwork of the eye Hueck's ligament BTO:0001605 cribiform ligament iridis ligamentum peactin-tum iridis ligamentum pectinatum ligamentum pectinatum anguli iridocornealis BTO:0001605 ligamentum pectinatum iridis pectinate ligament BTO:0001605 pectinate ligament of iris BTO:0001605 reticulum trabeculare sclerae scleral trabeculae scleral trabecular scleral trabecule scribiform ligament trabecular mesh trabecular meshwork BTO:0001605 GO:0002930 A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]. EMAPA:16076 amnionic fold uberon UBERON:0005971 amniotic fold ISBN:0073040584 A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]. ISBN:0073040584 amnionic fold The laminar structure of the heart uberon UBERON:0005983 heart layer The laminar structure of the heart MP:0010545 Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation TODO - change relation from part_of MESH:D003331 uberon UBERON:0005985 coronary vessel Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation MP:0010551 The supporting bundles of muscular fibers lining the walls of the atrial myocardium EMAPA:37432 ZFA:0005810 atrial trabecula atrium myocardial trabeculae trabecula of atrium trabecular layer of atrium trabecular layer of the atrium uberon UBERON:0005988 atrium myocardial trabecula ZFA The supporting bundles of muscular fibers lining the walls of the atrial myocardium MP:0010581 ZFA:0005810 EMAPA:37432 MA:th atrium myocardial trabeculae MP:0010581 trabecular layer of the atrium ZFA:0005810 The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve EMAPA:37431 FMA:7136 membranous atrioventricular septum uberon UBERON:0005989 atrioventricular septum Wikipedia The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve MP:0010592 EMAPA:37431 MA:th membranous atrioventricular septum FMA:7136 The paired arteries that carry blood to the yolk sac from the dorsal aorta EHDAA2:0002208 EMAPA:16207 uberon UBERON:0006002 Development notes:; the vitelline arteries give rise to the celiac artery, superior mesenteric artery, and inferior mesenteric artery in the adult[MP:0010664] vitelline artery http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png ventral branch The paired arteries that carry blood to the yolk sac from the dorsal aorta MP:0010664 Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] EMAPA:37883 body hair or bristle uberon adnexae cutis skin adnexa skin adnexal structure skin appendage UBERON:0006003 integumentary adnexa Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] MP:0010678 EMAPA:37883 MA:th body hair or bristle GO:GO adnexae cutis skin adnexa skin appendage A digit that is part of a digit 1 plus metapodial segment. 1 EMAPA:37285 MA:0003023 autopod digit 1 digit I limb digit 1 dewclaw uberon UBERON:0006048 digit 1 A digit that is part of a digit 1 plus metapodial segment. OBOL:automatic EMAPA:37285 MA:th digit I limb digit 1 MA:0003023 dewclaw A digit that is part of a digit 5 plus metapodial segment. 5 EMAPA:17441 EMAPA:37289 autopod digit 5 digit V fifth digit limb digit 5 uberon digiti minimi UBERON:0006052 digit 5 A digit that is part of a digit 5 plus metapodial segment. OBOL:automatic EMAPA:37289 MA:th digit V uberon UBERON:0006056 posterior surface of head A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions). uberon UBERON:0006058 multi-limb segment region https://github.com/obophenotype/uberon/issues/514 A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions). A process projection from a part of the vertebra such as centrum or arches. Examples: transverse process, diapophyses, parapophyses, and zygapophyses (both the cranial zygapophyses and the caudal zygapophyses). AAO:0000739 FMA:24530 NCIT:C116112 vertebra process vertebral process spinous process uberon UBERON:0006061 process of vertebra A process projection from a part of the vertebra such as centrum or arches. Examples: transverse process, diapophyses, parapophyses, and zygapophyses (both the cranial zygapophyses and the caudal zygapophyses). vertebral process FMA:24530 spinous process AAO:0000739 Any collection of muscles that is part of a hindlimb zeugopod. FMA:50211 leg musculature muscle group of leg set of muscles of leg uberon UBERON:0006067 musculature of hindlimb zeugopod Any collection of muscles that is part of a hindlimb zeugopod. OBOL:automatic leg musculature FMA:50211 muscle group of leg FMA:50211 set of muscles of leg FMA:50211 A bone that is part of a post-anal tail. MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future. EMAPA:18042 MA:0000696 uberon tail bone tail vertebra UBERON:0006068 bone of tail A bone that is part of a post-anal tail. OBOL:automatic MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future. MA tail bone MA:0000696 tail vertebra Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this. This region is reduced in humans and corresponds to the coccyx We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud XAO:0000087 uberon post-anal caudal region post-anal tail region postsacral region tail region UBERON:0006071 caudal region Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this. We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud XAO post-anal caudal region post-anal tail region postsacral region AAO:0000082 tail region AAO:0000082 That portion of the spine comprising the cervical vertebrae. The neck area of the spine. Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO] AAO:0000092 BTO:0004148 EHDAA2:0000238 EHDAA:5051 EMAPA:17215 FMA:24138 MA:0003154 NCIT:C69313 UMLS:C0728985 axial skeleton cervical region cervical skeleton cervical spinal column cervical spine cervical vertebrae series cervical vertebral column uberon skeletal system of neck UBERON:0006072 cervical region of vertebral column FMA That portion of the spine comprising the cervical vertebrae. The neck area of the spine. Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO] 2012-06-20 AAO:0000092 AAO AAO:Duellman_and_Trueb_1994 UMLS:C0728985 ncithesaurus:Cervical_Spine axial skeleton cervical region MA:0003154 cervical skeleton EHDAA2:0000238 cervical spinal column FMA:24138 cervical spine FMA:24138 cervical vertebral column FMA:24138 skeletal system of neck FMA:24138 That part of the spine comprising the thoracic vertebrae. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] AAO:0000612 BTO:0004150 EHDAA:5063 EMAPA:17396 FMA:9140 MA:0003155 NCIT:C69315 UMLS:C0581269 axial skeleton thoracic region columna vertebralis thoracicus thoracic spine thoracic vertebrae series thoracic vertebral column uberon UBERON:0006073 thoracic region of vertebral column FMA That part of the spine comprising the thoracic vertebrae. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] 2012-06-20 AAO:0000612 AAO AAO:Duellman_and_Trueb_1994 UMLS:C0581269 ncithesaurus:Thoracic_Spine axial skeleton thoracic region MA:0003155 columna vertebralis thoracicus FMA:9140 thoracic spine FMA:9140 thoracic vertebral column FMA:9140 Subdivision of vertebral column that corresponds to the lumbar subdivision of the body, containing the lumbar vertebrae. lumbar BTO:0004147 EHDAA2:0001037 EHDAA:5055 EMAPA:17393 FMA:16203 GAID:31 MA:0003156 NCIT:C69314 axial skeleton lumbar region lumbar skeleton lumbar spine lumbar vertebrae series lumbar vertebral column uberon UBERON:0006074 lumbar region of vertebral column Subdivision of vertebral column that corresponds to the lumbar subdivision of the body, containing the lumbar vertebrae. UBERONREF:0000006 axial skeleton lumbar region MA:0003156 lumbar skeleton EHDAA2:0001037 lumbar spine BTO:0004147 lumbar vertebral column FMA:16203 Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae. Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO] in AAO, this is posterior to the caudal-sacral region AAO:0000082 EMAPA:18043 MA:0003158 axial skeleton tail region caudal skeleton caudal vertebrae series uberon caudal region postsacral region tail region UBERON:0006076 caudal region of vertebral column Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae. UBERONREF:0000006 Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO] 2012-06-20 AAO:0000082 AAO AAO:Duellman_and_Trueb_1994 in AAO, this is posterior to the caudal-sacral region AAO axial skeleton tail region MA:0003158 caudal skeleton UBERONREF:0000006 caudal vertebrae series caudal region AAO:0000082 postsacral region AAO:0000082 tail region AAO:0000082 A collection of all skeletal elements in some subdivision of the vertebral column. FMA:16201 subdivision of vertebral skeleton vertebrae series vertebral column subdivision vertebral series uberon vertebral region vertebral subdivision UBERON:0006077 subdivision of vertebral column FMA A collection of all skeletal elements in some subdivision of the vertebral column. subdivision of vertebral skeleton vertebral column subdivision FMA:16201 The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. uberon UBERON:0006170 mesonephric capsule The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. GO:0061285 GOC:mtg_kidney_jan10 Acute angle occurring between the iris and the cornea at the periphery of the anterior chamber of the eye[MP]. FMA:58577 anterior chamber angle uberon UBERON:0006206 iridocorneal angle Acute angle occurring between the iris and the cornea at the periphery of the anterior chamber of the eye[MP]. MP:0004221 anterior chamber angle FMA:58577 The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. UBERON:0005999 CALOHA:TS-2409 EHDAA2:0000136 EHDAA:2592 EMAPA:16827 VHOG:0000502 aortico-pulmonary septum aorticopulmonary septum septum aorticopulmonale uberon aortic septum spiral septum UBERON:0006207 aortico-pulmonary spiral septum http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png Wikipedia The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. MP:0010650 aortico-pulmonary septum aorticopulmonary septum septum aorticopulmonale aortic septum spiral septum A collection of protruberances derived from pharyngeal arches 1 and 2 that develop into the folds of the pinna and gradually shift upwards and backwards to their final position on the head. EHDAA2:0000155 EHDAA:4685 EMAPA:17280 NCIT:C34110 VHOG:0001364 auditory hillock of Hiss uberon auditory tubercles auricular hillock hillock of Hiss UBERON:0006208 auditory hillocks A collection of protruberances derived from pharyngeal arches 1 and 2 that develop into the folds of the pinna and gradually shift upwards and backwards to their final position on the head. auditory tubercles VHOG:0001364 EHDAA2:0000179 EHDAA:3217 EMAPA:16893 uberon UBERON:0006210 body-wall mesenchyme The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. EHDAA2:0000189 EHDAA:536 EMAPA:16259 FMA:313607 VHOG:0000380 uberon oral membrane oral plate oropharyngeal membrane pharyngeal membrane UBERON:0006211 buccopharyngeal membrane http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png EHDAA2 The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. MP:0012521 oral membrane MP:0012521 oral plate MP:0012521 oropharyngeal membrane pharyngeal membrane MP:0012521 A cartilaginous condensation that has the potential to develop into a carpal bone. EHDAA2:0000221 EHDAA:8544 EMAPA:18102 VHOG:0001123 uberon carpal cartilage condensation UBERON:0006213 carpus cartilage element A cartilaginous condensation that has the potential to develop into a carpal bone. OBOL:automatic carpal cartilage condensation EMAPA:18102 A pre-cartilage condensation that has the potential to develop into a carpal bone. EHDAA2:0000222 EHDAA:6324 EMAPA:17724 VHOG:0000955 uberon carpal pre-cartilage condensation UBERON:0006214 carpus pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a carpal bone. OBOL:automatic carpal pre-cartilage condensation EMAPA:17724 the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO] UBERON:0013163 DHBA:10664 EHDAA2:0000231 EMAPA:17074 TAO:0001440 XAO:0004135 ZFA:0001440 uberon cerebellar anlage cerebellar primordium cerebellum primordium dorsal part of alar plate of metencephalon future cerebellum presumptive cerebellum rostral rhombic lip UBERON:0006215 rhombic lip EHDAA2 Wikipedia the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system MGI:anna MP:0012525 The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO] 2012-08-14 TAO:0001440 TAO ZFIN:curator cerebellar anlage MGI:anna cerebellar primordium EMAPA:17074 cerebellum primordium EHDAA2:0000231 EMAPA:17074 dorsal part of alar plate of metencephalon EMAPA:17074 future cerebellum presumptive cerebellum MGI:anna rostral rhombic lip MGI:anna The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] EHDAA2:0000257 EHDAA:214 EHDAA:2933 EMAPA:16832 FMA:295525 NCIT:C34128 UMLS:C0231056 VHOG:0001198 embryonic cloacal membrane uberon membrana cloacalis UBERON:0006217 cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png Wikipedia The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. MP:0011837 MP:anna A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] 2012-09-17 VHOG:0001198 VHOG In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] 2012-09-17 VHOG:0001198 VHOG PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002) UMLS:C0231056 ncithesaurus:Cloacal_Membrane membrana cloacalis EHDAA:1267 EMAPA:16342 RETIRED_EHDAA2:0000268 uberon UBERON:0006218 common atrial chamber The foremost region of the future forebrain that develops into the diencephalon. EFO:0003442 EHDAA2:0000600 EHDAA:844 EMAPA:16514 RETIRED_EHDAA2:0000386 TAO:0000574 ZFA:0000574 presumptive diencephalon uberon UBERON:0006222 future diencephalon EHDAA2 The foremost region of the future forebrain that develops into the diencephalon. UBERON:cjm presumptive diencephalon TAO:0000574 EHDAA2:0000431 EHDAA:8483 EMAPA:17710 uberon UBERON:0006224 elbow joint primordium EHDAA:1477 EMAPA:16660 RETIRED_EHDAA2:0000496 VHOG:0000715 uberon facio-acoustic preganglion complex UBERON:0006232 facio-acoustic VII-VIII preganglion complex EHDAA2 facio-acoustic preganglion complex EMAPA:16660 A differentiated genital tubercle that is part of a female reproductive system. EHDAA:8118 EMAPA:18680 RETIRED_EHDAA2:0000500 VHOG:0000666 genital tubercle of female uberon UBERON:0006233 female genital tubercle true A differentiated genital tubercle that is part of a female reproductive system. OBOL:automatic genital tubercle of female EMAPA:18680 A femur endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0000508 EMAPA:17502 VHOG:0000951 uberon femoral pre-cartilage condensation UBERON:0006234 femur pre-cartilage condensation A femur endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic femoral pre-cartilage condensation EMAPA:17502 An anatomical junctions that overlaps the foregut and midgut. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] EHDAA2:0000569 EHDAA:526 EMAPA:16363 VHOG:0000291 uberon UBERON:0006235 foregut-midgut junction An anatomical junctions that overlaps the foregut and midgut. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] 2012-09-17 VHOG:0000291 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 The embryonic precursor of the brain. The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) BAMS:Enc BTO:0004726 EFO:0003431 EHDAA:300 EHDAA:830 EMAPA:16089 FMA:312967 RETIRED_EHDAA2:0000591 TAO:0000146 ZFA:0000146 brain rudiment presumptive brain encephalon uberon embryonic brain UBERON:0006238 future brain The embryonic precursor of the brain. NLX:94995 The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) brain rudiment TAO:0000146 presumptive brain ZFA:0000146 encephalon NLX:94995 embryonic brain BTO:0004726 A tendon that has the potential to develop into a central tendon. The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. EHDAA2:0000593 EHDAA:4118 EMAPA:25035 uberon cranial derivative of septum transversum cranial part of septum transversum UBERON:0006239 future central tendon EHDAA2 mesenchyme cranial part Wikipedia A tendon that has the potential to develop into a central tendon. OBOL:automatic cranial derivative of septum transversum cranial part of septum transversum A presumptive structure that has the potential to develop into a forebrain. TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate) BAMS:Pros EFO:0003423 EHDAA2:0000661 EHDAA:2643 EMAPA:16640 TAO:0000062 ZFA:0000062 future prosencephalon presumptive forebrain presumptive prosencephalon uberon prosencephalon UBERON:0006240 future forebrain A presumptive structure that has the potential to develop into a forebrain. OBOL:automatic presumptive forebrain ZFA:0000062 presumptive prosencephalon TAO:0000062 prosencephalon EHDAA2:0000661 EFO:0003438 EHDAA2:0000674 EHDAA:898 EMAPA:16092 EMAPA:16755 TAO:0000417 ZFA:0000417 presumptive spinal cord presumptive spinal cord neural keel presumptive spinal cord neural plate presumptive spinal cord neural rod uberon UBERON:0006241 future spinal cord EHDAA2 presumptive spinal cord ZFA:0000417 presumptive spinal cord neural keel TAO:0000417 presumptive spinal cord neural plate TAO:0000417 presumptive spinal cord neural rod TAO:0000417 A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops. EHDAA2:0000700 EHDAA:3047 EMAPA:16713 XAO:0004205 uberon UBERON:0006242 gall bladder primordium cjm EMAPA EHDAA2 A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops. ISBN:0815318960 XAO:0004205 EHDAA2:0000785 EHDAA:8462 EMAPA:17739 uberon UBERON:0006244 hip joint primordium A humerus endochondral element that is composed primarily of cartilage tissue. EHDAA2:0000787 EHDAA:6240 EMAPA:17713 VHOG:0001120 uberon humeral cartilage condensation UBERON:0006245 humerus cartilage element EHDAA2 A humerus endochondral element that is composed primarily of cartilage tissue. OBOL:automatic humeral cartilage condensation EMAPA:17713 A humerus endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0000788 EHDAA:4192 EMAPA:17427 VHOG:0000950 uberon humeral pre-cartilage condensation UBERON:0006246 humerus pre-cartilage condensation A humerus endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic humeral pre-cartilage condensation EMAPA:17427 A iliac endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0000809 EHDAA:9568 EMAPA:18029 VHOG:0000964 uberon UBERON:0006247 iliac pre-cartilage condensation EHDAA2 A iliac endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG] Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] EHDAA2:0000996 EMAPA:17186 VHOG:0000449 uberon lingual swelling UBERON:0006260 the collection consisting of the two lateral swellings and the medial swelling lingual swellings EHDAA2 EHDAA2 Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG] 2012-09-17 VHOG:0000449 VHOG Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000449 VHOG DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002) lingual swelling EHDAA2:0000996 A differentiated genital tubercle that is part of a male reproductive system. EHDAA:8138 EMAPA:17969 RETIRED_EHDAA2:0001048 VHOG:0000667 genital tubercle of male uberon penis anlage UBERON:0006261 male genital tubercle true A differentiated genital tubercle that is part of a male reproductive system. OBOL:automatic genital tubercle of male EMAPA:17969 penis anlage EMAPA:17969 An anatomical junctions that overlaps the mouth and foregut. EHDAA:534 EMAPA:16258 RETIRED_EHDAA2:0001205 VHOG:0000592 uberon UBERON:0006264 mouth-foregut junction An anatomical junctions that overlaps the mouth and foregut. OBOL:automatic Groove between maxillary prominence and lateral nasal process. EHDAA2:0001238 EHDAA:4770 EMAPA:16679 FMA:300055 NCIT:C34218 UMLS:C1513875 VHOG:0001307 naso-lacrimal groove uberon s. lacrimalis maxillae UBERON:0006266 On the nasal surface of the body of the maxilla, in front of the opening of the sinus is a deep groove, the lacrimal groove (or lacrimal sulcus), which is converted into the nasolacrimal canal, by the lacrimal bone and inferior nasal concha; this canal opens into the inferior meatus of the nose and transmits the nasolacrimal duct[WP] See also: oblique facial cleft nasolacrimal groove http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray163.png EHDAA2 EHDAA2 EHDAA2 Groove between maxillary prominence and lateral nasal process. UMLS:C1513875 ncithesaurus:Nasolacrimal_Groove naso-lacrimal groove EMAPA:16679 s. lacrimalis maxillae The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 NCIT:C34231 UMLS:C1518429 VHOG:0001212 uberon UBERON:0006267 notochordal plate EHDAA2 EHDAA2 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] 2012-09-17 VHOG:0001212 VHOG UMLS:C1518429 ncithesaurus:Notochordal_Plate A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot EHDAA2:0001279 EHDAA:224 EMAPA:16102 FMA:293135 NCIT:C34232 UMLS:C1518430 VHOG:0001213 uberon chordamesoderm presumptive notochord UBERON:0006268 The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process EHDAA2 A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot UMLS:C1518430 ncithesaurus:Notochordal_Process In humans, the oronasal membrane ruptures during the seventh week, producing a single, large oronasal cavity EHDAA2:0001331 EHDAA:5882 EMAPA:17200 VHOG:0001352 uberon UBERON:0006272 oronasal cavity In humans, the oronasal membrane ruptures during the seventh week, producing a single, large oronasal cavity the pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG] UBERON:0009123 EHDAA2:0001336 EHDAA:929 EMAPA:16536 FMA:302911 NCIT:C34238 VHOG:0001147 otic cup uberon UBERON:0006273 otic pit EHDAA2 the pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles ISBN:0-683-40008-8 MP:0011172 A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG] 2012-09-17 VHOG:0001147 VHOG otic cup NCBIBook:NBK53175 Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity. Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG] EHDAA2:0001481 EHDAA:4128 EMAPA:17704 EMAPA:17707 VHOG:0001505 uberon pleuroperitoneal channel UBERON:0006279 pleuroperitoneal canal EHDAA2 EHDAA2 Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity. ISBN:0124020607 VHOG:0001505 Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0001505 VHOG pleuroperitoneal channel VHOG:0001505 Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. UBERON:0010226 embryonic ventricle EHDAA2:0001531 EMAPA:16350 FMA:71006 NCIT:C34160 TAO:0002231 ZFA:0001719 early heart ventricle embryonic heart ventricle future heart ventricle presumptive cardiac ventricle heart tube primitive ventricle primitive ventricle of heart primordial cardiac ventricle primordial ventricle uberon UBERON:0006283 The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] future cardiac ventricle ZFA EMAPA Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. ZFA:0001719 presumptive cardiac ventricle heart tube ZFA:0001719 primitive ventricle EHDAA2:0001531 primitive ventricle of heart EMAPA:16350 primordial cardiac ventricle FMA:71006 primordial ventricle FMA:71006 future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] DHBA:10595 EHDAA2:0001571 EHDAA:1356 EMAPA:16521 TAO:0001259 VHOG:0000644 ZFA:0001259 prosencephalic vesicle preevaginated forebrain vesicle uberon forebrain ventricle forebrain vesicle prosencephalic ventricle UBERON:0006284 early prosencephalic vesicle EHDAA2 future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000644 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 prosencephalic vesicle EHDAA2:0001571 forebrain ventricle VHOG:0000644 forebrain vesicle VHOG:0000644 prosencephalic ventricle VHOG:0000644 A rib endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001716 EHDAA:8347 EMAPA:17678 VHOG:0001122 uberon UBERON:0006288 rib cartilage element EHDAA2 EHDAA2 A rib endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A rib endochondral element that is composed primarily of a pre-cartilage condensation. EHDAA2:0001717 EHDAA:6026 EMAPA:17397 VHOG:0000681 uberon UBERON:0006289 rib pre-cartilage condensation EHDAA2 EHDAA2-abduced ZFA A rib endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A scapula endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001777 EHDAA:8368 EMAPA:18343 VHOG:0001125 uberon UBERON:0006290 scapula cartilage element EHDAA2 A scapula endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A scapula endochondral element that is composed primarily of a pre-cartilage condensation. the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005). EHDAA2:0001778 EHDAA:6041 EMAPA:18027 VHOG:0000960 uberon UBERON:0006291 scapula pre-cartilage condensation EHDAA2 A scapula endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005). this is part of the forelimb skeleton in EHDAA2, but this violates part-disjointness EHDAA2:0001836 EHDAA:8493 EMAPA:17712 uberon UBERON:0006292 shoulder joint primordium EHDAA2 this is part of the forelimb skeleton in EHDAA2, but this violates part-disjointness EHDAA2 A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]. check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme UBERON:0009750 EHDAA2:0001904 EHDAA:3003 EMAPA:18535 XAO:0000326 spleen mesenchyme splenic mesenchyme splenic primordium left spleen primordium uberon UBERON:0006293 spleen primordium XAO EHDAA2-modified XAO A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]. ISBN:0123747295 MP:0011263 check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme EMAPA spleen mesenchyme MP:0011263 splenic mesenchyme splenic primordium EHDAA2:0001904 left spleen primordium XAO:0000326 A stapes endochondral element that is composed primarily of a pre-cartilage condensation. independent of the mesenchymal condensation that will form the otic capsule EHDAA2:0001910 EHDAA:5699 EMAPA:17827 VHOG:0000956 stapedial anlage uberon UBERON:0006294 stapes pre-cartilage condensation EHDAA2 cranial end EHDAA2 A stapes endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic stapedial anlage A primordium that has the potential to develop into a submandibular gland. EHDAA2:0001939 EHDAA:9255 EMAPA:17755 uberon submaxillary gland primordium UBERON:0006298 submandibular gland primordium A primordium that has the potential to develop into a submandibular gland. OBOL:automatic submaxillary gland primordium EMAPA:17755 EHDAA:924 EMAPA:16663 RETIRED_EHDAA2:0002089 trigeminal V preganglion uberon trigeminal preganglion UBERON:0006304 See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model future trigeminal ganglion EHDAA2 trigeminal V preganglion EMAPA:16663 trigeminal preganglion EMAPA:16663 A segment of the eyeball that is filled with refractive media BTO:0002085 EMAPA:37529 FMA:58071 MA:0002459 NCIT:C32301 UMLS:C0459556 eye chamber eyeball chamber uberon chamber of eye UBERON:0006311 chamber of eyeball A segment of the eyeball that is filled with refractive media EMAPA:37529 MA:th UMLS:C0459556 ncithesaurus:Chamber_of_the_Eye eye chamber MA:0002459 eyeball chamber FMA:58071 chamber of eye BTO:0002085 Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. ocular refraction MA:0001911 uberon UBERON:0006312 ocular refractive media Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid fluid BIRNLEX:20 EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 galen:BodyFluid body fluid uberon UBERON:0006314 bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. MESH:A12.207 EMAPA:37441 MA:th body fluid GAID:266 A nucleus of brain that is part of a brainstem. EMAPA:32790 MA:0000821 uberon brain stem nucleus UBERON:0006331 brainstem nucleus A nucleus of brain that is part of a brainstem. OBOL:automatic brain stem nucleus EMAPA:32790 A choroid plexus stroma that is part of a lateral ventricle. definitions should be fixed to use generic stroma class MA:0000963 uberon UBERON:0006338 lateral ventricle choroid plexus stroma A choroid plexus stroma that is part of a lateral ventricle. OBOL:automatic A choroid plexus stroma that is part of a fourth ventricle. MA:0000985 uberon UBERON:0006340 fourth ventricle choroid plexus stroma A choroid plexus stroma that is part of a fourth ventricle. OBOL:automatic 2 2 An artery that connects two larger arteries. EMAPA:18598 MA:0001938 NCIT:C52851 UMLS:C1707451 uberon UBERON:0006347 Grouping for anterior and posterior communicating artery An artery that connects two larger arteries. ncithesaurus:Communicating_Artery UMLS:C1707451 ncithesaurus:Communicating_Artery inferred from artery EMAPA:18646 MA:0002227 uberon UBERON:0006355 superior vesical vein true MA the unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species found in most mammals, with the exception of humans EMAPA:29769 MA:0000406 baculum os baculum penile bone penis bone uberon UBERON:0006435 os penis the unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species MGI:anna MP:0009103 baculum penile bone penile bone MP:0009104 penis bone The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans; it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals EMAPA:30823 MA:0000387 baubellum clitoral bone clitoris bone os clitoridis uberon UBERON:0006440 os clitoris The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans; it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals MP:0011849 baubellum clitoral bone MP:0011849 os clitoridis A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended. this ontology contains a number of subtypes of seminal fluid, defined according to glands (which are more taxonomically restricted) we follow FMA and make this class a generic superclass of the secretions of different glands (prostate, bulbo-urethreal, seminal vesicle). MA (and ncit) follows a mixture model, where these secretions are part of the seminal fluid This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation seminal fluid may have a role in sperm capacitation, sperm motility BTO:0001232 CALOHA:TS-0918 EMAPA:36543 FMA:62967 MA:0002523 MAT:0000057 MIAA:0000057 seminal plasma uberon male genital fluid male genital secretion seminal fluid UBERON:0006530 seminal fluid A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended. This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation seminal plasma BTO:0001232 seminal fluid BTO:0001232 A portion of organism substance that secreted_by a zone of skin. MA:0002537 skin fluid/secretion uberon skin fluid skin substance UBERON:0006535 skin secretion A portion of organism substance that secreted_by a zone of skin. OBOL:automatic skin fluid/secretion MA:0002537 A portion of organism substance that is secreted by a male reproductive gland. EMAPA:36541 MA:0002521 male reproductive system fluid/secretion uberon male reproductive system fluid male reproductive system secretion UBERON:0006536 male reproductive gland secretion A portion of organism substance that is secreted by a male reproductive gland. UBERON:cjm male reproductive system fluid/secretion MA:0002521 A portion of organism substance that is secreted by a female reproductive gland. MA:0002510 female reproductive system fluid/secretion uberon female reproductive system fluid female reproductive system secretion UBERON:0006537 female reproductive gland secretion A portion of organism substance that is secreted by a female reproductive gland. UBERON:cjm female reproductive system fluid/secretion MA:0002510 A portion of organism substance that secreted_by a respiratory system. EMAPA:36550 MA:0002533 NCIT:C13722 UMLS:C1514899 uberon respiratory system fluid respiratory system secretion UBERON:0006538 respiratory system fluid/secretion A portion of organism substance that secreted_by a respiratory system. OBOL:automatic UMLS:C1514899 ncithesaurus:Respiratory_System_Fluid_or_Secretion A vasculature that is part of a kidney. EMAPA:28457 TAO:0005305 ZFA:0005305 uberon UBERON:0006544 kidney vasculature A vasculature that is part of a kidney. OBOL:automatic A tube in the kidney that collect and transport urine. in ZFA this is defined as part of mesonephros TAO:0005289 ZFA:0005289 uberon UBERON:0006553 renal duct A tube in the kidney that collect and transport urine. ZFIN:ZDB-PUB-071029-9 in ZFA this is defined as part of mesonephros ZFA A tube that is part of a excretory system. uberon UBERON:0006555 excretory tube A tube that is part of a excretory system. OBOL:automatic An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. consider merging with lymph vasculature Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] lymporeticular in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system AAO:0010522 CALOHA:TS-2024 EFO:0000870 EMAPA:18248 FMA:7162 MA:0002961 MESH:D008208 VHOG:0001761 lymphatic system lymphatic tree system uberon lymporeticular system UBERON:0006558 lymphatic part of lymphoid system AAO FMA MA An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] 2012-06-20 AAO:0010522 AAO AAO:BJB in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system FMA lymphatic system FMA:7162 MA:0002435 lymphatic tree system FMA:7162 lymporeticular system VHOG:0001761 The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. currently this is an extremely generic class, encompassing both protostomes and deuterostomes. branchial pharyngeal FBbt:00005380 MAT:0000049 MIAA:0000049 uberon anterior part of foregut pharyngeal tube UBERON:0006562 pharynx The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. GO:0060465 Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA] FMA:85030 uberon UBERON:0006563 tunica media of pulmonary trunk Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA] FMA:85030 FMA:FMA A urethral meatus that is part of a female urethra[Automatically generated definition]. The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts. EMAPA:36453 FMA:85266 MA:0002639 external orifice of female urethra external urethral orifice (female) female urethral meatus ostium urethrae externum (urethra feminina) urethral meatus of clitoral urethra uberon distal urethral opening of female urethral opening of clitoral urethra UBERON:0006565 female urethral meatus A urethral meatus that is part of a female urethra[Automatically generated definition]. OBOL:automatic The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts. external orifice of female urethra FMA:85266 external urethral orifice (female) FMA:85266 female urethral meatus FMA:85266 ostium urethrae externum (urethra feminina) FMA:85266 FMA:TA urethral meatus of clitoral urethra EMAPA:36453 distal urethral opening of female EMAPA:36453 urethral opening of clitoral urethra EMAPA:36453 A myocardium that is part of a left ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of aorta. EMAPA:17339 FMA:9558 MA:0002983 left ventricular myocardium myocardium of left ventricle uberon UBERON:0006566 left ventricle myocardium A myocardium that is part of a left ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of aorta. FMA:9558 left ventricular myocardium FMA:9558 myocardium of left ventricle FMA:9558 A myocardium that is part of a right ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. EMAPA:17342 FMA:9535 MA:0002984 myocardium of right ventricle right ventricular myocardium uberon UBERON:0006567 right ventricle myocardium A myocardium that is part of a right ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. FMA:9535 myocardium of right ventricle FMA:9535 right ventricular myocardium FMA:9535 A nucleus of brain that is part of a hypothalamus. BTO:0002449 EMAPA:35417 FMA:258762 MA:0002426 nucleus of hypothalamus uberon UBERON:0006568 hypothalamic nucleus A nucleus of brain that is part of a hypothalamus. OBOL:automatic nucleus of hypothalamus FMA:258762 A nucleus of brain that is part of a diencephalon. TAO:0002191 ZFA:0001659 uberon UBERON:0006569 diencephalic nucleus A nucleus of brain that is part of a diencephalon. OBOL:automatic The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line: FMA also has FMA:29321 but it's not clear how this differs EMAPA:19159 FMA:75383 NCIT:C34245 UMLS:C0821671 linea pectinata canalis analis pectinate line of anal canal uberon Hilton's 'white line' dentate line linea anocutanea recto-anal junction site of anal membrane UBERON:0006574 pectinate line http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line: FMA also has FMA:29321 but it's not clear how this differs FMA UMLS:C0821671 ncithesaurus:Pectinate_Line linea pectinata canalis analis FMA:75383 FMA:TA pectinate line of anal canal FMA:75383 Hilton's 'white line' EMAPA:19159 dentate line linea anocutanea recto-anal junction site of anal membrane EMAPA:19159 An organ that is part of a vestibular system. BIRNLEX:2519 UMLS:C0682674 balance organ uberon UBERON:0006585 vestibular organ NIFSTD An organ that is part of a vestibular system. OBOL:automatic UMLS:C0682674 BIRNLEX:2519 balance organ Presumptive structure of the blastula that will develop into endoderm. AAO:0000471 EFO:0003437 TAO:0000416 ZFA:0000416 uberon UBERON:0006595 presumptive endoderm Presumptive structure of the blastula that will develop into endoderm. AAO:0000468 EFO:0003439 TAO:0000568 ZFA:0000568 future blood uberon UBERON:0006596 presumptive blood Portion of embryonic tissue determined by fate mapping to become a structure. Consider merging with anlage AAO:0000479 TAO:0001116 ZFA:0001116 future structure presumptive structures uberon UBERON:0006598 presumptive structure Portion of embryonic tissue determined by fate mapping to become a structure. GOC:CVS GOC:YMB ZFA:0001116 presumptive structures ZFA:0001116 Presumptive structure of the blastula that will develop into ectoderm. AAO:0000470 EFO:0003466 TAO:0001376 XAO:0004132 ZFA:0001376 uberon presumptive epidermis UBERON:0006601 presumptive ectoderm Presumptive structure of the blastula that will develop into ectoderm. presumptive epidermis ZFA:0001376 Presumptive structure of the blastula that will develop into mesoderm. AAO:0000476 EFO:0003467 TAO:0001377 ZFA:0001377 uberon UBERON:0006603 presumptive mesoderm Presumptive structure of the blastula that will develop into mesoderm. 2 2 A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified]. this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO] in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible AAO:0000277 FMA:75779 MA:0001490 TAO:0001851 ZFA:0005488 dentary symphysis inter-dentary joint inter-mandibular joint symphysis menti uberon mental symphysis symphysis mandibulae UBERON:0006606 mandibular symphysis http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png FMA connects adjacent mandibles A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified]. TAO:wd ZFA:0005488 Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO] 2012-08-14 TAO:0001851 TAO TAO:wd in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible ISBN:0073040584 dentary symphysis TAO:0001851 inter-dentary joint TAO:0001851 inter-mandibular joint TAO:0001851 symphysis menti MA:0001490 mental symphysis symphysis mandibulae Exoskeleton or shell, including those of mollusks, turtles, insects and crustaceans. exoskeleton An external ear that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right auricular region EMAPA:37361 FMA:53643 uberon UBERON:0006616 right external ear An external ear that is in the right side of a multicellular organism. OBOL:automatic right auricular region FMA:53643 EMAPA:37361 MA:th An external ear that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left auricular region EMAPA:37360 FMA:53644 uberon UBERON:0006617 left external ear An external ear that is in the left side of a multicellular organism. OBOL:automatic left auricular region FMA:53644 EMAPA:37360 MA:th An artery with its origin in the lateral terminal branch of the internal thoracic artery, with distribution to the diaphragm and the intercostal muscles, and with anastomoses to the branches of the pericardiacophrenic and inferior phrenic. EMAPA:19215 FMA:10645 musculophrenic artery uberon UBERON:0006632 musculo-phrenic artery An artery with its origin in the lateral terminal branch of the internal thoracic artery, with distribution to the diaphragm and the intercostal muscles, and with anastomoses to the branches of the pericardiacophrenic and inferior phrenic. musculophrenic artery FMA:10645 A muscle layer that is part of a fallopian tube. EMAPA:29046 FMA:18318 muscle layer of fallopian tube muscle layer of oviduct muscle layer of uterine tube muscular coat of uterine tube muscular layer of uterine tube muscularis of uterine tube tunica muscularis (Tuba uterina) tunica muscularis tubae uterinae uterine tubal muscularis uberon UBERON:0006642 muscle layer of oviduct A muscle layer that is part of a fallopian tube. OBOL:automatic muscle layer of fallopian tube FMA:18318 muscle layer of oviduct FMA:18318 muscle layer of uterine tube FMA:18318 muscular coat of uterine tube FMA:18318 muscular layer of uterine tube FMA:18318 muscularis of uterine tube FMA:18318 tunica muscularis (Tuba uterina) FMA:18318 tunica muscularis tubae uterinae FMA:18318 FMA:TA uterine tubal muscularis FMA:18318 An adventitia that is part of a epididymis. EMAPA:30443 FMA:19136 epididymis adventitia uberon UBERON:0006645 adventitia of epididymis An adventitia that is part of a epididymis. OBOL:automatic epididymis adventitia FMA:19136 A muscle layer that is part of a epididymis. EMAPA:30747 FMA:19149 uberon UBERON:0006646 muscle layer of epididymis A muscle layer that is part of a epididymis. OBOL:automatic An adventitia that is part of a vas deferens. EMAPA:29767 FMA:19238 adventitia of deferent duct adventitia of ductus deferens adventitia of vas deferens deferent ductal adventitia tunica adventitia (ductus deferens) tunica adventitia ductus deferentis uberon UBERON:0006647 adventitia of ductus deferens An adventitia that is part of a vas deferens. OBOL:automatic adventitia of deferent duct FMA:19238 adventitia of ductus deferens FMA:19238 adventitia of vas deferens FMA:19238 deferent ductal adventitia FMA:19238 tunica adventitia (ductus deferens) FMA:19238 tunica adventitia ductus deferentis FMA:19238 FMA:TA An adventitia that is part of a seminal vesicle. EMAPA:29775 FMA:19403 adventitia of seminal gland seminal vesicle adventitia tunica adventitia (vesicula seminalis) tunica adventitia glandulae vesiculosae uberon UBERON:0006648 adventitia of seminal vesicle An adventitia that is part of a seminal vesicle. OBOL:automatic adventitia of seminal gland FMA:19403 seminal vesicle adventitia FMA:19403 tunica adventitia (vesicula seminalis) FMA:19403 tunica adventitia glandulae vesiculosae FMA:19403 FMA:TA EMAPA:30997 FMA:19976 muscular coat of vagina tunica muscularis vaginae vaginal muscularis uberon UBERON:0006652 muscular layer of vagina muscular coat of vagina FMA:19976 tunica muscularis vaginae FMA:19976 FMA:TA Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP]. BTO:0003117 EMAPA:19170 EMAPA:30829 FMA:19999 NCIT:C32681 UMLS:C0227769 clitoris glans glans of clitoris uberon glans clitoridis glans clitoris UBERON:0006653 glans clitoris http://upload.wikimedia.org/wikipedia/commons/8/8c/Clitoris_inner_anatomy.gif cjm Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP]. BTO:0003117 UMLS:C0227769 ncithesaurus:Glans_Clitoris clitoris glans FMA:19999 glans of clitoris FMA:19999 glans clitoridis glans clitoris Anatomical cavity for the proximal articular surface of the proximal limb or fin element with the scapulocoracoid or equivalent structure. Cavity for the articulation of the forelimb formed by the scapula, coracoid, and clavicle.[AAO] relationship loss: part_of scapular area (AAO:0000935)[AAO] The glenoid fossa can be associated with the metapterygium in sarcopterygians, or either the meso- or propterygium in basal gnathostomes such as Chondrichthyans FMA also has classes for the bony parts around the cavity - these may be more useful than the cavity term itself AAO:0000749 EMAPA:25122 FMA:23275 NCIT:C32682 UMLS:C1261046 cavitas glenoidalis scapulae cavitus glenoidalis glenoid cavity glenoid cavity of scapula glenoid facet uberon cavitas glenoidalis glenoid cavity UBERON:0006657 glenoid fossa http://upload.wikimedia.org/wikipedia/commons/e/ec/Gray328.png to be revised after scapulocoracoid fixes Anatomical cavity for the proximal articular surface of the proximal limb or fin element with the scapulocoracoid or equivalent structure. PHENOSCAPE:ad Cavity for the articulation of the forelimb formed by the scapula, coracoid, and clavicle.[AAO] 2012-06-20 AAO:0000749 AAO AAO:LAP relationship loss: part_of scapular area (AAO:0000935)[AAO] 2012-06-20 AAO:0000749 AAO The glenoid fossa can be associated with the metapterygium in sarcopterygians, or either the meso- or propterygium in basal gnathostomes such as Chondrichthyans ad FMA also has classes for the bony parts around the cavity - these may be more useful than the cavity term itself FMA UMLS:C1261046 ncithesaurus:Glenoid_Fossa cavitas glenoidalis scapulae FMA:23275 FMA:TA cavitus glenoidalis FMA:23275 glenoid cavity FMA:23275 glenoid cavity of scapula FMA:23275 cavitas glenoidalis glenoid cavity AAO:0000749 2 2 A joint that connects one phalanx to another along a proximodistal axis. Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint]. EMAPA:37884 FMA:42765 NCIT:C101527 galen:InterphalangealJoint inter-phalangeal joint inter-phalanx joint uberon UBERON:0006658 interphalangeal joint cjm two phalanges in series A joint that connects one phalanx to another along a proximodistal axis. Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint]. ncithesaurus:Interphalangeal_Joint EMAPA:37884 MA:th inter-phalangeal joint FMA:42765 A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies) An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle. BTO:0004838 UMLS:C0225358 muscular layer muscularis layer tunica muscularis uberon muscular coat muscularis muscularis externa muscularis propria transverse muscular fibers tunica externa tunica muscularis UBERON:0006660 muscular coat A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. BTO:0004838 UMLS:C0225358 ncithesaurus:Muscle_Layer muscular layer OBOL:automatic muscularis layer FMA:45634 tunica muscularis BTO:0004838 muscular coat muscularis externa BTO:0004838 muscularis propria transverse muscular fibers tunica externa BTO:0004838 tunica muscularis On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP]. EMAPA:18707 FMA:55805 uberon canalis caroticus UBERON:0006668 carotid canal http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP]. canalis caroticus the three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] EMAPA:17702 FMA:58279 NCIT:C34119 UMLS:C0230162 VHOG:0001399 central tendon centrum tendineum centrum tendineum diaphragmatis uberon UBERON:0006670 central tendon of diaphragm VHOG definitional the three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers MGI:csmith MP:0012061 In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] 2012-09-17 VHOG:0001399 VHOG UMLS:C0230162 ncithesaurus:Central_Tendon_of_the_Diaphragm central tendon FMA:58279 centrum tendineum FMA:58279 centrum tendineum diaphragmatis FMA:58279 FMA:TA A valve that is part of a vein. FMA:68095 valve of vein uberon UBERON:0006675 venous valve A valve that is part of a vein. OBOL:automatic valve of vein FMA:68095 An anatomical boundary that adjacent_to a epithelium. FMA:70997 epithelium surface uberon UBERON:0006677 surface of epithelium An anatomical boundary that adjacent_to a epithelium. OBOL:automatic epithelium surface FMA:70997 The hypoglossal canal is a bony canal in the occipital bone of the skull. EMAPA:19012 FMA:75370 uberon anterior condylar canal canalis nervi hypoglossi hyperglossal canal UBERON:0006682 hypoglossal canal The hypoglossal canal is a bony canal in the occipital bone of the skull. anterior condylar canal EMAPA:19012 canalis nervi hypoglossi hyperglossal canal A vein that is part of a vertebral column. EMAPA:18255 FMA:76735 MA:0002108 vena spinalis uberon spinal branch UBERON:0006686 spinal vein A vein that is part of a vertebral column. OBOL:automatic vena spinalis FMA:76735 FMA:TA spinal branch FMA:76735 A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes. TODO - check neural vs vertebral canal; embryonic vs adult? Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO] AAO:0000693 FMA:9680 GAID:242 NCIT:C33869 NCIT:C34221 UMLS:C0037922 UMLS:C1522467 uberon c. vertebralis foramen vertebrale neural canal spinal canal spinal cavity vertebral canal UBERON:0006692 vertebral canal http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes. Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO] 2012-06-20 AAO:0000693 AAO AAO:LAP UMLS:C0037922 ncithesaurus:Vertebral_Canal UMLS:C1522467 ncithesaurus:Neural_Canal c. vertebralis foramen vertebrale AAO:0000693 neural canal AAO:0000693 spinal canal AAO:0000693 spinal cavity vertebral canal A vasculature that is part of a cerebellum. FMA:268519 uberon UBERON:0006694 cerebellum vasculature A vasculature that is part of a cerebellum. OBOL:automatic The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus) Naming conventions for pod terms under discussion within phenoscape group carpus/tarsus mesopodial limb segment mesopodial segment uberon mesopod UBERON:0006716 mesopodium region MA:th The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus) MA:th mesopodial limb segment MA:th The collection of all skeletal elements in an autopodium region. Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO] Naming conventions for pod terms under discussion within phenoscape group VSAO:0005019 autopod skeleton autopodial skeleton skeletal parts of autopod skeleton of autopod uberon autopodium UBERON:0006717 autopodial skeleton The collection of all skeletal elements in an autopodium region. Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO] 2012-08-14 VSAO:0005019 VSAO VSAO:NI autopod skeleton autopodial skeleton VSAO:0005019 skeletal parts of autopod skeleton of autopod autopodium VSAO:0005019 VSAO:NI During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's]. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] EHDAA2:0001081 EMAPA:17187 FMA:312476 VHOG:0000730 median lingual swelling median tongue bud tuberculum impar tuberculum linguale mediale uberon UBERON:0006756 The thyroid initially develops caudal to the tuberculum impar . This embryonic swelling arises from the first pharyngeal arch and occurs midline on the floor of the developing pharynx, eventually helping form the tongue as the 2 lateral lingual swellings overgrow it. [http://emedicine.medscape.com/article/845125-overview] median lingual swelling http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png EHDAA2 During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's]. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000730 VHOG median lingual swelling EHDAA2:0001081 median tongue bud tuberculum linguale mediale During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] paired EHDAA2:0000911 EMAPA:17189 FMA:313628 VHOG:0000731 uberon lateral lingual prominence lateral swellings tuberculum laterale tuberculum linguale laterale UBERON:0006757 lateral lingual swelling http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line. Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] 2012-09-17 VHOG:0000731 VHOG DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002) lateral swellings tuberculum laterale tuberculum linguale laterale the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm EFO:0001403 EMAPA:37835 FMA:58342 GAID:896 MESH:D016850 ZFA:0005570 cornea limbus corneal limbus corneal-scleral limbus corneoscleral junction limbus corneae sclerocorneal junction sclerocorneal limbus uberon limbus corneae UBERON:0006761 This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343 corneo-scleral junction http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm MP:0013477 EMAPA:37835 MA:th corneal limbus FMA:58342 corneal limbus GAID:896 corneal-scleral limbus corneoscleral junction GAID:896 limbus corneae sclerocorneal junction FMA:58342 sclerocorneal limbus GAID:896 limbus corneae The hemispheric articular surface at the upper extremity of the thigh bone[Stedman, 26th ed]. The femur head is the highest part of the thigh bone. It is supported by the neck of the femur. The head is globular and forms rather more than a hemisphere, is directed upward, medialward, and a little forward, the greater part of its convexity being above and in front. Its surface is smooth, coated with cartilage in the fresh state, except over an ovoid depression, the fovea capitis femoris, which is situated a little below and behind the center of the head, and gives attachment to the ligament of head of femur. If there is a fracture of the neck of the femur, the blood supply through the ligament becomes crucial. In orthopedic surgery, the head of the femur is important because it can undergo avascular necrosis and consequent osteochondritis dissecans. The head is removed in total hip replacement surgery [WP]. Proximal head of the femur, which articulates with the acetabulum.[AAO] AAO:0000892 EMAPA:37541 FMA:32851 MA:0003050 MESH:A02.835.232.500.247.343 NCIT:C32718 UMLS:C0015813 galen:FemoralHead acetabular head femoral head kopf des Schenkelbeins uberon capital femoral epiphysis caput femoris femur head UBERON:0006767 head of femur http://upload.wikimedia.org/wikipedia/commons/9/97/Gray243.png The hemispheric articular surface at the upper extremity of the thigh bone[Stedman, 26th ed]. The femur head is the highest part of the thigh bone. It is supported by the neck of the femur. The head is globular and forms rather more than a hemisphere, is directed upward, medialward, and a little forward, the greater part of its convexity being above and in front. Its surface is smooth, coated with cartilage in the fresh state, except over an ovoid depression, the fovea capitis femoris, which is situated a little below and behind the center of the head, and gives attachment to the ligament of head of femur. If there is a fracture of the neck of the femur, the blood supply through the ligament becomes crucial. In orthopedic surgery, the head of the femur is important because it can undergo avascular necrosis and consequent osteochondritis dissecans. The head is removed in total hip replacement surgery [WP]. MESH:A02.835.232.500.247.343 Proximal head of the femur, which articulates with the acetabulum.[AAO] 2012-06-20 AAO:0000892 AAO AAO:LAP EMAPA:37541 MA:th UMLS:C0015813 ncithesaurus:Head_of_the_Femur acetabular head AAO:0000892 femoral head FMA:32851 kopf des Schenkelbeins FMA:32851 FMA:TA capital femoral epiphysis caput femoris AAO:0000892 caput femoris femur head MESH:A02.835.232.500.247.343 An epithelium that is composed primarily of secretory cells. consider splitting epithelium from epithelial tissue BTO:0002991 NCIT:C43370 NCIT:C45715 UMLS:C0682578 UMLS:C1708242 uberon UBERON:0006799 glandular epithelium An epithelium that is composed primarily of secretory cells. UMLS:C0682578 ncithesaurus:Glandular_Epithelium UMLS:C1708242 ncithesaurus:Glandular_Epithelial_Tissue Structural framework that provides support to the nasal sacs and ducts. AAO:0000320 FMA:60116 skeleton of nose uberon UBERON:0006813 nasal skeleton FMA FMA facial series Kardong-abduced Structural framework that provides support to the nasal sacs and ducts. AAO:0000320 skeleton of nose FMA:60116 Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand. Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO] relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] cushions body organs AAO:0000027 FMA:63897 loose areolar connective tissue uberon areolar tissue loose connective tissue UBERON:0006815 areolar connective tissue FMA Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand. FMA:63897 Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO] 2012-06-20 AAO:0000027 AAO AAO:LAP relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] 2012-06-20 AAO:0000027 AAO cushions body organs AAO loose areolar connective tissue FMA:63897 loose connective tissue AAO:0000027 An anatomical space that surrounded_by a trachea. FMA:7469 lumen of cartilaginous trachea tracheal lumen uberon UBERON:0006833 lumen of trachea An anatomical space that surrounded_by a trachea. OBOL:automatic lumen of cartilaginous trachea OBOL:automatic tracheal lumen FMA:7469 A furrow or an incomplete tube. AEO:0000161 EHDAA2_RETIRED:0003161 uberon groove UBERON:0006846 surface groove A furrow or an incomplete tube. AEO:0000161 AEO:JB groove AEO:0000161 Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage. Endochondral bone that is located medial to the cleithrum, and articulates ventrally with the coracoid, medially with the mesocoracoid when the later is present and posteriorly with the upper one to three proximal radials. The scapula develops from the scapulocoracoid cartilage and belongs to the primary pectoral girdle. It may be perforated by the scapular foramen or it may be notched ventr and forms together with a similar notch of the coracoid the scapulocoracoid foramen[TAO:0000583]. Paired bony elements of endochondral origin. They are situated at the level of the jaw articulation, in a vertical position, with the suprascapular margin being dorsal and the glenoid end being ventral.[AAO] relationship loss: has pars glenoidalis of scapula (AAO:0000753)[AAO] relationship loss: part_of scapular area (AAO:0000935)[AAO] scapular present in all tetrapods with even vestiges of anterior limbs, e.g., turtles & birds & mammals. chick scapula is of dual origin and segmentally organized UBERON:0001124 UBERON:0010904 AAO:0000751 BTO:0001218 CALOHA:TS-0897 EFO:0001400 EMAPA:18722 FMA:13394 GAID:186 MA:0001330 MESH:D012540 NCIT:C12783 OpenCyc:Mx4rvVji0JwpEbGdrcN5Y29ycA TAO:0000583 UMLS:C0036277 VHOG:0001398 VSAO:0000157 ZFA:0000583 galen:Scapula hypercoracocïde@fr hypercoracocïdeum@fr scapula@fr scapulae shoulder blade uberon scapula bone scapulas UBERON:0006849 scapula Pectoral:girdles-en.svg ZFA definitional Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage. VSAO:0000157 Endochondral bone that is located medial to the cleithrum, and articulates ventrally with the coracoid, medially with the mesocoracoid when the later is present and posteriorly with the upper one to three proximal radials. The scapula develops from the scapulocoracoid cartilage and belongs to the primary pectoral girdle. It may be perforated by the scapular foramen or it may be notched ventr and forms together with a similar notch of the coracoid the scapulocoracoid foramen[TAO:0000583]. TAO:0000583 Paired bony elements of endochondral origin. They are situated at the level of the jaw articulation, in a vertical position, with the suprascapular margin being dorsal and the glenoid end being ventral.[AAO] 2012-06-20 AAO:0000751 AAO AAO:LAP relationship loss: has pars glenoidalis of scapula (AAO:0000753)[AAO] 2012-06-20 AAO:0000751 AAO relationship loss: part_of scapular area (AAO:0000935)[AAO] 2012-06-20 AAO:0000751 AAO present in all tetrapods with even vestiges of anterior limbs, e.g., turtles & birds & mammals. ISBN:978-0-12-319060-4 UMLS:C0036277 ncithesaurus:Scapula hypercoracocïde@fr TAO:0000583 hypercoracocïdeum@fr TAO:0000583 scapula@fr TAO:0000583 scapulae ZFA:0000583 scapula bone BTO:0001218 scapulas TAO:0000583 A muscular coat that is part of a ureter. EMAPA:28811 FMA:15893 MA:0002654 muscular coat of ureter muscular layer of ureter muscularis of ureter tunica muscularis (ureter) tunica muscularis ureteris uberon ureteral smooth muscle layer UBERON:0006855 muscular coat of ureter FMA A muscular coat that is part of a ureter. OBOL:automatic muscular coat of ureter FMA:15893 muscular layer of ureter FMA:15893 muscularis of ureter FMA:15893 tunica muscularis (ureter) FMA:TA tunica muscularis ureteris FMA:TA ureteral smooth muscle layer EMAPA:28567 This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] keep this grouping class so long as it is required for GO All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] VHOG:0001141 adrenal gland - interrenal gland adrenal gland/interrenal tissue uberon adrenal - interrenal gland suprarenal gland - interrenal gland UBERON:0006858 adrenal/interrenal gland This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] GO:0030325 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0001141 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9 adrenal gland - interrenal gland VHOG:0001141 adrenal - interrenal gland VHOG:0001141 suprarenal gland - interrenal gland VHOG:0001141 Subdivision of long bone which forms the part of the bone between two metaphyses. Note that the diaphysis includes the metaphyses, but the diaphysis proper excludes these. The MA class is associated with EMAPA:35505 but we associate this with the more precise concept of diaphyseal plate FMA:32688 MA:0002803 body proper of long bone shaft proper of long bone uberon long bone diaphysis UBERON:0006861 diaphysis proper Subdivision of long bone which forms the part of the bone between two metaphyses. Note that the diaphysis includes the metaphyses, but the diaphysis proper excludes these. The MA class is associated with EMAPA:35505 but we associate this with the more precise concept of diaphyseal plate MA body proper of long bone FMA:32688 shaft proper of long bone FMA:32688 long bone diaphysis MA:0002803 A diaphysis that is part of a femur[Automatically generated definition]. The body of the femur (or shaft), almost cylindrical in form, is a little broader above than in the center, broadest and somewhat flattened from before backward below. It is slightly arched, so as to be convex in front, and concave behind, where it is strengthened by a prominent longitudinal ridge, the linea aspera. It presents for examination three borders, separating three surfaces. Of the borders, one, the linea aspera, is posterior, one is medial, and the other, lateral[Wikipedia:Body_of_femur]. EMAPA:37538 FMA:32847 MA:0003055 NCIT:C96209 body of femur corpus femoris femoral diaphysis femoral shaft shaft of femur uberon UBERON:0006862 diaphysis of femur http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray244.png A diaphysis that is part of a femur[Automatically generated definition]. OBOL:automatic The body of the femur (or shaft), almost cylindrical in form, is a little broader above than in the center, broadest and somewhat flattened from before backward below. It is slightly arched, so as to be convex in front, and concave behind, where it is strengthened by a prominent longitudinal ridge, the linea aspera. It presents for examination three borders, separating three surfaces. Of the borders, one, the linea aspera, is posterior, one is medial, and the other, lateral[Wikipedia:Body_of_femur]. EMAPA:37538 MA:th body of femur FMA:32847 corpus femoris FMA:32847 FMA:TA femoral diaphysis FMA:32847 shaft of femur FMA:32847 A proximal metaphysis that is part of a femur. FMA:32878 uberon UBERON:0006863 proximal metaphysis of femur A proximal metaphysis that is part of a femur. OBOL:automatic A distal metaphysis that is part of a femur. FMA:32881 uberon UBERON:0006864 distal metaphysis of femur A distal metaphysis that is part of a femur. OBOL:automatic A metaphysis that is part of a femur. EMAPA:37540 FMA:32875 MA:0003052 femoral metaphysis uberon UBERON:0006865 metaphysis of femur true A metaphysis that is part of a femur. OBOL:automatic EMAPA:37540 MA:th femoral metaphysis FMA:32875 The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. FBbt:00005756 WBbt:0005773 rectum uberon rectal part of digestive tract terminal section of digestive tract UBERON:0006866 terminal part of digestive tract The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. rectum FBbt:00005756 A gland that secretes a seminal fluid. FBbt:00004958 WBbt:0006870 uberon UBERON:0006868 seminal fluid secreting gland A gland that secretes a seminal fluid. OBOL:automatic the distal elements of the developing limb of vertebrates that will give rise to the pes (foot) EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER UBERON:0004343 EHDAA:5143 EHDAA:6096 EMAPA:17249 FMA:296800 NCIT:C34177 UMLS:C1517291 foot plate footplate uberon distal part of hindlimb bud foot disk UBERON:0006871 embryonic footplate the distal elements of the developing limb of vertebrates that will give rise to the pes (foot) MGI:csmith MP:0004576 UBERON:cjm EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER EHDAA2 UMLS:C1517291 ncithesaurus:Foot_Plate distal part of hindlimb bud EMAPA:17249 An apical ectodermal ridge that is part of a handplate. EHDAA2:0000729 EMAPA:17247 uberon UBERON:0006872 handplate apical ectodermal ridge An apical ectodermal ridge that is part of a handplate. OBOL:automatic the distal elements of the developing limb of vertebrates that will give rise to the manus (hand) EHDAA:4194 EHDAA:6242 EMAPA:17245 FMA:296794 NCIT:C34185 UMLS:C1512334 hand plate handplate uberon distal part of forelimb bud UBERON:0006875 embryonic handplate the distal elements of the developing limb of vertebrates that will give rise to the manus (hand) MGI:csmith MP:0004576 UBERON:cjm UMLS:C1512334 ncithesaurus:Hand_Plate distal part of forelimb bud EMAPA:17245 A vasculature that is part of a organ. FMA:74612 organ vasculature set of blood vessels of organ uberon UBERON:0006876 vasculature of organ A vasculature that is part of a organ. OBOL:automatic organ vasculature FMA:74612 set of blood vessels of organ FMA:74612 A vasculature that is part of a liver. the EHDAA2 term and the FMA term may not be exact equivalents - check EHDAA2:0003454 EMAPA:35501 FMA:73748 hepatic vasculature uberon hepatic vascular element liver vascular element liver vascular system UBERON:0006877 vasculature of liver A vasculature that is part of a liver. OBOL:automatic the EHDAA2 term and the FMA term may not be exact equivalents - check EHDAA2 hepatic vasculature FMA:73748 hepatic vascular element EMAPA:35501 liver vascular element EMAPA:35501 liver vascular system EHDAA2:0003454 A head mesenchyme that develops_from a mesoderm. merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme AAO:0011051 EFO:0003337 EFO:0003603 EHDAA2:0001118 EHDAA:655 EMAPA:16099 EMAPA_RETIRED:16270 FMA:293859 TAO:0000998 VHOG:0000185 XAO:0000053 ZFA:0000998 head mesenchyme derived from mesoderm head mesenchyme from head mesoderm head mesenchyme from mesoderm mesenchyme derived from head mesoderm mesenchyme from head mesoderm uberon cranial mesoderm head mesoderm UBERON:0006904 head mesenchyme from mesoderm ZFA EHDAA2 XAO A head mesenchyme that develops_from a mesoderm. OBOL:automatic head mesenchyme from head mesoderm EHDAA2:0001118 mesenchyme derived from head mesoderm EHDAA:1057 cranial mesoderm UBERON:0005280 head mesoderm AAO:0011051 UBERON:0005280 Mesenchyme that is part of a mandibular prominence. EHDAA2:0001062 EHDAA:5861 EHDAA:5873 EMAPA:17357 mesenchyme of mandibular process mesenchyme of mandibular prominence uberon UBERON:0006905 mandibular process mesenchyme Mesenchyme that is part of a mandibular prominence. OBOL:automatic mesenchyme of mandibular process EMAPA:17357 mesenchyme of mandibular prominence The lateral surface parts of the external nose, inferiorly, surrounding the naris[EoM]. FMA:59519 nasal ala uberon ala nasi ala of the nose wing of nose wing of the nose wings of the nose UBERON:0006906 ala of nose http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray852.png FMA-abduced-lr The lateral surface parts of the external nose, inferiorly, surrounding the naris[EoM]. nasal ala FMA:59519 ala nasi ala nasi ala of the nose wing of nose wing of the nose wings of the nose An anatomical space that surrounded_by a digestive tract. BTO:0000349 EMAPA:32908 FMA:45677 digestive tract lumen gut cavity gut lumen lumen of alimentary tract lumen of digestive tract lumen of gut uberon UBERON:0006909 lumen of digestive tract An anatomical space that surrounded_by a digestive tract. OBOL:automatic digestive tract lumen gut cavity BTO:0000349 gut lumen FMA:45677 lumen of alimentary tract lumen of digestive tract lumen of gut FMA:45677 An epithelium that is part of a lip. The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] BTO:0004468 TAO:0005334 ZFA:0005334 uberon UBERON:0006913 lip epithelium An epithelium that is part of a lip. OBOL:automatic The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] 2012-08-14 TAO:0005334 TAO ZFIN:ZDB-PUB-060921-12 An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 UMLS:C0221909 uberon UBERON:0006914 squamous epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium FBbt UMLS:C0221909 ncithesaurus:Squamous_Epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA] FMA:45563 NCIT:C13180 UMLS:C0836131 epithelium stratificatum squamosum uberon UBERON:0006915 stratified squamous epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA] FMA:45563 UMLS:C0836131 ncithesaurus:Stratified_Squamous_Epithelium epithelium stratificatum squamosum FMA:45563 A non-keratinized stratified squamous epithelium that is part of a tongue. FMA:62130 uberon UBERON:0006916 non-keratinized epithelium of tongue A non-keratinized stratified squamous epithelium that is part of a tongue. OBOL:automatic A squamous epithelium that is part of a tongue. this is a singleton subclass of tongue epithelium in MA MA:0002786 squamous epithelium of tongue uberon UBERON:0006919 tongue squamous epithelium A squamous epithelium that is part of a tongue. OBOL:automatic this is a singleton subclass of tongue epithelium in MA MA squamous epithelium of tongue OBOL:automatic A squamous epithelium that is part of a esophagus. MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass BTO:0003635 CALOHA:TS-1250 EMAPA:35324 MA:0001567 NCIT:C49222 UMLS:C1707950 uberon esophageal squamous epithelium squamous epithelium of esophagus squamous oesophageal epithelium UBERON:0006920 esophagus squamous epithelium A squamous epithelium that is part of a esophagus. OBOL:automatic MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass MA UMLS:C1707950 ncithesaurus:Esophageal_Squamous_Epithelium esophageal squamous epithelium OBOL:automatic squamous epithelium of esophagus OBOL:automatic squamous oesophageal epithelium MA:0001567 A squamous epithelium that is part of a stomach. EMAPA:35824 MA:0001611 uberon UBERON:0006921 stomach squamous epithelium A squamous epithelium that is part of a stomach. OBOL:automatic The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. MA:0001725 NCIT:C49219 UMLS:C1707351 cervical squamous epithelium uberon UBERON:0006922 cervix squamous epithelium The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane. UMLS:C1707351 ncithesaurus:Cervix_Squamous_Epithelium A squamous epithelium that is part of a vagina. EMAPA:37794 MA:0001731 NCIT:C49314 UMLS:C1711259 vaginal squamous epithelium uberon UBERON:0006923 vagina squamous epithelium A squamous epithelium that is part of a vagina. OBOL:automatic EMAPA:37794 MA:th UMLS:C1711259 ncithesaurus:Vaginal_Squamous_Epithelium A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland. EMAPA:17623 EMAPA:35814 FMA:63458 MA:0002784 epithelium of gastric gland uberon gastric gland epithelium UBERON:0006924 stomach glandular epithelium FMA A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. ISBN:0073040584 epithelium of gastric gland FMA:63458 gastric gland epithelium FMA:63458 Any gland that is part of the digestive system. AAO:0000130 BTO:0000345 uberon digestive gland UBERON:0006925 digestive system gland Any gland that is part of the digestive system. UBERON:cjm digestive gland BTO:0000345 Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA] FMA:64800 NCIT:C13182 UMLS:C0225337 uberon UBERON:0006929 glandular columnar epithelium Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA] FMA:64800 UMLS:C0225337 ncithesaurus:Columnar_Epithelium stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. EMAPA:27167 MA:0001614 stomach glandular region glandular mucous membrane uberon UBERON:0006931 stomach glandular region mucosa stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. stomach glandular region glandular mucous membrane EMAPA:27167 Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical CALOHA:TS-0682 FMA:62410 uberon neuroepithelium UBERON:0006934 sensory epithelium Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. BTO:0000314 note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical FMA neuroepithelium BTO:0000314 the epithelial cells lining the capsule and trabeculae of the thymus TODO - check whether this is part of the thymus or borders it MA:0000769 uberon UBERON:0006936 thymus subcapsular epithelium the epithelial cells lining the capsule and trabeculae of the thymus ISBN:0-8153-1691-7 MGI:cwg MP:0002369 the epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals EMAPA:32883 MA:0001189 uberon UBERON:0006937 inner ear epithelium the epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals MGI:csmith MP:0003308 An epithelium that is part of a pinna. EHDAA2:0001470 EHDAA:8983 EMAPA:17592 VHOG:0000632 uberon UBERON:0006938 pinna surface epithelium An epithelium that is part of a pinna. OBOL:automatic The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis. Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO] There are two basic designs for efferent ductule structure: a) multiple entries into the epididymis, as seen in most large mammals. In humans and other large mammals, there are approximately 15-20 efferent ducts, which also occupy nearly one third of the head of the epididymis. b) single entry, as seen in most small animals such as rodents, whereby the 3-6 ductules merge into a single small ductule prior to entering the epididymis Check EMAPA AAO:0010532 EMAPA:18993 FMA:19081 MA:0000398 NCIT:C32492 UMLS:C0228013 efferent ductule seminal duct uberon ductuli efferentes testis vasa efferentia UBERON:0006946 efferent duct http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg FMA The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis. Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO] 2012-06-20 AAO:0010532 AAO AAO:BJB Check EMAPA EMAPA UMLS:C0228013 ncithesaurus:Efferent_Ductule efferent ductule efferent ductule FMA:19081 ductuli efferentes testis ductuli efferentes testis vasa efferentia AAO:0010532 A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra. we use this as a generic grouping class for a number of taxa in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct UBERON:0010140 FMA:55678 TAO:0001268 ZFA:0001268 sperm duct sperm ducts uberon UBERON:0006947 male genital duct FMA-abduced-lr A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra. in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct FMA sperm duct ZFA:0001268 sperm ducts TAO:0001268 An epithelium that is part of a efferent duct. EMAPA:29747 FMA:19195 MA:0001734 epithelium of efferent ductule of testis uberon UBERON:0006948 efferent duct epithelium An epithelium that is part of a efferent duct. OBOL:automatic epithelium of efferent ductule of testis FMA:19195 The ejaculatory duct epithelium is composed of cuboidal to columnar cells between or through which project the terminal parts of the ducts of the unicellular prostate glands. TODO - split off insect classes BTO:0002618 EMAPA:29786 uberon UBERON:0006953 ejaculatory duct epithelium The ejaculatory duct epithelium is composed of cuboidal to columnar cells between or through which project the terminal parts of the ducts of the unicellular prostate glands. An epithelium that is part of a uterus. BTO:0003082 uberon uterus epithelium UBERON:0006955 uterine epithelium An epithelium that is part of a uterus. OBOL:automatic uterus epithelium BTO:0003082 The inner lining of the cheeks and lips. BTO:0003833 CALOHA:TS-2349 FMA:59785 NCIT:C12505 UMLS:C1578559 uberon UBERON:0006956 buccal mucosa The inner lining of the cheeks and lips. UMLS:C1578559 ncithesaurus:Buccal_Mucosa An epithelium that is part of a submandibular gland primordium. EHDAA2:0001940 EHDAA:9257 EMAPA:17756 uberon submaxillary gland primordium epithelium UBERON:0006957 submandibular gland primordium epithelium An epithelium that is part of a submandibular gland primordium. OBOL:automatic submaxillary gland primordium epithelium EMAPA:17756 The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. CALOHA:TS-1246 EMAPA:28880 FMA:18626 MA:0002991 NCIT:C33638 UMLS:C0737271 interstitial tissue of ovary ovarian stroma ovary stroma stroma of the ovary stroma ovarica uberon stroma ovarii UBERON:0006960 ovary stroma The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. UMLS:C0737271 ncithesaurus:Stroma_of_the_Ovarian_Cortex interstitial tissue of ovary FMA:18626 ovarian stroma FMA:18626 ovary stroma MA:0002991 stroma of the ovary stroma ovarica FMA:18626 stroma ovarii The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. EFO:0003709 TAO:0005077 ZFA:0005077 uberon UBERON:0006965 vascular cord The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. GO:0072360 ZFA:0005077 A capillary that is part of the coronary system. ZFA:0005813 heart capillary uberon UBERON:0006966 coronary capillary A capillary that is part of the coronary system. heart capillary GO:0003248 Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface. AAO:0010266 AEO:0000009 BILA:0000009 CARO:0000009 EHDAA2:0003009 FMA:9658 TAO:0001839 uberon UBERON:0006983 anatomical point Non-material anatomical entity of zero dimension, which forms a boundary of an anatomical line or surface. FMA:9658 A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n BILA:0000010 CARO:0001002 EHDAA2_RETIRED:0003192 FMA:24137 NCIT:C34022 UMLS:C1515977 uberon UBERON:0006984 Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface via morphological boundary in CARO A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n CARO:0001002 UMLS:C1515977 ncithesaurus:Anatomic_Surface The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. consider FBbt:00005541 ! cardiogenic mesoderm review EHDAA2 placement AAO:0011021 BILA:0000051 EFO:0000315 EHDAA2:0000214 EHDAA:385 FMA:293143 VHOG:0001641 XAO:0000235 cardiogenic splanchnopleure uberon cardiac mesoderm cardiogenic mesoderm cardiogenic region heart primordia UBERON:0007005 cardiogenic splanchnic mesoderm The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. XAO:0000235 cardiogenic splanchnopleure EHDAA2:0000214 cardiac mesoderm XAO:0000235 cardiogenic mesoderm cardiogenic region heart primordia XAO:0000235 Organism at the cleavage stage. BILA:0000058 uberon UBERON:0007010 cleaving embryo Organism at the cleavage stage. OBOL:automatic A multicellular organism that is at the juvenile stage. Whole organism that is not fully grown or sexually mature.[TAO] juvenile BILA:0000076 TAO:0002047 juvenile organism juveniles uberon UBERON:0007021 sexually immature organism A multicellular organism that is at the juvenile stage. OBOL:automatic Whole organism that is not fully grown or sexually mature.[TAO] 2012-08-14 TAO:0002047 TAO TAO:wd juvenile organism BILA:0000076 juveniles TAO:0002047 A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. Whole organism that is fully grown or sexually mature.[TAO] adult BILA:0000078 FBbt:00003004 HAO:0000087 NCIT:C17600 TAO:0002046 UMLS:C0001675 galen:Adult adults uberon UBERON:0007023 adult organism A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage. OBOL:automatic Whole organism that is fully grown or sexually mature.[TAO] 2012-08-14 TAO:0002046 TAO TAO:wd UMLS:C0001675 ncithesaurus:Adult adults TAO:0002046 The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 UMLS:C1514442 future digestive tract future digestive tube future gut primitive gut uberon embryonic digestive tube primordial digestive tube primordial gut UBERON:0007026 presumptive gut The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis NCBIBook:NBK10107 UMLS:C1514442 ncithesaurus:Primordial_Gut BILA:0000142 uberon UBERON:0007037 mechanosensory system Cranial neural crest that migrates into the mandibular arch. TAO:0007064 XAO:0000024 ZFA:0007064 uberon UBERON:0007098 mandibular neural crest ZFA ZFA Cranial neural crest that migrates into the mandibular arch. ZFA:0007064 Cranial neural crest that migrates into the hyoid arch. TAO:0007065 XAO:0000025 ZFA:0007065 hyoid crest uberon UBERON:0007099 hyoid neural crest ZFA ZFA Cranial neural crest that migrates into the hyoid arch. ZFA:0007065 hyoid crest XAO:0000025 A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis FBbt:00003154 SPD:0000130 TADS:0000147 dorsal tube heart uberon adult heart UBERON:0007100 Gene notes: Bmp, Nkx, Gata primary circulatory organ A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. GO:0007507 dorsal tube heart GO:0007507 adult heart FBbt:00003154 chorionic villus One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present. BTO:0001161 EHDAA2:0004717 MESH:A16.254.403.473.200 NCIT:C34125 UMLS:C0008508 uberon chorionic villi chorionic villous chorionic villus embryonic part of placenta embryonic placenta fetal part of placenta fetal placenta placental villi placental villous placental villus villous chorion villous of placenta UBERON:0007106 chorionic villus http://upload.wikimedia.org/wikipedia/commons/1/1e/Gray29.png BTO MP-def One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. BTO:0001161 UMLS:C0008508 ncithesaurus:Chorionic_Villus chorionic villi MESH:A16.254.403.473.200 chorionic villous chorionic villus GAID:1300 embryonic part of placenta embryonic placenta fetal part of placenta fetal placenta placental villi GAID:1300 placental villus GAID:1300 The femur neck or neck of the femur is a flattened pyramidal process of bone, connecting the femoral head with the femoral shaft, and forming with the latter a wide angle opening medialward. FMA:42385 GAID:201 MESH:A02.835.232.500.247.510 NCIT:C61563 UMLS:C0015815 galen:NeckOfFemur femoral neck uberon collum femoris femur neck neck of the femur UBERON:0007119 neck of femur http://upload.wikimedia.org/wikipedia/commons/9/97/Gray243.png The femur neck or neck of the femur is a flattened pyramidal process of bone, connecting the femoral head with the femoral shaft, and forming with the latter a wide angle opening medialward. UMLS:C0015815 ncithesaurus:Femoral_Neck femoral neck FMA:42385 collum femoris femur neck neck of the femur A pharyngeal pouch that is between pharyngeal arches 1 and 2. . [][VHOG] In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery we use adjacency relations rather than part_of, as in EHDAA2. UBERON:0005718 AAO:0011114 EFO:0003631 EHDAA2:0000016 EMAPA:16124 EMAPA:16125 FMA:295668 NCIT:C34176 TAO:0001128 UMLS:C0231068 VHOG:0000555 VHOG:0000970 XAO:0000102 ZFA:0001128 1st arch branchial pouch 1st arch branchial pouch endoderm 1st arch pouch endoderm 1st branchial pouch 1st pharyngeal pouch endoderm first arch pharyngeal pouch first visceral pouch hyomandibular pouch pharyngeal pouches 1 visceral pouch 1 uberon first pharyngeal pouch UBERON:0007122 pharyngeal pouch 1 A pharyngeal pouch that is between pharyngeal arches 1 and 2. ISBN:0124020607 VHOG:0000970 . [][VHOG] 2012-09-17 VHOG:0000970 VHOG In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG] 2012-09-17 VHOG:0000970 VHOG DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010) The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery WP we use adjacency relations rather than part_of, as in EHDAA2. EHDAA2 UMLS:C0231068 ncithesaurus:First_Pharyngeal_Pouch 1st arch branchial pouch EHDAA2:0000013 1st arch branchial pouch endoderm EHDAA2:0000016 1st arch pouch endoderm EHDAA2:0000016 1st pharyngeal pouch endoderm VHOG:0000555 first arch pharyngeal pouch OBOL:automatic first visceral pouch XAO:0000102 pharyngeal pouches 1 ZFA:0001128 visceral pouch 1 XAO:0000102 first pharyngeal pouch VHOG:0000970 A pharyngeal puch that is between the pharyngeal arches 2 and 3. A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG] Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract. Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve UBERON:0005715 AAO:0011115 EFO:0003633 EHDAA2:0000058 EMAPA:16275 EMAPA:16276 FMA:295676 NCIT:C34289 RETIRED_EHDAA2:0000060 TAO:0001130 UMLS:C0231069 VHOG:0000561 VHOG:0000967 XAO:0000247 ZFA:0001130 2nd arch branchial pouch 2nd arch branchial pouch endoderm 2nd arch pouch endoderm 2nd branchial pouch 2nd pharyngeal pouch endoderm pharyngeal pouches 2 second arch pharyngeal pouch second visceral pouch visceral pouch 2 uberon second pharyngeal pouch UBERON:0007123 pharyngeal pouch 2 A pharyngeal puch that is between the pharyngeal arches 2 and 3. ISBN:0124020607 A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0000967 VHOG Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] 2012-06-20 AAO:0011115 AAO ISBN:0-226-55763-4 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000967 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve WP UMLS:C0231069 ncithesaurus:Second_Pharyngeal_Pouch 2nd arch branchial pouch RETIRED_EHDAA2:0000060 2nd arch branchial pouch endoderm EHDAA2:0000061 2nd arch pouch endoderm EHDAA2:0000058 2nd pharyngeal pouch endoderm VHOG:0000561 pharyngeal pouches 2 ZFA:0001130 second arch pharyngeal pouch OBOL:automatic second visceral pouch XAO:0000247 visceral pouch 2 XAO:0000247 second pharyngeal pouch VHOG:0000967 A pharyngeal pouch that between pharyngeal arches 3 and 4. A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG] Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve UBERON:0005716 AAO:0011116 EFO:0003634 EHDAA2:0000077 EMAPA:16586 FMA:295682 NCIT:C34311 RETIRED_EHDAA2:0000076 TAO:0001131 UMLS:C0231070 VHOG:0000966 VHOG:0001030 XAO:0000251 ZFA:0001131 3rd arch branchial pouch 3rd arch branchial pouch endoderm 3rd branchial pouch 3rd pharyngeal pouch endoderm pharyngeal pouches 3 third arch pharyngeal pouch third visceral pouch visceral pouch 3 uberon third pharyngeal pouch UBERON:0007124 pharyngeal pouch 3 A pharyngeal pouch that between pharyngeal arches 3 and 4. ISBN:0124020607 A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0000966 VHOG Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] 2012-06-20 AAO:0011116 AAO ISBN:0-226-55763-4 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000966 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve WP UMLS:C0231070 ncithesaurus:Third_Pharyngeal_Pouch 3rd arch branchial pouch RETIRED_EHDAA2:0000076 3rd arch branchial pouch endoderm EHDAA2:0000077 3rd pharyngeal pouch endoderm VHOG:0001030 pharyngeal pouches 3 ZFA:0001131 third arch pharyngeal pouch OBOL:automatic third visceral pouch XAO:0000251 visceral pouch 3 XAO:0000251 third pharyngeal pouch VHOG:0000966 Ganglion which is located in the trunk. EFO:0000901 MAT:0000344 MIAA:0000344 TAO:0001573 ZFA:0001573 body ganglion trunk ganglia uberon UBERON:0007134 trunk ganglion Ganglion which is located in the trunk. ZFIN:curator body ganglion MAT:0000344 trunk ganglia ZFA:0001573 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 uberon presumptive central nervous system UBERON:0007135 neural keel An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000131 TAO ZFIN:curator presumptive central nervous system ZFA:0000131 An internal carotid artery that branching_part_of a left common carotid artery plus branches. EMAPA:16329 FMA:4062 arteria caritis interna sinistra uberon UBERON:0007142 left internal carotid artery An internal carotid artery that branching_part_of a left common carotid artery plus branches. OBOL:automatic arteria caritis interna sinistra FMA:4062 An internal carotid artery that branching_part_of a right common carotid artery plus branches. EMAPA:16330 FMA:3949 arteria carotis interna dextra uberon UBERON:0007143 right internal carotid artery An internal carotid artery that branching_part_of a right common carotid artery plus branches. OBOL:automatic arteria carotis interna dextra FMA:3949 An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx). EMAPA:16748 FMA:85540 embryo tail tail of embryo uberon embryonic tail UBERON:0007144 embryonic post-anal tail An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. embryo tail FMA:85540 tail of embryo FMA:85540 embryonic tail FMA:85540 An anatomical cavity that surrounded_by a midgut. EMAPA:18377 FMA:54366 midgut lumen uberon UBERON:0007147 lumen of midgut An anatomical cavity that surrounded_by a midgut. OBOL:automatic midgut lumen FMA:54366 An anatomical cavity that surrounded_by a hindgut. EMAPA:18396 FMA:54367 hindgut lumen uberon UBERON:0007148 lumen of hindgut An anatomical cavity that surrounded_by a hindgut. OBOL:automatic hindgut lumen FMA:54367 An anatomical cavity that surrounded_by a anal canal. EMAPA:18836 FMA:17357 anal canal lumen uberon UBERON:0007158 lumen of anal canal An anatomical cavity that surrounded_by a anal canal. OBOL:automatic anal canal lumen FMA:17357 An anatomical cavity that surrounded_by a colon. EMAPA:18945 FMA:18374 colon lumen uberon colonic lumen UBERON:0007159 lumen of colon An anatomical cavity that surrounded_by a colon. OBOL:automatic colon lumen FMA:18374 colonic lumen FMA:18374 EMAPA:25124 FMA:23797 scapular border uberon UBERON:0007171 border of scapula scapular border FMA:23797 The medial border of the scapula (vertebral border, medial margin) is the longest of the three borders, and extends from the medial to the inferior angle. It is arched, intermediate in thickness between the superior and the axillary borders, and the portion of it above the spine forms an obtuse angle with the part below. This border presents an anterior and a posterior lip, and an intermediate narrow area. The anterior lip affords attachment to the Serratus anterior; the posterior lip, to the Supraspinatus above the spine, the Infraspinatus below; the area between the two lips, to the Levator scapulC& above the triangular surface at the commencement of the spine, to the Rhomboideus minor on the edge of that surface, and to the Rhomboideus major below it; this last is attached by means of a fibrous arch, connected above to the lower part of the triangular surface at the base of the spine, and below to the lower part of the border. consider merging with UBERON:1500000 scapular blade, depending on https://github.com/obophenotype/uberon/issues/339. See also http://www.ncbi.nlm.nih.gov/pubmed/20136669 EMAPA:25127 FMA:23242 margo medialis (scapula) margo medialis scapulae medial part of scapula vertebral border of scapula uberon medial border of the scapula medial margin of the scapula vertebral border vertebral border of the scapula UBERON:0007174 medial border of scapula EMAPA-modified The medial border of the scapula (vertebral border, medial margin) is the longest of the three borders, and extends from the medial to the inferior angle. It is arched, intermediate in thickness between the superior and the axillary borders, and the portion of it above the spine forms an obtuse angle with the part below. This border presents an anterior and a posterior lip, and an intermediate narrow area. The anterior lip affords attachment to the Serratus anterior; the posterior lip, to the Supraspinatus above the spine, the Infraspinatus below; the area between the two lips, to the Levator scapulC& above the triangular surface at the commencement of the spine, to the Rhomboideus minor on the edge of that surface, and to the Rhomboideus major below it; this last is attached by means of a fibrous arch, connected above to the lower part of the triangular surface at the base of the spine, and below to the lower part of the border. margo medialis (scapula) FMA:23242 margo medialis scapulae FMA:23242 FMA:TA medial part of scapula FMA:23242 vertebral border of scapula FMA:23242 medial border of the scapula medial margin of the scapula vertebral border vertebral border of the scapula A lamina propria that is part of a colonic mucosa. EMAPA:27395 FMA:15657 MA:0003196 colonic lamina propria lamina propria mucosae of colon lamina propria of colonic mucosa lamina propria of colonic mucous membrane uberon UBERON:0007177 lamina propria of mucosa of colon A lamina propria that is part of a colonic mucosa. OBOL:automatic colonic lamina propria FMA:15657 lamina propria mucosae of colon FMA:15657 lamina propria of colonic mucosa FMA:15657 lamina propria of colonic mucous membrane FMA:15657 A serous membrane that is part of a uterine tube infundibulum. EMAPA:29903 FMA:18324 serosa of infundibulum of fallopian tube serosa of infundibulum of oviduct uberon UBERON:0007181 serosa of infundibulum of uterine tube A serous membrane that is part of a uterine tube infundibulum. OBOL:automatic serosa of infundibulum of fallopian tube FMA:18324 serosa of infundibulum of oviduct FMA:18324 A muscle layer that is part of a uterine tube infundibulum. EMAPA:31264 FMA:18336 muscle layer of infundibulum of fallopian tube muscle layer of infundibulum of oviduct muscularis of infundibulum of uterine tube uberon UBERON:0007182 muscle layer of infundibulum of uterine tube A muscle layer that is part of a uterine tube infundibulum. OBOL:automatic muscle layer of infundibulum of fallopian tube FMA:18336 muscle layer of infundibulum of oviduct FMA:18336 muscularis of infundibulum of uterine tube FMA:18336 A mesothelium that is part of a serous pericardium. BTO:0003157 EMAPA:16133 FMA:18149 mesothelium of pericardium pericardial mesothelium serous pericardium mesothelium uberon UBERON:0007188 mesothelium of serous pericardium A mesothelium that is part of a serous pericardium. OBOL:automatic mesothelium of pericardium FMA:18149 pericardial mesothelium FMA:18149 serous pericardium mesothelium FMA:18149 The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis. CALOHA:TS-0085 FMA:21426 bone marrow stroma uberon UBERON:0007195 stroma of bone marrow The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis. bone marrow stroma FMA:21426 The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. UBERON:0004102 FMA:7393 NCIT:C117875 arbor tracheobronchialis uberon tracheobronchial system UBERON:0007196 tracheobronchial tree Wikipedia The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. arbor tracheobronchialis FMA:7393 FMA:TA tracheobronchial system HP:0005607 multicellular organism that can produce both male and female gametes. AAO:0010035 BILA:0000029 CARO:0000029 HAO:0000029 TADS:0000601 WBbt:0007849 uberon dioecious organism hermaphrodite UBERON:0007197 hermaphroditic organism multicellular organism that can produce both male and female gametes. dioecious organism BILA:0000029 hermaphrodite WBbt:0007849 The vasculature consisting of brachiocephalic arteries and veins. uberon UBERON:0007204 brachiocephalic vasculature The vasculature consisting of brachiocephalic arteries and veins. Mesenchyme that develops_from a cranial neural crest. EFO:0003572 EHDAA2:0000735 EMAPA:16169 EMAPA:16271 EMAPA_RETIRED:16271 TAO:0000787 ZFA:0000787 head mesenchyme from cranial neural crest head mesenchyme from neural crest head neural crest derived mesenchyme uberon UBERON:0007213 mesenchyme derived from head neural crest ZFA Mesenchyme that develops_from a cranial neural crest. OBOL:automatic head mesenchyme from neural crest EHDAA2:0000735 Mesenchyme that develops_from a trunk neural crest. EHDAA2:0002093 EMAPA:16182 TAO:0000999 ZFA:0000999 trunk mesenchyme from neural crest trunk neural crest derived mesenchyme uberon UBERON:0007214 mesenchyme derived from trunk neural crest Mesenchyme that develops_from a trunk neural crest. OBOL:automatic trunk mesenchyme from neural crest EHDAA2:0002093 An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. EV:0300011 EVM:2990031 FBdv:00005333 FMA:63631 MIAA:0000399 MmusDv:0000031 OGES:000023 embryo late (growth) stage fetal stage fetus fetus stage uberon embryo late growth stage embryo late stage UBERON:0007220 late embryonic stage https://github.com/obophenotype/uberon/issues/355 https://github.com/obophenotype/uberon/issues/565 An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. BGEE:ANiknejad embryo late (growth) stage MIAA:0000399 fetal stage fetus MIAA:0000399 fetus stage embryo late growth stage BTO:0000449 embryo late stage BTO:0000449 relationship to Meckel's cartilage to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000031 EHDAA:583 EMAPA:16382 VHOG:0000510 ventral pharyngeal arch 1 uberon ventral mandibular arch ventral visceral arch 1 UBERON:0007237 1st arch mandibular component EHDAA2 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000510 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) ventral pharyngeal arch 1 VHOG:0000510 ventral mandibular arch VHOG:0000510 ventral visceral arch 1 VHOG:0000510 relationship to palatoquadrate to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000038 EHDAA:595 EMAPA:16388 VHOG:0000511 uberon UBERON:0007238 1st arch maxillary component EHDAA2 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000511 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) A tunica media that is part of a artery. EMAPA:36294 EV:0100029 FMA:14273 NCIT:C49321 UMLS:C1710627 arterial media tunica media (arteriae) uberon UBERON:0007239 tunica media of artery A tunica media that is part of a artery. OBOL:automatic UMLS:C1710627 ncithesaurus:Venous_System_Smooth_Muscle_Tissue arterial media EV:0100029 tunica media (arteriae) FMA:14273 A tunica adventitia that is part of a artery. EMAPA:36295 EV:0100030 FMA:14274 arterial adventitia tunica externa (adventitia)(arteriae) uberon UBERON:0007240 tunica adventitia of artery A tunica adventitia that is part of a artery. OBOL:automatic arterial adventitia EV:0100030 tunica externa (adventitia)(arteriae) FMA:14274 A tunica adventitia that is part of a vein. EMAPA:36310 EV:0100034 FMA:14355 tunica externa (adventitia)(venae) venous adventitia uberon UBERON:0007241 tunica adventitia of vein A tunica adventitia that is part of a vein. OBOL:automatic tunica externa (adventitia)(venae) FMA:14355 venous adventitia EV:0100034 A tunica intima that is part of a vein. EMAPA:36308 EV:0100032 FMA:14353 tunica interna (intima)(venae) venous intima uberon UBERON:0007242 tunica intima of vein A tunica intima that is part of a vein. OBOL:automatic tunica interna (intima)(venae) FMA:14353 venous intima EV:0100032 A tunica media that is part of a vein. EMAPA:36309 EV:0100033 FMA:14354 tunica media (venae) venous media uberon UBERON:0007243 tunica media of vein A tunica media that is part of a vein. OBOL:automatic tunica media (venae) FMA:14354 venous media EV:0100033 Gray matter of the central nervous system which is a collection of clustered nuclei. FMA:256381 FMA:84059 uberon cluster of neural nuclei neural nuclei nuclear complex UBERON:0007245 nuclear complex of neuraxis Gray matter of the central nervous system which is a collection of clustered nuclei. Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future. FMA:72246 superior olivary complex nucleus uberon UBERON:0007247 nucleus of superior olivary complex Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. superior olivary complex nucleus FMA:72246 An intervertebral disk that is part of a cervical region of vertebral column. A cervical intervertebral disk connects at least one cervical vertebra, either to another cervical vertebra, or at one point on the vertebral colummn, to a thoracic vertebra EMAPA:19415 FMA:13895 cervical intervertebral disc intervertebral disc of cervical region uberon UBERON:0007252 intervertebral disk of cervical vertebra An intervertebral disk that is part of a cervical region of vertebral column. A cervical intervertebral disk connects at least one cervical vertebra, either to another cervical vertebra, or at one point on the vertebral colummn, to a thoracic vertebra cervical intervertebral disc FMA:13895 intervertebral disc of cervical region EMAPA:19415 An intervertebral disk that is part of a thoracic region of vertebral column. A thoracic intervertebral disk connects at least one thoracic vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a lumbar vertebra EMAPA:19489 FMA:10455 intervertebral disc of thoracic region uberon UBERON:0007254 intervertebral disk of thoracic vertebra An intervertebral disk that is part of a thoracic region of vertebral column. A thoracic intervertebral disk connects at least one thoracic vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a lumbar vertebra intervertebral disc of thoracic region EMAPA:19489 An intervertebral disk that is part of a lumbar region of vertebral column. A lumbar intervertebral disk connects at least one lumbar vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a sacral vertebra EMAPA:19468 FMA:13894 intervertebral disc of lumbar region uberon UBERON:0007255 intervertebral disk of lumbar vertebra An intervertebral disk that is part of a lumbar region of vertebral column. A lumbar intervertebral disk connects at least one lumbar vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a sacral vertebra intervertebral disc of lumbar region EMAPA:19468 A pre-cartilage condensation that is part of a trachea. EHDAA2:0002070 EHDAA:7082 uberon UBERON:0007267 trachea pre-cartilage rings A pre-cartilage condensation that is part of a trachea. OBOL:automatic Any collection of muscles that is part of a pectoral appendage. currently defined by location rather than attachment EFO:0003540 TAO:0000563 ZFA:0000563 pectoral fin muscle pectoral fin musculature uberon UBERON:0007269 pectoral appendage musculature Any collection of muscles that is part of a pectoral appendage. OBOL:automatic pectoral fin muscle ZFA:0000563 pectoral fin musculature ZFA:0000563 Any collection of muscles that is part of a pelvic appendage. currently defined by location rather than attachment Musculature that is part of the pelvic fin.[TAO] TAO:0000258 ZFA:0000258 pelvic fin musculature uberon UBERON:0007270 pelvic appendage musculature Any collection of muscles that is part of a pelvic appendage. OBOL:automatic Musculature that is part of the pelvic fin.[TAO] 2012-08-14 TAO:0000258 TAO TAO:curator pelvic fin musculature ZFA:0000258 Any collection of muscles that is part of an appendage. currently defined by location rather than attachment TAO:0000207 ZFA:0000207 fin musculature uberon UBERON:0007271 appendage musculature Any collection of muscles that is part of an appendage. OBOL:automatic fin musculature ZFA:0000207 Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. VSAO:0005000 uberon cheiropterygium UBERON:0007272 pectoral appendage skeleton VSAO Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle. VSAO:0005000 VSAO:NI cheiropterygium VSAO:0005000 VSAO:NI The collection of all skeletal elements in a pelvic appendage region. uberon UBERON:0007273 pelvic appendage skeleton VSAO The collection of all skeletal elements in a pelvic appendage region. The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. TODO - unify naming conventions The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. BAMS:HB CALOHA:TS-2118 EFO:0003440 EHDAA2:0001630 FMA:295640 TAO:0000569 ZFA:0000569 presumptive rhombencephalon uberon embryonic rhombencephalon future hindbrain rhombencephalon UBERON:0007277 presumptive hindbrain XAO-abduced cjm The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. NPX:PDR presumptive rhombencephalon ZFA:0000569 embryonic rhombencephalon CALOHA:TS-2118 future hindbrain rhombencephalon EHDAA2:0001630 Portion of tissue that is part of the heart tube and will become the sinus venosus. TAO:0002234 ZFA:0001722 uberon UBERON:0007278 presumptive sinus venosus ZFA Portion of tissue that is part of the heart tube and will become the sinus venosus. ZFA:0001722 A presumptive structure that has the potential to develop into a endocardium. Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] TAO:0002233 ZFA:0001724 uberon UBERON:0007280 presumptive endocardium A presumptive structure that has the potential to develop into a endocardium. OBOL:automatic Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] 2012-08-14 TAO:0002233 TAO ZFIN:curator Embryonic structure that gives rise to the midbrain hindbrain boundary. EFO:0003446 TAO:0001187 XAO:0004086 ZFA:0001187 presumptive MHB presumptive midbrain-hindbrain boundary uberon UBERON:0007281 presumptive midbrain hindbrain boundary ZFA Embryonic structure that gives rise to the midbrain hindbrain boundary. ZFA:0001187 presumptive MHB presumptive midbrain-hindbrain boundary ZFA:0001187 A presumptive structure that has the potential to develop into a presomitic mesoderm. EFO:0003421 TAO:0000053 ZFA:0000053 uberon presumptive segmental plates UBERON:0007282 presumptive segmental plate https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 A presumptive structure that has the potential to develop into a presomitic mesoderm. OBOL:automatic presumptive segmental plates ZFA:0000053 A presumptive structure that has the potential to develop into a neural plate. consider merging Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 prospective neuroectoderm prospective vegetal ectoderm uberon UBERON:0007284 presumptive neural plate A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic Region of the gastrula which gives rise to the neural plate.[TAO] 2012-08-14 TAO:0000063 TAO ZFIN:curator prospective neuroectoderm ZFA:0000063 prospective vegetal ectoderm ZFA:0000063 The part of the blastula that has the potential to develop into a paraxial mesoderm. EFO:0003443 TAO:0000591 XAO:0004134 ZFA:0000591 future paraxial mesenchyme future paraxial mesoderm uberon UBERON:0007285 presumptive paraxial mesoderm The part of the blastula that has the potential to develop into a paraxial mesoderm. UBERON:cjm future paraxial mesenchyme UBERON:cjm A presumptive structure that has the potential to develop into a forebrain-midbrain boundary. EFO:0003463 TAO:0001368 ZFA:0001368 uberon UBERON:0007288 presumptive forebrain midbrain boundary A presumptive structure that has the potential to develop into a forebrain-midbrain boundary. OBOL:automatic A presumptive structure that has the potential to develop into a pronephric mesoderm. EFO:0003619 TAO:0001070 ZFA:0001070 nephron primordium uberon UBERON:0007297 presumptive pronephric mesoderm A presumptive structure that has the potential to develop into a pronephric mesoderm. OBOL:automatic nephron primordium ZFA:0001070 A blood vessel that is part of a pectoral appendage. TAO:0005301 ZFA:0005301 pectoral fin blood vessel uberon UBERON:0007300 pectoral appendage blood vessel A blood vessel that is part of a pectoral appendage. OBOL:automatic pectoral fin blood vessel ZFA:0005301 A blood vessel that is part of a limb/fin. TAO:0005299 ZFA:0005299 fin blood vessel limb blood vessel uberon UBERON:0007301 appendage blood vessel A blood vessel that is part of a limb/fin. OBOL:automatic fin blood vessel ZFA:0005299 limb blood vessel A vasculature that is part of a pectoral appendage. TAO:0005096 ZFA:0005096 pectoral fin vasculature uberon UBERON:0007302 pectoral appendage vasculature A vasculature that is part of a pectoral appendage. OBOL:automatic pectoral fin vasculature ZFA:0005096 A vasculature that is part of a chordate pharynx. TAO:0005003 ZFA:0005003 branchial vasculature uberon UBERON:0007303 pharyngeal vasculature A vasculature that is part of a chordate pharynx. OBOL:automatic branchial vasculature ZFA:0005003 A vasculature that is part of a limb/fin. TAO:0005095 ZFA:0005095 fin vasculature uberon UBERON:0007304 appendage vasculature A vasculature that is part of a limb/fin. OBOL:automatic fin vasculature ZFA:0005095 A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans. TODO - check In mice many lobules lack islets, in contrast to other mammals including humans EMAPA:37710 FMA:16012 MA:0000721 lobulus pancreaticus pancreas lobe pancreatic lobule uberon UBERON:0007324 pancreatic lobule A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans. ISBN:0123813611 EMAPA:37710 MA:th lobulus pancreaticus FMA:16012 pancreas lobe MA:0000721 pancreatic lobule FMA:16012 A duct that collects and carries secretions of the exocrine pancreas to the intestine. this class groups together accessory (dorsal) and main (ventral) pancreatic ducts Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms EHDAA:9194 EMAPA:32952 FMA:10419 MA:0000124 TAO:0001372 VHOG:0000254 ZFA:0001372 duct of pancreas pancreas duct uberon ductus pancreaticus UBERON:0007329 pancreatic duct http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png ZFA MA A duct that collects and carries secretions of the exocrine pancreas to the intestine. GOC:cvs GOC:ymb ORCiD:0000-0002-2244-7917 ORCiD:0000-0002-9900-7880 Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000254 VHOG These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] 2012-09-17 VHOG:0000254 VHOG DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005) in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms EHDAA2 duct of pancreas OBOL:accepted pancreas duct OBOL:accepted ductus pancreaticus An anatomical surface that is part of a tongue. FMA:54647 tongue surface uberon UBERON:0007367 surface of tongue An anatomical surface that is part of a tongue. OBOL:automatic tongue surface FMA:54647 The upper (superior) side of the tongue. check superior/dorsal FMA:54646 dorsal surface of tongue uberon UBERON:0007371 superior surface of tongue The upper (superior) side of the tongue. dorsal surface of tongue FMA:54646 The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. this grouping class exists primarily to align with GO - see GO:0008544. BSA:0000073 BTO:0000313 FBbt:00004993 HAO:0000298 TADS:0000109 WBbt:0005733 epidermis epidermis (sensu Metazoa) outer epidermal layer outer epithelial layer uberon hypoderm hypodermis UBERON:0007376 outer epithelium The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. GO:0008544 epidermis GO:0008544 hypoderm BTO:0000313 hypodermis GO:0008544 WBbt:0005733 The yellow spheroidal mass of stored food that forms the inner portion of the egg of a bird or reptile and is surrounded by the white. egg yolk http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0215 egg yolk egg (with shell) The hard-shelled reproductive body produced by a bird and especially by the common domestic chicken; also: its contents used as food. whole egg in shell http://langual.org Note that this is cross referenced to both LanguaL "egg" as well as "whole egg in shell" http://www.langual.org/langual_thesaurus.asp?termid=C0128 http://www.langual.org/langual_thesaurus.asp?termid=C0274 LanguaL curation note: The egg shell functions as a container. Therefore, the physical state of a raw egg in the shell is *LIQUID, HIGH VISCOSITY, WITH NO VISIBLE PARTICLES*. shelled egg Outermost layer of cells surrounding the embryo. Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm. EFO:0003425 TAO:0000086 ZFA:0000086 EVL enveloping layer uberon UBERON:0007383 enveloping layer of ectoderm Outermost layer of cells surrounding the embryo. Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000086 TAO ZFIN:curator relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] 2012-08-14 TAO:0000086 TAO EVL ZFA:0000086 enveloping layer ZFIN:ZDB-PUB-961014-576 A lymphatic vessel that is part of a limb/fin. TAO:0005300 ZFA:0005300 uberon UBERON:0007384 appendage lymph vessel A lymphatic vessel that is part of a limb/fin. OBOL:automatic A lymphatic vessel that is part of a pectoral appendage. TAO:0005302 ZFA:0005302 uberon UBERON:0007385 pectoral appendage lymph vessel A lymphatic vessel that is part of a pectoral appendage. OBOL:automatic A lymphatic vessel that is part of a pelvic appendage. uberon UBERON:0007386 pelvic appendage lymph vessel A lymphatic vessel that is part of a pelvic appendage. OBOL:automatic A cartilage tissue that is part of a paired limb or fin. Cartilage which is part of one of the paired fins.[TAO] TAO:0001543 ZFA:0001543 uberon UBERON:0007389 paired limb/fin cartilage A cartilage tissue that is part of a paired limb or fin. Cartilage which is part of one of the paired fins.[TAO] 2012-08-14 TAO:0001543 TAO ZFIN:curator A cartilage tissue that is part of a pectoral appendage. Cartilage which is part of the pectoral fin.[TAO] TAO:0000257 ZFA:0000257 uberon pectoral fin cartilage UBERON:0007390 pectoral appendage cartilage tissue A cartilage tissue that is part of a pectoral appendage. OBOL:automatic Cartilage which is part of the pectoral fin.[TAO] 2012-08-14 TAO:0000257 TAO ZFIN:curator pectoral fin cartilage TAO:0000257 A cartilage tissue that is part of a pelvic appendage. Cartilage which is part of the pelvic fin.[TAO] TAO:0001459 ZFA:0001459 uberon pelvic fin cartilage UBERON:0007391 pelvic appendage cartilage tissue A cartilage tissue that is part of a pelvic appendage. OBOL:automatic Cartilage which is part of the pelvic fin.[TAO] 2012-08-14 TAO:0001459 TAO ZFIN:curator pelvic fin cartilage TAO:0001459 A nucleus of brain that spans a midbrain tegmentum. this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species UBERON:0012277 FMA:258768 ZFA:0005577 tegmental nuclei tegmental nucleus uberon UBERON:0007414 nucleus of midbrain tegmentum A nucleus of brain that spans a midbrain tegmentum. OBOL:automatic tegmental nuclei tegmental nucleus ZFA:0005577 The space within an epithelial sphere. EHDAA2:0003079 AEO:0000079 cavity of vesicle uberon UBERON:0007473 lumen of epithelial sac The space within an epithelial sphere. AEO:JB cavity of vesicle AEO:0000079 An epithelial tube that is open at one end only. AEO:0000115 EHDAA2:0003115 uberon UBERON:0007499 epithelial sac AEO An epithelial tube that is open at one end only. AEO:JB UBERONREF:0000001 An epithelial tube open at both ends that allows fluid flow. AEO_RETIRED:0000116 RETIRED_EHDAA2:0003116 uberon UBERON:0007500 epithelial tube open at both ends AEO An epithelial tube open at both ends that allows fluid flow. AEO:JB UBERONREF:0000001 A collection of connected epithelial tubes with a single portal. EHDAA2:0003117 AEO:0000117 EHDAA2:0003117 arborising epithelial duct system uberon UBERON:0007501 arborizing epithelial duct system AEO AEO A collection of connected epithelial tubes with a single portal. AEO:JB UBERONREF:0000001 arborising epithelial duct system AEO:0000117 A closed epithelium with a lumen. EHDAA2:0003119 AEO:0000119 EHDAA2:0003119 uberon UBERON:0007503 epithelial vesicle AEO A closed epithelium with a lumen. AEO:JB A ring of smooth muscle cells whose contraction closes the opening of the ring. AEO:0000143 EHDAA2:0003143 uberon UBERON:0007521 smooth muscle sphincter A ring of smooth muscle cells whose contraction closes the opening of the ring. AEO:JB Mesenchyme with little extracellular matrix. EHDAA2:0003146 AEO:0000146 EHDAA2:0003146 uberon UBERON:0007524 dense mesenchyme tissue AEO Mesenchyme with little extracellular matrix. AEO:JB Mesenchyme whose cells are embedded in obvious amounts of extracellular matrix. EHDAA2:0003151 AEO:0000151 EHDAA2:0003151 uberon UBERON:0007529 loose mesenchyme tissue AEO Mesenchyme whose cells are embedded in obvious amounts of extracellular matrix. AEO:JB Mesenchymal cells that are migrating. this class will be an important part of the NC reorganization EHDAA2:0003152 AEO:0000152 EHDAA2:0003152 uberon UBERON:0007530 migrating mesenchyme population Mesenchymal cells that are migrating. AEO:JB A ciliated columnar epithelium that is part of a oviduct. in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA:62016 MA:0001719 uberon epithelium of uterine tube uterine tube epithelium UBERON:0007589 ciliated columnar oviduct epithelium MA FMA A ciliated columnar epithelium that is part of a oviduct. OBOL:automatic in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label FMA epithelium of uterine tube FMA:62016 uterine tube epithelium FMA:62016 A cuboidal epithelium that is part of a oviduct. MA:0001720 uberon UBERON:0007590 cuboidal oviduct epithelium MA A cuboidal epithelium that is part of a oviduct. OBOL:automatic Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html] FMA:64798 uberon UBERON:0007592 ciliated columnar epithelium FMA Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] FMA:64798 Epithelium bearing vibratile cilia on the free surface. uberon UBERON:0007601 ciliated epithelium Epithelium bearing vibratile cilia on the free surface. Stratified columnar epithelia is a rare type of epithelial tissue composed of column shaped cells arranged in multiple layers. Stratified columnar epithelia are found in the ocular conjunctiva of the eye, in parts of the pharynx and anus, the female's uterus, the male urethra and vas deferens. Also found in intralobular ducts in salivary glands.[WP] FMA:45564 NCIT:C33620 UMLS:C0836132 epithelium stratificatum columnare uberon UBERON:0007602 stratified columnar epithelium FMA Stratified columnar epithelia is a rare type of epithelial tissue composed of column shaped cells arranged in multiple layers. Stratified columnar epithelia are found in the ocular conjunctiva of the eye, in parts of the pharynx and anus, the female's uterus, the male urethra and vas deferens. Also found in intralobular ducts in salivary glands.[WP] UMLS:C0836132 ncithesaurus:Stratified_Columnar_Epithelium epithelium stratificatum columnare FMA:45564 A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 CALOHA:TS-0998 FMA:66762 synovium stratum synoviale synovial layer synovial membrane uberon synovial tissue UBERON:0007616 layer of synovial tissue BTO A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 synovium CALOHA:TS-0998 stratum synoviale FMA:TA synovial layer FMA:66762 synovial membrane FMA:66762 synovial tissue BTO:0001338 An anatomical cavity that surrounded_by a synovial joint. FMA:11356 articular cavity (synovial joint) cavitas articularis (junctura synovialis) cavity of synovial joint uberon joint cavity synovial cavity UBERON:0007617 synovial cavity of joint An anatomical cavity that surrounded_by a synovial joint. OBOL:automatic articular cavity (synovial joint) FMA:11356 cavitas articularis (junctura synovialis) FMA:11356 cavity of synovial joint FMA:11356 joint cavity FMA:11356 synovial cavity FMA:11356 A synovial cavity of joint that is part of a hip joint. EMAPA:19021 FMA:9701 uberon UBERON:0007618 synovial cavity of hip joint FMA A synovial cavity of joint that is part of a hip joint. OBOL:automatic epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. GAID:907 MESH:D010857 uberon eye pigment epithelium UBERON:0007625 pigment epithelium of eye epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. MP:0005200 eye pigment epithelium MESH:A09.371.670 A neural nucleus that is part of a medulla oblongata. FMA:258772 uberon UBERON:0007635 nucleus of medulla oblongata A neural nucleus that is part of a medulla oblongata. OBOL:automatic The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. BIRNLEX:4096 BM:V CALOHA:TS-2077 DHBA:266441713 FMA:71248 HBA:9203 UMLS:C0040999 trigeminal nuclei uberon nuclei trigemini UBERON:0007641 trigeminal nuclear complex http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png FMA FMA The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. MA UMLS:C0040999 BIRNLEX:4096 trigeminal nuclei FMA:71248 nuclei trigemini A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes FMA:12772 NCIT:C33769 UMLS:C0229745 lymph node of thorax uberon deep thoracic lymph node UBERON:0007644 thoracic lymph node A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes OBOL:automatic UMLS:C0229745 ncithesaurus:Thoracic_Lymph_Node lymph node of thorax FMA:12772 deep thoracic lymph node FMA:12772 A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx. decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d UBERON:0004065 EHDAA2:0004453 primary meninx uberon meninx primitiva primitive meninx primordial meninx UBERON:0007645 future meninx EHDAA2 ISBN:0073040584 A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx. the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d MP:0009726 primary meninx EHDAA2:0004453 meninx primitiva MP:0009726 The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx. future leptomeninges future leptomeninx uberon UBERON:0007646 endomeninx ISBN:9781607950325 The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx. ISBN:9781607950325 The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer). UBERON:0010115 EHDAA2:0004317 future dura mater uberon UBERON:0007647 ectomeninx ISBN:9781607950325 The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer). ISBN:9781607950325 future dura mater EHDAA2:0004317 2 An anatomical structure that connects two structures junction FMA:5898 anatomical junction uberon UBERON:0007651 anatomical junction FMA An anatomical structure that connects two structures A sphincter that is part of an esophagus. check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here uberon UBERON:0007652 esophageal sphincter A sphincter that is part of an esophagus. functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule. FMA:17691 uberon UBERON:0007684 uriniferous tubule functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule. ISBN:0073040584 region of the embryo into the area in which the kidney rudiment will develop. uberon kidney anlage UBERON:0007687 kidney field region of the embryo into the area in which the kidney rudiment will develop. GO:0072004 GOC:mtg_kidney_jan10 kidney anlage GOC:mtg_kidney_jan10 Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. field AEO:0000170 EFO:0001649 EHDAA2:0003170 FBbt:00005426 developmental field uberon future organ organ field UBERON:0007688 anlage FBbt AEO FBbt Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. FBbt:00005426 JB:DEF endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]. uberon diverticulum thyroideum saccus thyroideus UBERON:0007689 thyroid diverticulum VHOG endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]. MP:0004662 diverticulum thyroideum saccus thyroideus . EFO:0003626 EHDAA2:0001457 EHDAA:962 EMAPA:32754 FMA:293087 TAO:0001104 ZFA:0001104 early pharyngeal arch endoderm uberon pharyngeal arch endoderm pharyngeal endoderm pharyngeal region endoderm UBERON:0007690 relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' early pharyngeal endoderm cjm . early pharyngeal arch endoderm EHDAA2:0001457 pharyngeal endoderm ZFA:0001104 pharyngeal region endoderm EHDAA2:0001456 The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. FMA:63589 NCIT:C33738 UMLS:C0226971 porus gustatorius taste pore uberon UBERON:0007691 gustatory pore Taste:bud.svg FMA FMA The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. UMLS:C0226971 ncithesaurus:Taste_Pore porus gustatorius taste pore FMA:63589 A nucleus of brain that is part of a thalamus. TODO - consider splitting nucleus and complex BTO:0002452 EMAPA:35859 FMA:256693 MA:0002992 thalamic nucleus uberon nuclear complex of thalamus UBERON:0007692 nucleus of thalamus A nucleus of brain that is part of a thalamus. OBOL:automatic thalamic nucleus MA:0002992 nuclear complex of thalamus FMA:256693 A bone that is part of a reproductive organ. baculum uberon os penis/os clitoris UBERON:0007719 bone of reproductive organ A bone that is part of a reproductive organ. OBOL:automatic 2 2 The interphalangeal articulations of the foot (articulations of the phalanges) are ginglymoid joints, and each has a plantar and two collateral ligaments. The arrangement of these ligaments is similar to that in the metatarsophalangeal articulations: the Extensor tendons supply the places of dorsal ligaments. EMAPA:36337 FMA:35225 MESH:D014033 NCIT:C32867 NCIT:C33789 UMLS:C0040356 foot interphalangeal joint hindlimb digit inter-phalangeal joint interphalangeal joint of foot interphalangeal joint of toe uberon toe joint UBERON:0007721 interphalangeal joint of pes two in series The interphalangeal articulations of the foot (articulations of the phalanges) are ginglymoid joints, and each has a plantar and two collateral ligaments. The arrangement of these ligaments is similar to that in the metatarsophalangeal articulations: the Extensor tendons supply the places of dorsal ligaments. UMLS:C0040356 ncithesaurus:Interphalangeal_Joint_of_the_Foot foot interphalangeal joint MESH:A02.835.583.378.900 hindlimb digit inter-phalangeal joint EMAPA:36337 interphalangeal joint of foot FMA:35225 interphalangeal joint of toe FMA:35225 NCBITaxon:9606 toe joint MESH:A02.835.583.378.900 2 2 The interphalangeal articulations of hand are hinge-joints of the phalanges of the hand. There are two sets (except in the thumb): 'proximal interphalangeal joints' (PIP), those between the first (also called proximal) and second (intermediate) phalanges 'distal interphalangeal joints' (DIP), those between the second and third (distal) phalanges A similar group of articulations also function in the toes. consider renaming: 'finger' is ambiguous as the term in some usages excludes the thumb (we include it) EMAPA:36336 FMA:35285 NCIT:C32868 UMLS:C0016125 articulationes digitorum manus articulationes interphalangeae manus interphalangeal joint of hand interphalangeal joint of finger uberon IP joint articulations of the digits interphalangeal articulations of hand interphalangeal joints of hand UBERON:0007722 interphalangeal joint of manus two in series The interphalangeal articulations of hand are hinge-joints of the phalanges of the hand. There are two sets (except in the thumb): 'proximal interphalangeal joints' (PIP), those between the first (also called proximal) and second (intermediate) phalanges 'distal interphalangeal joints' (DIP), those between the second and third (distal) phalanges A similar group of articulations also function in the toes. UMLS:C0016125 ncithesaurus:Interphalangeal_Joint_of_the_Hand articulationes digitorum manus articulationes interphalangeae manus interphalangeal joint of hand FMA:35285 interphalangeal joint of finger FMA:35285 NCBITaxon:9606 IP joint FMA:35285 articulations of the digits interphalangeal articulations of hand interphalangeal joints of hand 2 2 An interphalangeal joint of manus that is part of a manual digit 1. in humans, this connects proximal and distal phalanges of the thumb, so there is only a single inter-phalangeal joint - i.e. there is no distinct proximal and distal joints EMAPA:25058 FMA:35312 NCIT:C102306 interphalangeal joint of first digit of hand interphalangeal joint of hand digit 1 interphalangeal joint of manual digit 1 interphalangeal joint of manual digit I interphalangeal joint of pollex interphalangeal joint of thumb uberon UBERON:0007723 interphalangeal joint of manual digit 1 An interphalangeal joint of manus that is part of a manual digit 1. OBOL:automatic interphalangeal joint of first digit of hand FMA:35312 interphalangeal joint of manual digit I interphalangeal joint of thumb FMA:35312 NCBITaxon:9606 2 2 An interphalangeal joint of pes that is part of a pedal digit 1. EMAPA:26430 FMA:35353 interphalangeal joint of first digit of foot interphalangeal joint of first digit of pes interphalangeal joint of foot digit 1 interphalangeal joint of great toe interphalangeal joint of hallux interphalangeal joint of pedal digit 1 interphalangeal joint of pedal digit I interphalangeal joint of big toe uberon interphalangeal joint of first toe UBERON:0007724 interphalangeal joint of pedal digit 1 An interphalangeal joint of pes that is part of a pedal digit 1. OBOL:automatic interphalangeal joint of first digit of foot FMA:35353 interphalangeal joint of first digit of pes FMA:35353 interphalangeal joint of great toe FMA:35353 interphalangeal joint of pedal digit I interphalangeal joint of big toe FMA:35353 NCBITaxon:9606 interphalangeal joint of first toe FMA:35353 2 2 An interphalangeal joint of pes that is part of a pedal digit 5. EMAPA:26478 FMA:35365 interphalangeal joint of fifth digit of foot interphalangeal joint of fifth toe interphalangeal joint of pedal digit V interphalangeal joint of little toe uberon UBERON:0007728 interphalangeal joint of pedal digit 5 An interphalangeal joint of pes that is part of a pedal digit 5. OBOL:automatic interphalangeal joint of fifth digit of foot FMA:35365 interphalangeal joint of fifth toe FMA:35365 interphalangeal joint of pedal digit V interphalangeal joint of little toe FMA:35365 NCBITaxon:9606 2 2 An interphalangeal joint of manus that is part of a manual digit 5. EMAPA:25070 FMA:35407 interphalangeal joint of fifth digit of hand interphalangeal joint of fifth finger interphalangeal joint of manual digit V interphalangeal joint of little finger uberon UBERON:0007732 interphalangeal joint of manual digit 5 An interphalangeal joint of manus that is part of a manual digit 5. OBOL:automatic interphalangeal joint of fifth digit of hand FMA:35407 interphalangeal joint of fifth finger FMA:35407 interphalangeal joint of manual digit V interphalangeal joint of little finger FMA:35407 NCBITaxon:9606 A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 1. EMAPA:25057 FMA:35249 metacarpophalangeal joint of digit 1 metacarpophalangeal joint of first digit of hand metacarpophalangeal joint of manual digit I metacarpo-phalangeal joint of digit 1 of fore-paw metacarpophalangeal joint of thumb uberon UBERON:0007735 metacarpophalangeal joint of manual digit 1 FMA A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 1. OBOL:automatic metacarpophalangeal joint of first digit of hand FMA:35249 metacarpophalangeal joint of manual digit I metacarpo-phalangeal joint of digit 1 of fore-paw EMAPA:25057 metacarpophalangeal joint of thumb FMA:35249 NCBITaxon:9606 A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 5. EMAPA:25069 FMA:35261 metacarpophalangeal joint of digit 5 metacarpophalangeal joint of fifth digit of hand metacarpophalangeal joint of fifth finger metacarpophalangeal joint of manual digit V metacarpo-phalangeal joint of digit 5 of fore-paw metacarpophalangeal joint of little finger uberon UBERON:0007747 metacarpophalangeal joint of manual digit 5 FMA A skeletal joint that connects a metacarpal bone and connects a proximal phalanx of manual digit 5. OBOL:automatic metacarpophalangeal joint of fifth digit of hand FMA:35261 metacarpophalangeal joint of fifth finger FMA:35261 metacarpophalangeal joint of manual digit V metacarpo-phalangeal joint of digit 5 of fore-paw EMAPA:25069 metacarpophalangeal joint of little finger FMA:35261 NCBITaxon:9606 A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 1. the name of the structure in EMAPA is incorrect EMAPA:26436 FMA:35228 NCIT:C102321 first metatarsophalangeal joint metatarsophalangeal joint of first digit of foot metatarsophalangeal joint of great toe metatarsophalangeal joint of pedal digit I metatarsophalangeal joint of big toe uberon metatarsophalangeal joint of first toe UBERON:0007750 metatarsophalangeal joint of pedal digit 1 FMA A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 1. OBOL:automatic the name of the structure in EMAPA is incorrect EMAPA metatarsophalangeal joint of first digit of foot FMA:35228 metatarsophalangeal joint of great toe FMA:35228 metatarsophalangeal joint of pedal digit I metatarsophalangeal joint of big toe FMA:35228 NCBITaxon:9606 metatarsophalangeal joint of first toe FMA:35228 A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 5. the name of the structure in EMAPA is incorrect EMAPA:26484 FMA:35240 metatarsophalangeal joint of fifth digit of foot metatarsophalangeal joint of fifth toe metatarsophalangeal joint of pedal digit V metatarsophalangeal joint of little toe uberon UBERON:0007762 metatarsophalangeal joint of pedal digit 5 FMA A skeletal joint that connects a metatarsal bone and connects a distal phalanx of pedal digit 5. OBOL:automatic the name of the structure in EMAPA is incorrect EMAPA metatarsophalangeal joint of fifth digit of foot FMA:35240 metatarsophalangeal joint of fifth toe FMA:35240 metatarsophalangeal joint of pedal digit V metatarsophalangeal joint of little toe FMA:35240 NCBITaxon:9606 A gland that is part of a epidermis. FMA:59153 epidermal gland gland of epidermis uberon UBERON:0007771 epidermis gland A gland that is part of a epidermis. OBOL:automatic gland of epidermis FMA:59153 Any portion of sweat that is produced by a sweat gland of the scrotum. FMA:73266 scrotum sweat sweat of scrotal sac sweat of scrotum uberon UBERON:0007772 scrotal sweat Any portion of sweat that is produced by a sweat gland of the scrotum. OBOL:automatic scrotum sweat OBOL:automatic sweat of scrotal sac OBOL:automatic sweat of scrotum FMA:73266 Any sweat gland that is part of a scrotum. EMAPA:29743 uberon UBERON:0007773 scrotal sweat gland Any sweat gland that is part of a scrotum. OBOL:automatic An endothelium that is part of a umbilical artery. BTO:0000857 uberon UBERON:0007778 umbilical artery endothelium BTO An endothelium that is part of a umbilical artery. OBOL:automatic Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces transudative characteristically low in protein and cellular content (unless there has been secondary concentration) FMA:12276 GAID:1195 MESH:D005122 ncithesaurus:Transudate uberon plasma ultrafiltrate UBERON:0007779 transudate Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces Any fluid produced by a serous gland. serous fluid serosal fluid serous gland fluid uberon UBERON:0007794 secretion of serous gland Any fluid produced by a serous gland. UBERON:cjm serosal fluid Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905 MA:0002718 NCIT:C33854 UMLS:C0489903 uberon Gefaesssystem@de UBERON:0007798 vascular system MA Anatomical system that consists of all blood and lymph vessels. The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. ncithesaurus:Vascular_System in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system MA UMLS:C0489903 ncithesaurus:Vascular_System Gefaesssystem@de BTO:0001085 A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord. TODO - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels BTO:0004705 NCIT:C34132 UMLS:C1516792 uberon UBERON:0007806 connecting stalk EHDAA2 EHDAA2 A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord. UMLS:C1516792 ncithesaurus:Connecting_Stalk A vasculature that is part of a connecting stalk. EHDAA2:0000313 connecting stalk blood vessels uberon connecting stalk blood vessel vasculature of connecting stalk UBERON:0007807 connecting stalk vasculature EHDAA2 A vasculature that is part of a connecting stalk. OBOL:automatic connecting stalk blood vessels EHDAA2:0000313 Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:TS-0002 EFO:0003771 uberon abdominal adipose tissue abdominal fat intra-abdominal fat UBERON:0007808 adipose tissue of abdominal region Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:paula MGI:csmith abdominal adipose tissue BTO:0004041 abdominal fat BTO:0004041 intra-abdominal fat BTO:0004041 The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. CALOHA:TS-2356 EV:0100009 FMA:280881 MA:0000006 NCIT:C12418 UMLS:C0460004 WikipediaCategory:Head_and_neck galen:HeadAndNeck uberon cephalic area cephalic part of animal cephalic region head and neck head or neck UBERON:0007811 craniocervical region MA The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. UMLS:C0460004 ncithesaurus:Head_and_Neck cephalic area cephalic part of animal cephalic region head and neck FMA:280881 A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton. Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO] Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO] present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species) AAO:0010338 EMAPA:16748 MA:0000008 NCIT:C77663 TAO:0001117 UMLS:C0039259 XAO:0003026 ZFA:0001117 muscular postanal tail postanal tail post-anal fin tail uberon post-vent region UBERON:0007812 post-anal tail A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton. Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO] 2012-06-20 AAO:0010338 AAO AAO:EJS Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO] 2012-08-14 TAO:0001117 TAO ZFIN:curator UMLS:C0039259 ncithesaurus:Tail post-anal fin tail post-vent region TAO:0001117 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). this encompasses non-skeletal tissue An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] UBERON:0007824 girdle girdle region EMAPA:37854 FMA:24874 VSAO:0000303 uberon fin girdle fin girdle region limb girdle limb girdle region UBERON:0007823 appendage girdle region An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). UBERONREF:0000003 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] 2012-08-14 VSAO:0000303 VSAO EMAPA:37854 MA:th fin girdle fin girdle region limb girdle limb girdle region Mesentery that is located in the peritoneum. FMA:20570 TAO:0005129 XAO:0000138 ZFA:0005129 uberon UBERON:0007826 peritoneal mesentery FMA Mesentery that is located in the peritoneum. UBERON:cjm External part of the nose containing the external nares. Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae[FMA:59515]. EMAPA:37831 FMA:59515 NCIT:C32566 UMLS:C0458561 uberon nose UBERON:0007827 external nose External part of the nose containing the external nares. Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae[FMA:59515]. FMA:59515 EMAPA:37831 MA:th UMLS:C0458561 ncithesaurus:External_Nose A bone that is part of a appendage girdle region. EMAPA:35379 MA:0000291 girdle bone uberon UBERON:0007828 girdle bone/zone A bone that is part of a appendage girdle region. OBOL:automatic girdle bone MA:0000291 A bone that is part of a pectoral girdle region. EMAPA:35669 MA:0000292 bone of pectoral girdle uberon UBERON:0007829 pectoral girdle bone MA A bone that is part of a pectoral girdle region. OBOL:automatic A bone element or fused bone that is part of pelvic girdle. check sacrum, coccyx (MA does NOT include these) typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone EMAPA:18028 MA:0000293 NCIT:C33287 UMLS:C0030786 bone of pelvic girdle pelvic girdle bone uberon UBERON:0007830 pelvic girdle bone/zone MA A bone element or fused bone that is part of pelvic girdle. UMLS:C0030786 ncithesaurus:Pelvic_Bone pelvic girdle bone MA:0000293 A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons. Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO] Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO] Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO] The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG] Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically. AAO:0000422 AAO:0000754 EFO:0000946 EHDAA2:0001420 FMA:24141 MAT:0000181 MIAA:0000181 NCIT:C33547 TAO:0000407 UMLS:C0427245 VHOG:0001156 VSAO:0000156 XAO:0003063 ZFA:0000407 skeletal parts of pectoral girdle skeleton of pectoral girdle uberon cingulum pectorale pectoral girdle scapular girdle UBERON:0007831 pectoral girdle skeleton http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons. Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO] 2012-08-14 TAO:0000407 TAO TAO:wd Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO] 2012-08-14 VSAO:0000156 VSAO Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO] 2012-06-20 AAO:0000422 AAO AAO:LAP The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG] 2012-09-17 VHOG:0001156 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18 Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically. VSAO UMLS:C0427245 ncithesaurus:Shoulder_Girdle skeletal parts of pectoral girdle skeleton of pectoral girdle cingulum pectorale pectoral girdle VSAO:0000156 scapular girdle TAO:0000407 Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts AAO:0000426 AAO:0000768 EFO:0000947 EHDAA2:0001426 EHDAA:7149 EHDAA:8324 EMAPA:18028 FMA:87592 MAT:0000182 MIAA:0000182 TAO:0000565 VHOG:0000305 VSAO:0000155 XAO:0003064 ZFA:0000565 galen:PelvicGirdle pelvic girdle skeleton skeletal parts of pelvic girdle skeleton of pelvic girdle uberon pelvic girdle UBERON:0007832 pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. VSAO:0000155 Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] 2012-06-20 AAO:0000426 AAO AAO:LAP Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] 2012-08-14 TAO:0000565 TAO TAO:wd Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] 2012-08-14 VSAO:0000155 VSAO The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] 2012-09-17 VHOG:0000305 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333 Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts VSAO pelvic girdle skeleton VSAO:0000155 skeletal parts of pelvic girdle skeleton of pelvic girdle pelvic girdle VSAO:0000155 Bone element that arises as a result of intramembranous ossification. Bone element that arises as a result of intramembranous ossification.[VSAO] Intramembranous bone that forms deep in the organism.[TAO] AEO:0000085 EHDAA2:0003085 TAO:0001645 VSAO:0000023 XAO:0004014 ZFA:0001636 uberon membrane bones UBERON:0007842 membrane bone VSAO Bone element that arises as a result of intramembranous ossification. GO_REF:0000034 VSAO:0000023 Bone element that arises as a result of intramembranous ossification.[VSAO] 2012-08-14 VSAO:0000023 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Intramembranous bone that forms deep in the organism.[TAO] 2012-08-14 TAO:0001645 TAO TAO:wd membrane bones ZFA:0001636 Skeletal element that is composed of cartilage tissue and may be permanent or transient. TAO still mixes tissue and element AAO:0011130 CALOHA:TS-0118 EMAPA:32730 FMA:55107 VSAO:0000000 XAO:0004013 ZFA:0001501 cartilage organ cartilaginous element chondrogenic element uberon cartilage UBERON:0007844 cartilage element VSAO VSAO VSAO Skeletal element that is composed of cartilage tissue and may be permanent or transient. GO_REF:0000034 PSPUB:0000170 VSAO:0000000 TAO still mixes tissue and element TAO cartilage organ FMA:55107 cartilaginous element chondrogenic element VSAO:0000000 cartilage VSAO:0000000 Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification). FMA:20103 uberon UBERON:0007845 regular connective tissue FMA Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. FMA:20103 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] FMA:64781 NCIT:C33453 UMLS:C0225333 VSAO:0000050 XAO:0004030 dense fibrous connective tissue dense regular collagenous connective tissue dense regular collagenous tissue regular dense connective tissue typus regularis (textus connectivus collagenosus compactus) uberon UBERON:0007846 dense regular connective tissue FMA ncithesaurus Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). GO_REF:0000034 PSPUB:0000170 VSAO:0000050 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] 2012-08-14 VSAO:0000050 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] 2012-08-29 FMA:64781 FMA UMLS:C0225333 ncithesaurus:Regular_Dense_Connective_Tissue dense fibrous connective tissue FMA:64781 dense regular collagenous connective tissue FMA:64781 dense regular collagenous tissue FMA:64781 typus regularis (textus connectivus collagenosus compactus) FMA:64781 A bone that is part of a craniocervical region. EMAPA:37245 MA:0000569 head or neck bone uberon cranial bone UBERON:0007914 bone of craniocervical region MA MA A bone that is part of a craniocervical region. OBOL:automatic EMAPA:37245 MA:th head or neck bone MA:0000569 The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. FMA:7477 NCIT:C32881 UMLS:C0502414 os irregulare uberon os irregulare UBERON:0008001 irregular bone FMA The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. UMLS:C0502414 ncithesaurus:Irregular_Bone os irregulare A skeletal joint that is part of a appendage girdle region. MA:0001505 girdle joint uberon UBERON:0008114 joint of girdle MA A skeletal joint that is part of a appendage girdle region. OBOL:automatic girdle joint OBOL:automatic A anatomical surface that is part of a cartilage element. FMA:76668 cartilage surface uberon UBERON:0008115 surface of cartilage A anatomical surface that is part of a cartilage element. OBOL:automatic cartilage surface FMA:76668 A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. subclasses of this should be checked for taxonomic consistency Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity] FMA:7478 galen:PneumaticBone os pneumaticum pneumatic bone uberon hollow bone UBERON:0008193 pneumatized bone A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. os pneumaticum FMA:7478 pneumatic bone FMA:7478 Any muscle organ that is part of a pectoral girdle region. EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate EMAPA:17748 FMA:37347 muscle of shoulder girdle pectoral girdle muscle uberon UBERON:0008196 muscle of pectoral girdle Any muscle organ that is part of a pectoral girdle region. OBOL:automatic EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate EMAPA muscle of shoulder girdle FMA:37347 pectoral girdle muscle FMA:37347 todo - consider obsoletion in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone EMAPA:37308 FMA:42854 MA:0000655 uberon UBERON:0008202 bone of hip region MA in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone MA EMAPA:37308 MA:th The part of the ventral body cavity that is within the pelvis. EMAPA:37235 FMA:9738 MA:0003089 space of pelvic compartment uberon cavitas pelvis UBERON:0008203 pelvic cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the ventral body cavity that is within the pelvis. UBERON:cjm EMAPA:37235 MA:th space of pelvic compartment FMA:9738 cavitas pelvis Musculature system of the pharyngeal and head regions. in MA this is restricted to skeletal muscles EMAPA:37259 MA:0000571 TAO:0000328 ZFA:0000328 head or neck muscle uberon head muscles head or neck muscle UBERON:0008229 craniocervical region musculature MA MA Musculature system of the pharyngeal and head regions. ZFA:0000328 ZFA:curator in MA this is restricted to skeletal muscles MA EMAPA:37259 MA:th head or neck muscle MA:0000571 head muscles ZFA:0000328 head or neck muscle MA:0000571 Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. EMAPA:37234 FMA:24217 MA:0000028 dorsum of thorax posterior part of thorax thoracic back thoracic part of back upper back uberon back of thorax UBERON:0008231 dorsal thoracic segment of trunk FMA MA FMA Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. FMA:24217 EMAPA:37234 MA:th dorsum of thorax FMA:24217 posterior part of thorax FMA:24217 thoracic back FMA:24217 thoracic part of back FMA:24217 upper back MA:0000028 back of thorax FMA:24217 A muscle of back that is part of a lower back. EMAPA:37262 MA:0000502 uberon UBERON:0008242 lower back muscle MA MA A muscle of back that is part of a lower back. OBOL:automatic EMAPA:37262 MA:th A muscle of back that is part of a dorsal thoracic segment of trunk. EMAPA:37261 MA:0000508 uberon UBERON:0008243 upper back muscle MA MA A muscle of back that is part of a dorsal thoracic segment of trunk. OBOL:automatic EMAPA:37261 MA:th A knoblike tooth primordium that develops into the mature tooth and consists of enamel organ, dental papilla, and dental sac enclosing them. BTO:0001838 FMA:306006 MESH:A14.254.900.720 NCIT:C34313 UMLS:C0040442 dental bud dental germ tooth germ uberon UBERON:0008281 tooth bud A knoblike tooth primordium that develops into the mature tooth and consists of enamel organ, dental papilla, and dental sac enclosing them. UBERON:cjm UMLS:C0040442 ncithesaurus:Tooth_Bud dental bud FMA:306006 dental germ tooth germ An endothelium that is part of a heart [Automatically generated definition]. this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class. BTO:0004293 uberon cardiac endothelium UBERON:0008307 heart endothelium An endothelium that is part of a heart [Automatically generated definition]. OBOL:automatic cardiac endothelium BTO:0004293 A gland that is part of a nasopharynx. FMA:55076 uberon UBERON:0008310 nasopharyngeal gland A gland that is part of a nasopharynx. OBOL:automatic with numerous vascular spaces that may become engorged with blood uberon UBERON:0008324 Examples: corpus cavernosum or penis or clitoris erectile tissue with numerous vascular spaces that may become engorged with blood A smooth muscle tissue that is part of a clitoris. BTO:0005000 uberon clitoris smooth muscle UBERON:0008331 clitoral smooth muscle A smooth muscle tissue that is part of a clitoris. OBOL:automatic clitoris smooth muscle BTO:0005000 An intestinal villus in the duodenum. FMA:63300 uberon UBERON:0008342 intestinal villus of duodenum An intestinal villus in the duodenum. OBOL:automatic An intestinal villus in the ileum. FMA:63302 uberon UBERON:0008344 intestinal villus of ileum An intestinal villus in the ileum. OBOL:automatic An epithelium that is part of a ileum. EMAPA:35423 FMA:17233 MA:0003217 epithelium of ileum uberon UBERON:0008345 ileal epithelium FMA An epithelium that is part of a ileum. OBOL:automatic epithelium of ileum FMA:17233 An epithelium that is part of a duodenum. CALOHA:TS-2087 EMAPA:19078 FMA:17231 MA:0003208 epithelium of duodenum uberon UBERON:0008346 duodenal epithelium FMA An epithelium that is part of a duodenum. OBOL:automatic epithelium of duodenum FMA:17231 An epithelium that is part of a breast. BTO:0001428 uberon UBERON:0008367 breast epithelium An epithelium that is part of a breast. OBOL:automatic Epithelium pertaining to the trachea and bronchi. BTO:0002925 CALOHA:TS-1063 uberon bronchotracheal epithelium UBERON:0008397 tracheobronchial epithelium Epithelium pertaining to the trachea and bronchi. Dorlands_Medical_Dictionary:MerckMedicus bronchotracheal epithelium BTO:0002925 An epithelium that is part of a buccal mucosa. BTO:0004803 uberon UBERON:0008420 buccal epithelium BTO An epithelium that is part of a buccal mucosa. OBOL:automatic A vertebral foramen that is part of a cervical vertebra. FMA:13480 uberon UBERON:0008429 cervical vertebral foramen A vertebral foramen that is part of a cervical vertebra. OBOL:automatic A vertebral foramen that is part of a lumbar vertebra. FMA:24826 uberon UBERON:0008430 lumbar vertebral foramen A vertebral foramen that is part of a lumbar vertebra. OBOL:automatic A vertebral foramen that is part of a thoracic vertebra. FMA:9143 uberon UBERON:0008432 thoracic vertebral foramen A vertebral foramen that is part of a thoracic vertebra. OBOL:automatic 2 2 Intertarsal articulations are the joints of the tarsus. The specific intertarsal articulations are: Talocalcaneal articulation Talocalcaneonavicular articulation Calcaneocuboid articulation Cuneonavicular articulation Cuboideonavicular articulation Intercuneiform articulation Cuneocuboid articulation EMAPA:37762 FMA:44281 GAID:259 MA:0003112 MESH:D013640 NCIT:C33735 UMLS:C1527245 uberon articulationes intertarsale articulationes intertarsales articulationes intertarseae intermetatarsal joint intertarsal intertarsal articulation intertarsal joint tarsal joint tarsal joints UBERON:0008447 intertarsal joint http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray360.png two adjacent tarsals Intertarsal articulations are the joints of the tarsus. The specific intertarsal articulations are: Talocalcaneal articulation Talocalcaneonavicular articulation Calcaneocuboid articulation Cuneonavicular articulation Cuboideonavicular articulation Intercuneiform articulation Cuneocuboid articulation EMAPA:37762 MA:th UMLS:C1527245 ncithesaurus:Tarsal_Joint articulationes intertarsale MESH:A02.835.583.378.831 articulationes intertarsales articulationes intertarseae MESH:A02.835.583.378.831 intermetatarsal joint MESH:A02.835.583.378.831 intertarsal intertarsal articulation intertarsal joint MESH:A02.835.583.378.831 tarsal joint MESH:A02.835.583.378.831 tarsal joints Any muscle organ that is part of an nose. FMA:73758 NCIT:C33158 UMLS:C0224219 muscle of nose uberon UBERON:0008522 nasal muscle FMA Any muscle organ that is part of an nose. OBOL:automatic UMLS:C0224219 ncithesaurus:Nasal_Muscle muscle of nose OBOL:automatic EHDAA2:0001421 EMAPA:17748 RETIRED_EHDAA2:0001422 uberon UBERON:0008713 pectoral girdle and thoracic body wall skeletal muscle A muscle tissue that is part of a prostate gland. NCIT:C13100 UMLS:C1183911 prostate gland muscle tissue prostate muscle tissue prostatic muscle prostatic musclular tissue uberon UBERON:0008715 muscle tissue of prostate A muscle tissue that is part of a prostate gland. OBOL:automatic UMLS:C1183911 ncithesaurus:Prostatic_Muscular_Tissue prostate gland muscle tissue OBOL:automatic prostate muscle tissue OBOL:automatic An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers EHDAA2:0000444 EHDAA:42 EHDAA:75 EMAPA:16050 NCIT:C34164 UMLS:C1516906 uberon embryonic epiblast UBERON:0008780 The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5. inner cell mass derived epiblast Wikipedia An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers MP:0003886 UMLS:C1516906 ncithesaurus:Epiblast embryonic epiblast MP:0003886 The dorsal venous arch of the foot is a superficial vein that connects the small saphenous vein and the great saphenous vein. Anatomically, it is defined by where the dorsal veins of the first and fifth digit, respectively, meet the great saphenous vein and small saphenous vein. EMAPA:37521 FMA:44356 MA:0002110 arcus venosus dorsalis pedis dorsal venous arch of foot uberon arcus venosus dorsalis pedis UBERON:0008783 dorsal venous arch http://upload.wikimedia.org/wikipedia/commons/4/4e/Gray581.png MA The dorsal venous arch of the foot is a superficial vein that connects the small saphenous vein and the great saphenous vein. Anatomically, it is defined by where the dorsal veins of the first and fifth digit, respectively, meet the great saphenous vein and small saphenous vein. EMAPA:37521 MA:th arcus venosus dorsalis pedis dorsal venous arch of foot FMA:44356 arcus venosus dorsalis pedis A limb segment that is part of a hindlimb. FMA:24877 free lower limb segment free lower limb subdivision segment of free lower limb subdivision of free lower limb uberon UBERON:0008784 lower limb segment A limb segment that is part of a hindlimb. OBOL:automatic free lower limb segment FMA:24877 free lower limb subdivision FMA:24877 segment of free lower limb FMA:24877 subdivision of free lower limb FMA:24877 A limb segment that is part of a forelimb. FMA:24876 free upper limb segment free upper limb subdivision segment of free upper limb subdivision of free upper limb uberon UBERON:0008785 upper limb segment A limb segment that is part of a forelimb. OBOL:automatic free upper limb segment FMA:24876 free upper limb subdivision FMA:24876 segment of free upper limb FMA:24876 subdivision of free upper limb FMA:24876 Any of the three large depressions in the posterior, middle, and anterior aspects of the floor of the cranial cavity todo - review the relationships for this and its subclasses; the relation should be bounded rather than part of, and contains should be used for the brain parts contained by the fossae FMA:321144 uberon UBERON:0008789 cranial fossa true Any of the three large depressions in the posterior, middle, and anterior aspects of the floor of the cranial cavity A zone of skin that is part of a cheek. FMA:24759 cheek skin uberon UBERON:0008803 skin of cheek A zone of skin that is part of a cheek. OBOL:automatic cheek skin FMA:24759 An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]. this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO] AAO:0010255 FBbt:00004850 HAO:0000091 TAO:0002036 TGMA:0000585 aedeagus penis uberon copulatory organ UBERON:0008811 intromittent organ An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]. Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO] 2012-08-14 TAO:0002036 TAO TAO:wd aedeagus FBbt:00004850 A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing EHDAA2:0000187 FMA:293041 NCIT:C34248 UMLS:C1519038 embryonic pharyngeal complex pharyngeal apparatus pharyngeal system uberon pharyngeal arch complex pharyngeal arch region pharyngeal arches and clefts pharyngeal complex UBERON:0008814 pharyngeal arch system A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. GO:0060037 GOC:dph UMLS:C1519038 ncithesaurus:Pharyngeal_Apparatus pharyngeal system GO:0060037 pharyngeal arch region EHDAA2:0000187 A head that is part of a embryo. CALOHA:TS-0246 FBbt:00000155 FMA:293011 uberon UBERON:0008816 embryonic head A head that is part of a embryo. OBOL:automatic An endoderm that is part of a thymus primordium. uberon UBERON:0008817 thymus primordium endoderm An endoderm that is part of a thymus primordium. OBOL:automatic A brain that develops_from a neural tube. a reasoner should automatically classify all the vertebrate ontology brain classes here vertebrate brain uberon UBERON:0008823 neural tube derived brain https://github.com/obophenotype/uberon/issues/338 ZFA FMA A brain that develops_from a neural tube. OBOL:automatic Any duct branching of of the main epididymis duct. EMAPA:36525 FMA:18297 MA:0001735 NCIT:C32484 UMLS:C0458632 epididymal duct epididymis duct uberon UBERON:0008824 duct of epididymis FMA Any duct branching of of the main epididymis duct. UMLS:C0458632 ncithesaurus:Duct_of_the_Epididymis epididymal duct MA:0001735 epididymis duct FMA:18297 An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10 The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. AAO:0011057 EHDAA2:0000740 EHDAA:1530 NCIT:C34187 UMLS:C1512407 XAO:0000101 liver diverticulum uberon diverticulum hepaticum UBERON:0008835 hepatic diverticulum http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png EHDAA2 caudal part EHDAA2 EHDAA2 An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. MP:MP UMLS:C1512407 ncithesaurus:Hepatic_Diverticulum liver diverticulum XAO:0000101 diverticulum hepaticum BTO:0001642 uberon UBERON:0008836 liver bud cjm A ligament that does not connect two skeletal elements. Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625]. this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus. FMA:25625 MA:0003004 non-skeletal ligament uberon fibrous ligament UBERON:0008845 nonskeletal ligament cjm A ligament that does not connect two skeletal elements. Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625]. FMA:25625 this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus. FMA fibrous ligament Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified]. logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71 Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO] Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624]. ligament AAO:0010444 AEO:0000090 CALOHA:TS-2146 EHDAA2:0003232 EV:0100144 FMA:25624 GAID:118 MA:0003005 VSAO:0000072 articular larua articular ligament true ligament uberon UBERON:0008846 skeletal ligament Knee:diagram.svg bones or cartilage organs VSAO Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified]. GO_REF:0000034 Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO] 2012-08-14 VSAO:0000072 VSAO PSPUB:0000170 Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624]. FMA:25624 ligament VSAO:0000072 ZFA:0001675 articular larua articular ligament true ligament The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two FMA:14909 gastric muscularis muscle layer of stomach muscularis externa of stomach tunica muscularis (gaster) tunica muscularis gastris uberon UBERON:0008856 stomach muscularis externa MA-abduced The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines MP:0010779 the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two WP gastric muscularis FMA:14909 muscle layer of stomach FMA:14909 muscularis externa of stomach FMA:14909 tunica muscularis (gaster) FMA:14909 The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter EMAPA:37944 FMA:14580 canalis pyloricus uberon canalis pyloricus UBERON:0008858 pyloric canal Illu:stomach.jpg FMA Wikipedia The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter MP:0010791 EMAPA:37944 MA:th canalis pyloricus canalis pyloricus A gastric gland in the cardiac region of the stomach; cardiac glands are fewer in number than in the fundus and body, and secrete mucin which coats the stomach and protects it[MP] The cardiac glands of the stomach secrete primarily mucus. They are few in number and occur close to the cardiac orifice where the esophagus joins the stomach. In general, they are more shallow than those in the other parts of the stomach. They are of two kinds: (1) simple tubular glands resembling those of the pyloric end of the stomach, but with short ducts. (2) compound racemose glands resembling the duodenal glands. The cardiac gland is both innervated by the parasympathetic and symapthetic nerve fibres of the autonomic nervous system[Wikipedia:Cardiac_glands]. Kardong places this in the glandular epithelium, FMA more generally in the mucosa EMAPA:37459 FMA:14920 gardiac gland gastric cardiac gland gastric cardiac mucuous gland gastric gland of cardia glandula cardiaca (gaster) uberon cardiac gland UBERON:0008859 cardiac gastric gland MP FMA A gastric gland in the cardiac region of the stomach; cardiac glands are fewer in number than in the fundus and body, and secrete mucin which coats the stomach and protects it[MP] MP:0010795 The cardiac glands of the stomach secrete primarily mucus. They are few in number and occur close to the cardiac orifice where the esophagus joins the stomach. In general, they are more shallow than those in the other parts of the stomach. They are of two kinds: (1) simple tubular glands resembling those of the pyloric end of the stomach, but with short ducts. (2) compound racemose glands resembling the duodenal glands. The cardiac gland is both innervated by the parasympathetic and symapthetic nerve fibres of the autonomic nervous system[Wikipedia:Cardiac_glands]. Kardong places this in the glandular epithelium, FMA more generally in the mucosa FMA EMAPA:37459 MA:th gardiac gland ISBN:0073040584 gastric cardiac gland FMA:14920 gastric gland of cardia FMA:14920 glandula cardiaca (gaster) FMA:14920 cardiac gland FMA:14920 The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]. check relationship to pylorus vs antrum EMAPA:27211 FMA:14922 NCIT:C33431 UMLS:C0227239 glandula pylorica pyloric antrum gland pyloric gland pyloric mucuous gland uberon UBERON:0008861 pyloric gastric gland http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png MP The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]. MP:0010797 UMLS:C0227239 ncithesaurus:Pyloric_Gland glandula pylorica FMA:14922 pyloric antrum gland OBOL:automatic pyloric gland FMA:14922 Any skeletal muscle organ in the hypodermis / superficial fascia We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this UBERON:0010934 EMAPA:18188 MA:0003140 hypodermal muscle layer hypodermis muscle layer superficial fascia muscular layer panniculus carnosus uberon UBERON:0008876 hypodermis skeletal muscle layer MP-def Any skeletal muscle organ in the hypodermis / superficial fascia ISBN:0123813611 MP:0011157 hypodermal muscle layer MP:0011157 hypodermis muscle layer MP:0011157 panniculus carnosus MP:0011157 The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA:45621 pulmonary circulatory system pulmonary system uberon UBERON:0008886 pulmonary vascular system Obol The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. ISBN:0073040584 Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA FMA:45621 pulmonary circulatory system FMA:45621 pulmonary system ISBN:0073040584 The hemorrhoidal plexus (or rectal venous plexus) surrounds the rectum, and communicates in front with the vesical venous plexus in the male, and the uterovaginal plexus in the female. A free communication between the portal and systemic venous systems is established through the hemorrhoidal plexus. FMA:18933 NCIT:C32728 UMLS:C0226766 uberon haemorrhoidal plexus hemorrhoidal plexus plexus haemorrhoidalis plexus venosus rectalis UBERON:0008887 rectal venous plexus http://upload.wikimedia.org/wikipedia/commons/6/69/Gray587.png FMA The hemorrhoidal plexus (or rectal venous plexus) surrounds the rectum, and communicates in front with the vesical venous plexus in the male, and the uterovaginal plexus in the female. A free communication between the portal and systemic venous systems is established through the hemorrhoidal plexus. UMLS:C0226766 ncithesaurus:Hemorrhoidal_Plexus haemorrhoidal plexus hemorrhoidal plexus plexus haemorrhoidalis plexus venosus rectalis Subdivision of endoskeleton derived from pharyngeal arches Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both AAO:0010157 TAO:0001216 VHOG:0000315 VSAO:0000149 XAO:0003176 ZFA:0001216 pharyngeal endoskeleton viscerocranium uberon branchial arch skeleton gill arch skeleton pharyngeal arch pharyngeal arch skeleton pharyngeal skeleton visceral cranium visceral skeletal system visceral skeleton UBERON:0008895 splanchnocranium http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg redundant Grays Subdivision of endoskeleton derived from pharyngeal arches ISBN:0073040584 Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] 2012-08-14 TAO:0001216 TAO ZFIN:curator Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] 2012-06-20 AAO:0010157 AAO AAO:EJS The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] 2012-09-17 VHOG:0000315 VHOG The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000315 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235 VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. VSAO pharyngeal endoskeleton viscerocranium VHOG:0000315 ZFA:0001216 pharyngeal arch VSAO:0000149 pharyngeal arch skeleton ZFA:0001216 pharyngeal skeleton ZFA:0001216 visceral cranium visceral skeletal system visceral skeleton UBERONREF:0000007 A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher. Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO] AAO:0010362 BTO:0002152 EFO:0003694 TAO:0001597 XAO:0000099 ZFA:0001613 branchial arch branchial arches branchial bar branchial bars gill arch gill arches 1-5 pharyngeal arch 3-7 visceral arches 3-7 uberon gill bar UBERON:0008896 post-hyoid pharyngeal arch A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher. Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO] 2012-06-20 AAO:0010362 AAO AAO:EJS branchial arch ZFA:0001613 branchial arches ZFA:0001613 branchial bar ZFA:0001613 branchial bars ZFA:0001613 gill arch ZFA:0001613 gill arches 1-5 ZFA:0001613 pharyngeal arch 3-7 ZFA:0001613 visceral arches 3-7 ZFA:0001613 gill bar Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. Intramembranous bone that forms superficially in the organism.[TAO] other AOs are not yet in sync with this classification AAO:0010769 TAO:0001590 VSAO:0000130 XAO:0004015 ZFA:0001590 uberon dermal bones UBERON:0008907 dermal bone wd VSAO VSAO Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. GO_REF:0000034 VSAO:0000130 Intramembranous bone that forms superficially in the organism.[TAO] 2012-08-14 TAO:0001590 TAO TAO:wd dermal bones ZFA:0001590 Bone element that is adjacent to the notochord. We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] AAO:0010777 TAO:0001639 VSAO:0000307 ZFA:0001629 perichordal bones uberon perichordal bone UBERON:0008909 perichordal bone not in VSAO ZFA Bone element that is adjacent to the notochord. GO_REF:0000034 VSAO:0000307 Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] 2012-08-14 TAO:0001639 TAO TAO:wd perichordal bones ZFA:0001629 perichordal bone ZFA:0001629 Albumen is the clear liquid contained within an egg and consists of water and proteins, among which are ovomucin and ovomucoid. It protects the egg yolk and provides additional nutrition for the growth of the embryo. egg white, albumen http://langual.org http://www.langual.org/langual_thesaurus.asp?termid=C0241 egg white albumen A parenchyma that is part of a lung. EMAPA:35522 FMA:27360 MA:0003168 respiratory portion of lung uberon parenchyma of lung pulmonary parenchyma UBERON:0008946 lung parenchyma FMA FMA A parenchyma that is part of a lung. OBOL:automatic respiratory portion of lung FMA:27360 parenchyma of lung BTO:0000763 pulmonary parenchyma EMAPA:35522 EHDAA2:0004069 NCIT:C34283 UMLS:C1514898 uberon UBERON:0008947 respiratory primordium Obol UMLS:C1514898 ncithesaurus:Respiratory_Primordium A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder. GAID:178 MESH:D001133 NCIT:C12983 UMLS:C0003793 free forelimb bone wing bone uberon UBERON:0008962 forelimb bone A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder. UMLS:C0003793 ncithesaurus:Bone_of_the_Upper_Extremity free forelimb bone UBERONREF:0000003 wing bone Geisha:syn NCBITaxon:8782 wing bone NCBITaxon:8782 OBOL:automatic The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 parenchyma of kidney uberon kidney parenchyma UBERON:0008987 renal parenchyma FMA FMA The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 parenchyma of kidney FMA:15574 kidney parenchyma BTO:0003604 One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed. BTO:0003634 FMA:9404 NCIT:C32536 UMLS:C0227178 esophageal gland glandulae oesophageae mucous gland of submucosa of esophagus uberon UBERON:0008989 submocosal esophageal gland http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed. BTO:0003634 UMLS:C0227178 ncithesaurus:Esophageal_Gland esophageal gland FMA:9404 glandulae oesophageae mucous gland of submucosa of esophagus FMA:9404 System pertaining to blood vessels in the brain. UBERON:0005284 BTO:0003840 EFO:0003491 EMAPA:35186 FMA:242007 FMA:61935 TAO:0000099 ZFA:0000099 brain vasculature cerebrovascular system intracerebral vasculature uberon UBERON:0008998 vasculature of brain System pertaining to blood vessels in the brain. BTO:0003840 cerebrovascular system BTO:0003840 intracerebral vasculature FMA:61935 Any portion of tissue that surrounds a urethra. BTO:0005081 uberon UBERON:0009010 periurethral tissue Any portion of tissue that surrounds a urethra. UBERON:cjm A zone of skin that is part of a lower back. EMAPA:37281 MA:0000504 uberon UBERON:0009014 lower back skin MA A zone of skin that is part of a lower back. OBOL:automatic EMAPA:37281 MA:th A zone of skin that is part of a dorsal thoracic segment of trunk. EMAPA:37280 MA:0000510 uberon UBERON:0009015 upper back skin MA A zone of skin that is part of a dorsal thoracic segment of trunk. OBOL:automatic EMAPA:37280 MA:th An artery that supplies blood to the urinary bladder. EMAPA:37131 MA:0002078 arteria vesicali vesical arteries uberon UBERON:0009027 vesical artery An artery that supplies blood to the urinary bladder. EMAPA:37131 MA:th arteria vesicali vesical arteries Vein that drains left lung and returns blood to the heart. A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. EMAPA:37165 MA:0002207 NCIT:C48946 UMLS:C0226670 uberon UBERON:0009030 left pulmonary vein Vein that drains left lung and returns blood to the heart. A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. ncithesaurus:Left_Pulmonary_Vein EMAPA:37165 MA:th UMLS:C0226670 ncithesaurus:Left_Pulmonary_Vein Vein that drains right lung and returns blood to the heart. A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. EMAPA:37379 MA:0002208 NCIT:C48947 UMLS:C0226669 uberon UBERON:0009032 right pulmonary vein Vein that drains right lung and returns blood to the heart. A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. ncithesaurus:Right_Pulmonary_Vein EMAPA:37379 MA:th UMLS:C0226669 ncithesaurus:Right_Pulmonary_Vein The prostatic veins form a well-marked prostatic plexus which lies partly in the fascial sheath of the prostate and partly between the sheath and the prostatic capsule. It communicates with the pudendal and vesical plexuses. FMA:29711 uberon plexus venosus prostaticus pudendal venous plexus UBERON:0009042 prostatic venous plexus http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png The prostatic veins form a well-marked prostatic plexus which lies partly in the fascial sheath of the prostate and partly between the sheath and the prostatic capsule. It communicates with the pudendal and vesical plexuses. plexus venosus prostaticus pudendal venous plexus FMA:29711 An organism containing a developing embryo, fetus, or unborn offspring within the body. BTO:0004733 uberon gravid pregnant adult pregnant adult stage pregnant organism pregnant stage UBERON:0009097 gravid organism An organism containing a developing embryo, fetus, or unborn offspring within the body. BTO:0004733 gravid BTO:0004733 pregnant adult BTO:0004733 pregnant adult stage BTO:0004733 pregnant stage BTO:0004733 The uterus in pregnancy NCIT:C12406 UMLS:C1514389 ncithesaurus:Gravid_Uterus uberon womb UBERON:0009098 gravid uterus The uterus in pregnancy UMLS:C1514389 ncithesaurus:Pregnant_Uterus A mature thymus that is entirely part of the cervical region. A cervical thymus is a pathological structure in a human - it can form during the migration of the thymus to its location in the mediastinum. Some mice have a cervical thymus. There are examples of cervical thymi in marsupials and prosimians[ISBN:0781714125] uberon UBERON:0009114 cervical thymus A mature thymus that is entirely part of the cervical region. A mature thymus that is entirely part of thoracic region. uberon UBERON:0009115 thoracic thymus A mature thymus that is entirely part of thoracic region. A gonad prior to differentiating into a definitive testis or ovary. EHDAA2:0000716 NCIT:C34192 UMLS:C1512703 uberon gonad rudiment UBERON:0009117 typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] indifferent gonad A gonad prior to differentiating into a definitive testis or ovary. UMLS:C1512703 ncithesaurus:Indifferent_Gonad The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke's pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke's pouch, the anlage of the adenohypophysis. Rathke's pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009) EFO:0000229 TAO:0001198 XAO:0004208 ZFA:0001198 uberon pituitary placode UBERON:0009122 adenohypophyseal placode NCBIBook:NBK53175 ZFA The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary pituitary placode ZFA:0001198 Rostralmost epibranchial placode. Associated with 1st branchial cleft. EHDAA2:0004206 TAO:0001295 XAO:0004211 ZFA:0001295 epibranchial placode 1 facial epibranchial placode facial placode uberon facial VII placode hyoid VII placode hyoid placode UBERON:0009124 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to geniculate ganglion geniculate placode ZFA Rostralmost epibranchial placode. Associated with 1st branchial cleft. NCBIBook:NBK53175 epibranchial placode 1 EHDAA2:0004206 facial epibranchial placode XAO:0004211 facial placode ZFA:0001295 hyoid VII placode ISBN:0471888893 hyoid placode ISBN:0471888893 Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. EHDAA2:0004207 TAO:0001296 XAO:0004212 ZFA:0001296 epibranchial placode 2 glossopharyngeal IX placode glossopharyngeal epibranchial placode glossopharyngeal placode uberon UBERON:0009125 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion petrosal placode ZFA Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. NCBIBook:NBK53175 epibranchial placode 2 EHDAA2:0004207 glossopharyngeal IX placode ISBN:0471888893 glossopharyngeal epibranchial placode XAO:0004212 glossopharyngeal placode ISBN:0471888893 ZFA:0001296 Cranial ganglion which develops from an epibranchial placode. TAO:0001555 ZFA:0001555 epibranchial ganglia uberon UBERON:0009127 Epibranchial ganglia orchestrate the development of the cranial neurogenic crest epibranchial ganglion ZFA NCBIBook:NBK53175 Cranial ganglion which develops from an epibranchial placode. ZFIN:curator epibranchial ganglia ZFA:0001555 Endocardium that is part of the right atrium. EHDAA2:0000274 FMA:7281 NCIT:C102339 VHOG:0001228 endocardium of right atrium right atrial endocardium uberon right atrium endocardial tissue UBERON:0009129 right atrium endocardium EHDAA2 EHDAA2 Endocardium that is part of the right atrium. endocardium of right atrium FMA:7281 right atrial endocardium FMA:7281 right atrium endocardial tissue VHOG:0001228 A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] UBERON:0009146 EHDAA2:0001483 EMAPA:17709 NCIT:C34256 UMLS:C1283968 VHOG:0000757 pleuroperitoneal fold pleuroperitoneal membranes uberon UBERON:0009133 pleuroperitoneal membrane EHDAA2 A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000757 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 UMLS:C1283968 ncithesaurus:Pleuroperitoneal_Membrane pleuroperitoneal fold VHOG:0000757 pleuroperitoneal membranes EHDAA2:0001483 A vein that is part of a craniocervical region. EHDAA2:0004542 craniocervical vein head and neck veins vein of head and neck uberon UBERON:0009141 craniocervical region vein A vein that is part of a craniocervical region. OBOL:automatic head and neck veins EHDAA2:0004542 Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 uberon UBERON:0009142 entire embryonic mesenchyme EHDAA2 Sum total of mesenchyme in the embryo. EMAPA:16549 RETIRED_EHDAA2:0001454 pharyngeal region uberon UBERON:0009145 pharyngeal region of foregut EHDAA2 pharyngeal region EMAPA:16549 EHDAA2:0004021 uberon UBERON:0009196 indifferent external genitalia cjm 2 Any suture between cranial and/or facial bones. we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA joint of the skull bones uberon articulation of skull bones UBERON:0009198 craniofacial suture Any suture between cranial and/or facial bones. GO:0097094 joint of the skull bones OBOL:automatic articulation of skull bones OBOL:automatic 2 Any suture between facial bones. uberon UBERON:0009199 facial suture between two adjacent facial bones Any suture between facial bones. GO:0097096 The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium. EMAPA:32728 uberon UBERON:0009200 limb epidermis The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium. GOC:dph GOC:sdb_2009 GOC:tb A nephric duct is a tube that drains a primitive kidney[GO]. EMAPA:16577 uberon UBERON:0009201 pronephric duct or mesonephric duct nephric duct EHDAA2 A nephric duct is a tube that drains a primitive kidney[GO]. GO:0072176 Mesenchyme that is part of a lateral nasal prominence. EHDAA2:0000917 EMAPA:16807 FMA:312665 mesenchyme of latero-nasal process uberon UBERON:0009205 lateral nasal process mesenchyme Mesenchyme that is part of a lateral nasal prominence. OBOL:automatic mesenchyme of latero-nasal process EMAPA:16807 An ectoderm that is part of a lateral nasal prominence. EHDAA2:0000918 EMAPA:16806 ectoderm of latero-nasal process uberon UBERON:0009206 lateral nasal process surface ectoderm EHDAA2 An ectoderm that is part of a lateral nasal prominence. OBOL:automatic ectoderm of latero-nasal process EMAPA:16806 A thin fold of ectoderm and endoderm that separates the pharyngeal pouches from the pharyngeal clefts in a developing embryo. In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG] EMAPA:32749 FMA:295758 NCIT:C34251 UMLS:C1519040 branchial arch membrane branchial membrane pharyngeal membrane uberon UBERON:0009210 each membrane is initially composed of an inner layer formed by the endodermal lining of a branchial pouch and an outer layer formed by the ectodermal lining of the branchial groove; later, these two layers become separated by a thin layer of mesoderm; only the first branchial membrane contributes to the formation of an adult structure, i.e. the tympanic membrane (aka eardrum); the second, third, and fourth membranes are obliterated[MP] pharyngeal membrane EMAPA A thin fold of ectoderm and endoderm that separates the pharyngeal pouches from the pharyngeal clefts in a developing embryo. In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG] 2012-09-17 VHOG:0001427 VHOG ISBN:978-0124020603 Kaufman MH, Bard JBL, The anatomical basis of mouse development (1999) p.72 UMLS:C1519040 ncithesaurus:Pharyngeal_Membrane branchial arch membrane EMAPA:32749 A pharyngeal membrane that separates the first pharyngeal cleft from the first pharyngeal pouch. check EMAPA - 3 terms appear to match. We follow EMAPA in making each membrane part of the arch with the same number, though in fact it is between these arches EHDAA:3788 EMAPA:16121 EMAPA:16992 EMAPA:17281 VHOG:0001427 1st branchial membrane 1st pharyngeal membrane future tympanic membrane tympanic membrane primordium uberon UBERON:0009213 pharyngeal membrane of 1st arch EMAPA A pharyngeal membrane that separates the first pharyngeal cleft from the first pharyngeal pouch. 1st branchial membrane EMAPA:16992 1st pharyngeal membrane VHOG:0001427 future tympanic membrane EMAPA:17281 tympanic membrane primordium ISBN:1416037055 Cartilaginous form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]. cartilaginous centrum of vertebra postcaudal cartilaginous centrum uberon UBERON:0009291 cartilaginous centrum of vertebra[PMID:11746457] cartilaginous vertebral centrum Cartilaginous form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]. VSAO:0000183 VSAO:curator postcaudal cartilaginous centrum medial or lateral; in EHDAA2 also frontonasal or intermaxillary EHDAA2:0000581 EHDAA:4776 EMAPA:16680 FMA:293971 uberon nasal placode UBERON:0009292 embryonic nasal process medial or lateral; in EHDAA2 also frontonasal or intermaxillary EHDAA2 The superior surface of the tongue divided by the sulcus terminalis into an anterior two-thirds, the presulcal part (pars presulcalis). and a posterior one-third, the postsulcal part (pars postsulcalis). FMA:54651 NCIT:C32482 UMLS:C0226952 dorsal tongue dorsum linguae tongue dorsum uberon UBERON:0009471 dorsum of tongue FMA The superior surface of the tongue divided by the sulcus terminalis into an anterior two-thirds, the presulcal part (pars presulcalis). and a posterior one-third, the postsulcal part (pars postsulcalis). UMLS:C0226952 ncithesaurus:Dorsum_of_the_Tongue dorsal tongue FMA:54651 dorsum linguae tongue dorsum FMA:54651 Mesenchyme that is part of a otic placode. EHDAA2:0001340 EMAPA:16196 uberon UBERON:0009477 associated mesenchyme of otic placode Mesenchyme that is part of a otic placode. OBOL:automatic An ectoderm that is part of a buccopharyngeal membrane. EHDAA2:0000190 EMAPA:16260 uberon UBERON:0009479 ectoderm of buccopharyngeal membrane An ectoderm that is part of a buccopharyngeal membrane. OBOL:automatic An endoderm that is part of a buccopharyngeal membrane. EHDAA2:0000191 EMAPA:16261 uberon UBERON:0009480 endoderm of buccopharyngeal membrane An endoderm that is part of a buccopharyngeal membrane. OBOL:automatic Mesenchyme that is part of a foregut-midgut junction. EHDAA2:0000570 EMAPA:16364 uberon UBERON:0009482 associated mesenchyme of foregut-midgut junction Mesenchyme that is part of a foregut-midgut junction. OBOL:automatic A mesentery that is part of a foregut-midgut junction. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EHDAA2:0000575 EMAPA:16365 VHOG:0000430 foregut-midgut junction mesentery uberon UBERON:0009483 mesentery of foregut-midgut junction A mesentery that is part of a foregut-midgut junction. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000430 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 foregut-midgut junction mesentery VHOG:0000430 A portion of mesenchymal tissue associated with an individual pharyngeal arch. this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. EMAPA:32755 FMA:295694 branchial arch mesenchyme pharyngeal arch mesenchyme uberon UBERON:0009494 pharyngeal arch mesenchymal region EHDAA2 cjm A portion of mesenchymal tissue associated with an individual pharyngeal arch. this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. MP:0011262 branchial arch mesenchyme MP:0011262 pharyngeal arch mesenchyme An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 uberon UBERON:0009497 epithelium of foregut-midgut junction EHDAA2 An epithelium that is part of a foregut-midgut junction. OBOL:automatic Anatomical region that surrounds the otic vesicle. EHDAA2:0001343 EMAPA:16670 XAO:0004474 otocyst associated mesenchyme otocyst mesenchyme uberon periotic region UBERON:0009500 periotic mesenchyme XAO EHDAA2 Anatomical region that surrounds the otic vesicle. XAO:0004474 XAO:curators otocyst associated mesenchyme EHDAA2:0001343 otocyst mesenchyme EMAPA:16670 periotic region XAO:0004474 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head EHDAA2:0004109 EMAPA:16683 FMA:295821 frontonasal mesenchyme naso-frontal mesenchyme uberon UBERON:0009501 mesenchyme of fronto-nasal process The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head MP:0011266 frontonasal mesenchyme MP:0011266 naso-frontal mesenchyme MP:0011266 Mesenchyme that is part of a developing hindgut. EHDAA2:0000780 EMAPA:16716 hindgut associated mesenchyme uberon UBERON:0009503 mesenchyme of hindgut Mesenchyme that is part of a developing hindgut. OBOL:automatic hindgut associated mesenchyme EHDAA2:0000780 Mesenchyme that is part of a developing trachea. EHDAA2:0002067 EMAPA:16854 trachea associated mesenchyme uberon UBERON:0009505 mesenchyme of trachea EHDAA2 Mesenchyme that is part of a developing trachea. OBOL:automatic trachea associated mesenchyme EHDAA2:0002067 Mesenchyme that is part of a developing middle ear. Also 1st arch maxillary mesenchyme in EHDAA2 otic mesenchyme EHDAA2:0001182 EMAPA:17001 middle ear associated mesenchyme uberon UBERON:0009506 mesenchyme of middle ear EHDAA2 EHDAA2 EHDAA2 Mesenchyme that is part of a developing middle ear. OBOL:automatic Also 1st arch maxillary mesenchyme in EHDAA2 EHDAA2 middle ear associated mesenchyme EHDAA2:0001182 An endoderm that is part of a anal region. EHDAA2:0004020 EMAPA:17177 uberon UBERON:0009521 anal membrane endodermal component An endoderm that is part of a anal region. OBOL:automatic An epithelium that is part of a lateral lingual swelling. EHDAA2:0000913 EMAPA:17190 FMA:313717 uberon UBERON:0009522 lateral lingual swelling epithelium An epithelium that is part of a lateral lingual swelling. OBOL:automatic Mesenchyme that is part of a handplate. We group two EMAPA classes here but these may need to be separated EHDAA2:0000731 EMAPA:17248 EMAPA:17457 hand plate mesenchyme handplate mesenchyme uberon UBERON:0009523 mesenchyme of handplate EHDAA2 Mesenchyme that is part of a handplate. OBOL:automatic We group two EMAPA classes here but these may need to be separated EMAPA handplate mesenchyme EHDAA2:0000731 Mesenchyme that is part of a maxillary prominence. EHDAA2:0001071 EMAPA:17361 FMA:312691 mesenchyme of maxillary process mesenchyme of maxillary prominence uberon UBERON:0009526 maxillary process mesenchyme Mesenchyme that is part of a maxillary prominence. OBOL:automatic mesenchyme of maxillary process EMAPA:17361 mesenchyme of maxillary prominence A vascular plexus that is part of a left lung. EHDAA2:0000963 EMAPA:17660 uberon UBERON:0009536 vascular element of left lung A vascular plexus that is part of a left lung. OBOL:automatic A vascular plexus that is part of a right lung. EHDAA2:0001757 EMAPA:17668 uberon UBERON:0009537 vascular element of right lung A vascular plexus that is part of a right lung. OBOL:automatic Mesenchyme that is part of a submandibular gland primordium. EHDAA2:0001941 EMAPA:17757 uberon submaxillary gland primordium mesenchyme UBERON:0009539 mesenchyme of submandibular gland primordium Mesenchyme that is part of a submandibular gland primordium. OBOL:automatic submaxillary gland primordium mesenchyme EMAPA:17757 A hepatic sinusoid that is part of a left lobe of liver. EHDAA2:0001001 EMAPA:18309 VHOG:0000709 left lobe hepatic sinusoids uberon UBERON:0009548 hepatic sinusoid of left of lobe of liver A hepatic sinusoid that is part of a left lobe of liver. OBOL:automatic left lobe hepatic sinusoids VHOG:0000709 A hepatic sinusoid that is part of a right lobe of liver. EHDAA2:0001009 EMAPA:18316 VHOG:0000710 right lobe hepatic sinusoids uberon UBERON:0009549 hepatic sinusoid of right of lobe of liver A hepatic sinusoid that is part of a right lobe of liver. OBOL:automatic right lobe hepatic sinusoids VHOG:0000710 An endoderm that is part of a foregut-midgut junction. EHDAA2:0000572 EMAPA:18403 uberon UBERON:0009550 endoderm of foregut-midgut junction An endoderm that is part of a foregut-midgut junction. OBOL:automatic A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium). Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults digit tip distal digit segment tip of digit uberon UBERON:0009551 distal segment of digit cjm A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium). digit tip distal digit segment tip of digit A segment of the manual digit containing the distal phalanx UBERON:0004093 OpenCyc:Mx4rvVjpf5wpEbGdrcN5Y29ycA finger digit tip finger distal segment finger tip fingertip forelimb digit tip tip of finger uberon UBERON:0009552 distal segment of manual digit A segment of the manual digit containing the distal phalanx finger digit tip finger distal segment finger tip fingertip HP:0001211 forelimb digit tip A segment of the pedal digit containing the distal phalanx. Note this class represents a digit segment and thus includes tissues in addition to bone. hindlimb digit tip tip of toe toe digit tip toe distal segment uberon P3 segment of pedal digit distalmost part of toe UBERON:0009553 distal segment of pedal digit A segment of the pedal digit containing the distal phalanx. Note this class represents a digit segment and thus includes tissues in addition to bone. hindlimb digit tip tip of toe toe digit tip toe distal segment P3 segment of pedal digit distalmost part of toe A skeletal joint that connects a mesopodium bone and connects a proximal phalanx. We include these joints as being part of the digits; this is consistent with the FMA, and makes classification easier. Note that digit and metapodial regions are part-disjoint metacarpo-tarsophalangeal joint metapodial-phalangeal joint metapodium-phalanx joint fetlock uberon UBERON:0009559 metacarpal/tarsal-phalangeal joint A skeletal joint that connects a mesopodium bone and connects a proximal phalanx. OBOL:automatic metacarpo-tarsophalangeal joint metapodial-phalangeal joint metapodium-phalanx joint fetlock NCBITaxon:9788 A submucosa that is part of a intestine. FMA:15696 submucosa of intestine uberon UBERON:0009566 intestinal submucosa FMA A submucosa that is part of a intestine. OBOL:automatic submucosa of intestine FMA:15696 Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] AAO:0000612 FMA:72066 NCIT:C92597 thoracolumbar column thoracolumbar region of vertebral column thoracolumbar vertebrae set thoracolumbar vertebral column trunk vertebrae series trunk vertebral column uberon presacral region thoracolumbar region trunk region trunk skeleton trunk spine UBERON:0009568 trunk region of vertebral column Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions. UBERONREF:0000006 Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] 2012-06-20 AAO:0000612 AAO AAO:Duellman_and_Trueb_1994 thoracolumbar vertebrae set FMA:72066 presacral region AAO:0000612 thoracolumbar region AAO:0000612 trunk region AAO:0000612 FMA:25054 region of trunk trunk subdivision uberon UBERON:0009569 subdivision of trunk region of trunk FMA:25054 trunk subdivision FMA:25054 A sulcus limitans of neural tube that is part of a future spinal cord. EHDAA2:0001265 EMAPA:17584 VHOG:0001548 spinal cord lateral wall sulcus limitans uberon UBERON:0009570 spinal cord sulcus limitans A sulcus limitans of neural tube that is part of a future spinal cord. OBOL:automatic spinal cord lateral wall sulcus limitans EHDAA2:0001265 A sulcus limitans of neural tube that is part of a future medulla oblongata. EHDAA2:0001100 EMAPA:17561 uberon UBERON:0009576 medulla oblongata sulcus limitans EHDAA2 A sulcus limitans of neural tube that is part of a future medulla oblongata. OBOL:automatic A sulcus limitans of neural tube that is part of a future metencephalon. EHDAA2:0001161 EMAPA:17567 uberon UBERON:0009577 metencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future metencephalon. OBOL:automatic A sulcus limitans of neural tube that is part of a future myelencephalon. EHDAA2:0001945 uberon UBERON:0009578 myelencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future myelencephalon. OBOL:automatic EHDAA2:0000397 EMAPA:16906 VHOG:0000912 diencephalon lateral wall mantle layer mantle layer lateral wall diencephalon uberon UBERON:0009580 diencephalon mantle layer mantle layer lateral wall diencephalon VHOG:0000912 EHDAA2:0001172 EMAPA:16977 VHOG:0000910 mantle layer lateral wall midbrain midbrain lateral wall mantle layer uberon mantle layer lateral wall mesencephalon UBERON:0009581 midbrain mantle layer mantle layer lateral wall midbrain VHOG:0000910 mantle layer lateral wall mesencephalon VHOG:0000910 EMAPA:17580 VHOG:0000911 mantle layer lateral wall spinal cord spinal cord lateral wall mantle layer uberon UBERON:0009583 spinal cord mantle layer mantle layer lateral wall spinal cord VHOG:0000911 Mesenchyme that is part of a 1st arch mandibular component. UBERON:0010043 EHDAA2:0000034 EMAPA:16385 mesenchymal region of mandibular component of first pharyngeal arch mesenchyme of mandibular component uberon mandibular component mesenchyme mandibular mesenchyme UBERON:0009584 1st arch mandibular mesenchyme EMAPA Mesenchyme that is part of a 1st arch mandibular component. OBOL:automatic mesenchymal region of mandibular component of first pharyngeal arch mesenchyme of mandibular component EMAPA:16385 Mesenchyme that is part of a developing left lung. EHDAA2:0000944 EMAPA:16730 EMAPA:17654 left lung mesenchyme uberon UBERON:0009602 left lung associated mesenchyme Mesenchyme that is part of a developing left lung. OBOL:automatic left lung mesenchyme EMAPA:17654 Mesenchyme that is part of a developing right lung. EHDAA2:0001739 EMAPA:17662 right lung mesenchyme uberon UBERON:0009603 right lung associated mesenchyme Mesenchyme that is part of a developing right lung. OBOL:automatic right lung mesenchyme EMAPA:17662 A neural plate that develops_from a future forebrain. TAO:0007018 ZFA:0007018 uberon UBERON:0009610 forebrain neural plate ZFA ZFA A neural plate that develops_from a future forebrain. OBOL:automatic A neural plate that develops_from a presumptive midbrain. TAO:0007019 ZFA:0007019 uberon UBERON:0009611 midbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive midbrain. OBOL:automatic A neural plate that develops_from a presumptive hindbrain. TAO:0007022 ZFA:0007022 uberon UBERON:0009614 hindbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive hindbrain. OBOL:automatic TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 MHB neural plate midbrain-hindbrain boundary neural plate uberon UBERON:0009615 midbrain hindbrain boundary neural plate ZFA https://github.com/obophenotype/uberon/issues/438 Bgee:AN MHB neural plate midbrain-hindbrain boundary neural plate ZFA:0007044 A presumptive structure that has the potential to develop into a midbrain. TODO - unify naming conventions BAMS:MES EFO:0003432 EHDAA2:0000615 EMAPA:16140 TAO:0000148 ZFA:0000148 presumptive mesencephalon uberon early midbrain future midbrain mesencephalon UBERON:0009616 presumptive midbrain ZFA ZFA A presumptive structure that has the potential to develop into a midbrain. OBOL:automatic presumptive mesencephalon ZFA:0000148 early midbrain future midbrain mesencephalon EHDAA2:0000615 Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. A major contributor to neurocranium [PMID:16313393] EHDAA2:0000736 EHDAA:364 EMAPA:16171 cephalic paraxial mesenchyme cephalic paraxial mesoderm cranial paraxial mesenchyme cranial paraxial mesoderm head paraxial mesenchyme uberon somitomere somitomeric mesoderm UBERON:0009617 head paraxial mesoderm Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. cephalic paraxial mesenchyme cephalic paraxial mesoderm cranial paraxial mesenchyme cranial paraxial mesoderm head paraxial mesenchyme EHDAA2:0000736 EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon trunk paraxial mesenchyme UBERON:0009618 trunk paraxial mesoderm trunk and cervical paraxial mesenchyme EHDAA2:0002094 trunk paraxial mesenchyme A somite that is part of a tail. AAO:0010383 EMAPA:16860 XAO:0003143 uberon UBERON:0009621 tail somite A somite that is part of a tail. OBOL:automatic The lumbar nerves are the five spinal nerves emerging from the lumbar vertebrae. They are divided into posterior and anterior divisions. FMA:5861 NCIT:C33015 UMLS:C0228897 lumbar spinal nerve nervus lumbalis uberon nervi lumbales UBERON:0009624 lumbar nerve http://upload.wikimedia.org/wikipedia/commons/d/d1/Gray802.png The lumbar nerves are the five spinal nerves emerging from the lumbar vertebrae. They are divided into posterior and anterior divisions. UMLS:C0228897 ncithesaurus:Lumbar_Nerve lumbar spinal nerve FMA:5861 nervus lumbalis FMA:5861 FMA:TA nervi lumbales EMAPA:35878 MA:0001859 uberon UBERON:0009644 trachea non-cartilage connective tissue MA A sympathetic nerve trunk that is part of a lower back. EMAPA:37655 FMA:6263 MA:0001163 NCIT:C52828 UMLS:C1708762 lumbar sympathetic trunk uberon lumbar part of sympathetic trunk lumbar sympathetic chain UBERON:0009646 lumbar sympathetic nerve trunk A sympathetic nerve trunk that is part of a lower back. OBOL:automatic EMAPA:37655 MA:th UMLS:C1708762 ncithesaurus:Lumbar_Sympathetic_Nerve_Trunk lumbar sympathetic trunk FMA:6263 lumbar part of sympathetic trunk FMA:6263 lumbar sympathetic chain FMA:6263 One of the two epithelia which make up the tympanic membrane (along with the fibrous layer) EMAPA:19064 MA:0001224 NCIT:C49308 UMLS:C1711401 tympanic epithelium tympanic membrane epithelial layer uberon UBERON:0009647 tympanic membrane epithelium One of the two epithelia which make up the tympanic membrane (along with the fibrous layer) UMLS:C1711401 ncithesaurus:Tympanic_Epithelium tympanic epithelium MA:0001224 A basement membrane that is part of a nephron tubule. EMAPA:37490 MA:0001680 NCIT:C49273 UMLS:C1709901 kidney tubule basement membrane renal tubular basement membrane renal tubule basement membrane uberon UBERON:0009651 nephron tubule basement membrane true A basement membrane that is part of a nephron tubule. OBOL:automatic EMAPA:37490 MA:th UMLS:C1709901 ncithesaurus:Renal_Tubule_Basement_Membrane kidney tubule basement membrane MA:0001680 renal tubule basement membrane MA:0001680 A basement membrane that is part of a bronchus. MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108 EMAPA:37809 MA:0001832 NCIT:C49208 UMLS:C1707051 bronchial basement membrane uberon UBERON:0009652 bronchus basement membrane true A basement membrane that is part of a bronchus. OBOL:automatic MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108 MA EMAPA:37809 MA:th UMLS:C1707051 ncithesaurus:Bronchus_Basement_Membrane bronchial basement membrane A basement membrane that is part of a trachea. EMAPA:37552 MA:0001854 NCIT:C49302 UMLS:C1710455 uberon UBERON:0009653 trachea basement membrane true MA-modified A basement membrane that is part of a trachea. OBOL:automatic EMAPA:37552 MA:th UMLS:C1710455 ncithesaurus:Trachea_Basement_Membrane An artery that supplies oxygenated blood to the ear. add child terms EMAPA:37072 MA:0001918 NCIT:C52849 UMLS:C1706858 uberon UBERON:0009655 auricular artery An artery that supplies oxygenated blood to the ear. ncithesaurus:Auricular_Artery EMAPA:37072 MA:th UMLS:C1706858 ncithesaurus:Auricular_Artery EMAPA:37092 MA:0001987 NCIT:C52947 UMLS:C1708633 labial artery uberon UBERON:0009657 artery of lip EMAPA:37092 MA:th UMLS:C1708633 ncithesaurus:Labial_Artery labial artery MA:0001987 Nucleus located in the midbrain. TAO:0002209 ZFA:0001665 uberon UBERON:0009661 midbrain nucleus Nucleus located in the midbrain. ZFIN:curator Nucleus located within the hindbrain. TAO:0002177 ZFA:0001658 uberon UBERON:0009662 hindbrain nucleus Nucleus located within the hindbrain. ZFIN:curator A nucleus of brain that is part of a telencephalon. TAO:0002178 ZFA:0001660 uberon UBERON:0009663 telencephalic nucleus A nucleus of brain that is part of a telencephalon. OBOL:automatic EHDAA2:0004566 EMAPA:32911 MA:0003203 uberon peritoneal cavity mesentary peritoneal mesentary UBERON:0009664 gut mesentery https://github.com/obophenotype/uberon/issues/509 EHDAA2 peritoneal cavity mesentary peritoneal mesentary Ventral mesentery is the part of the peritoneum closest to the navel. degenerates during development except foregut portion EHDAA2:0004569 uberon UBERON:0009668 ventral mesentery EHDAA2 Ventral mesentery is the part of the peritoneum closest to the navel. An anatomical space that surrounded_by a embryonic cloaca. EHDAA2:0004586 uberon UBERON:0009669 embryonic cloacal lumen An anatomical space that surrounded_by a embryonic cloaca. OBOL:automatic An anatomical space that surrounded_by a rectum. EHDAA2:0004587 EMAPA:18388 FMA:14598 lumen of rectum uberon UBERON:0009670 rectal lumen cjm EHDAA2 An anatomical space that surrounded_by a rectum. OBOL:automatic lumen of rectum FMA:14598 The nasal fin is an epithelial seam that develops by fusion between the epithelial linings of the medial and lateral nasal swellings. Shortly after its formation the nasal fin regresses and is replaced by mesenchyme, with exception of its most posterior portion which remains as the bucconasal membrane. EHDAA2:0004548 FMA:295940 uberon UBERON:0009671 nasal fin The nasal fin is an epithelial seam that develops by fusion between the epithelial linings of the medial and lateral nasal swellings. Shortly after its formation the nasal fin regresses and is replaced by mesenchyme, with exception of its most posterior portion which remains as the bucconasal membrane. The oronasal membrane separates the oral cavity and nasal cavity. split into two? In humans, the oronasal membrane ruptures during the seventh week, producing a single, large oronasal cavity EHDAA2:0000188 EHDAA:7840 EHDAA:7984 FMA:295942 bucconasal membrane uberon UBERON:0009672 oronasal membrane EHDAA2 EHDAA2 EHDAA2 posterior portion EHDAA2 The oronasal membrane separates the oral cavity and nasal cavity. bucconasal membrane EHDAA:7840 EFO:0003562 EHDAA2:0001981 EHDAA:1993 EHDAA:2671 EMAPA:16914 early telencephalic vesicle uberon early telencephalic ventricle UBERON:0009676 early telencephalic vesicle EHDAA2 EHDAA2 early telencephalic vesicle EHDAA2:0001981 Anatomical cluster consisting of adjacent teeth constituting a row. FMA:59415 TAO:0001667 ZFA:0001642 dental arcade row of teeth tooth rows uberon UBERON:0009678 tooth row Anatomical cluster consisting of adjacent teeth constituting a row. ZFIN:curator dental arcade FMA:59415 row of teeth tooth rows ZFA:0001642 A tooth row that is part of a skeleton of lower jaw. EHDAA2:0001029 FMA:55635 arcus dentalis inferior lower dental arcade lower jaw teeth set of all lower teeth uberon mandibular dental arcade UBERON:0009679 set of lower jaw teeth A tooth row that is part of a skeleton of lower jaw. OBOL:automatic arcus dentalis inferior FMA:TA lower dental arcade FMA:55635 lower jaw teeth EHDAA2:0001029 set of all lower teeth FMA:55635 mandibular dental arcade FMA:55635 A epithelium that is part of a hypopharynx. EHDAA2:0004575 FMA:62454 epithelium of laryngeal pharynx laryngopharynx epithelium uberon UBERON:0009695 epithelium of laryngopharynx EHDAA2 A epithelium that is part of a hypopharynx. OBOL:automatic epithelium of laryngeal pharynx FMA:62454 laryngopharynx epithelium FMA:62454 A epithelium that is part of a vermiform appendix. CALOHA:TS-2062 EHDAA2:0004561 FMA:63581 appendix epithelium epithelium of vermiform appendix uberon UBERON:0009697 epithelium of appendix A epithelium that is part of a vermiform appendix. OBOL:automatic appendix epithelium FMA:63581 epithelium of vermiform appendix FMA:63581 EHDAA2:0001371 uberon pancreatis dorsalis UBERON:0009708 dorsal pancreas EHDAA2 EHDAA2 EHDAA2 cjm EHDAA2:0001393 uberon pancreatis ventralis UBERON:0009709 ventral pancreas EHDAA2 EHDAA2 EHDAA2 cjm Any endocardium that is part of the right ventricle of the heart. Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. EHDAA2:0002188 EMAPA:17341 FMA:9536 NCIT:C102343 VHOG:0001235 right ventricle endocardium right ventricular endocardium uberon endocardial lining of right ventricle right ventricle endocardial tissue UBERON:0009712 endocardium of right ventricle EHDAA2 FMA Any endocardium that is part of the right ventricle of the heart. Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. FMA:9536 right ventricle endocardium VHOG:0001235 right ventricular endocardium FMA:9536 endocardial lining of right ventricle EMAPA:17341 right ventricle endocardial tissue VHOG:0001235 Any endocardium that is part of the left ventricle of the heart. Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. EHDAA2:0002182 EMAPA:17338 FMA:9559 VHOG:0001233 left ventricle endocardium left ventricular endocardium uberon endocardial lining of left ventricle left ventricle endocardial tissue UBERON:0009713 endocardium of left ventricle FMA Any endocardium that is part of the left ventricle of the heart. Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. FMA:9559 left ventricle endocardium VHOG:0001233 left ventricular endocardium FMA:9559 endocardial lining of left ventricle EMAPA:17338 left ventricle endocardial tissue VHOG:0001233 An anatomical cavity that surrounded_by a stomodeum. lumen of stomatodaeum lumen of stomodeum stomatodeal cavity uberon UBERON:0009715 stomodeal lumen An anatomical cavity that surrounded_by a stomodeum. OBOL:automatic EHDAA2:0004621 EMAPA:32754 FMA:293087 uberon pharyngeal arch endoderm UBERON:0009722 entire pharyngeal arch endoderm pharyngeal arch endoderm EHDAA2:0004621 The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels medullary sinus EMAPA:37898 FMA:312359 uberon lymph node medullary sinusoid UBERON:0009744 Lymph flows into the medullary sinuses from cortical sinuses, and into efferent lymphatic vessels. Medullary sinuses contain histiocytes (immobile macrophages) and reticular cells.[WP] lymph node medullary sinus The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels MP:0011222 EMAPA:37898 MA:th The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node medullary cord EMAPA:37897 uberon UBERON:0009745 lymph node medullary cord The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node MP:0011224 EMAPA:37897 MA:th The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells. EMAPA mapping from TH EMAPA:32705 uberon limb mesoderm UBERON:0009749 limb mesenchyme The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells. MP:0011261 EMAPA mapping from TH EMAPA limb mesoderm Geisha:syn NCBITaxon:8782 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts EHDAA2:0004162 EMAPA:36438 heart mesenchyme uberon UBERON:0009751 cardiac mesenchyme The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures MP:0011264 heart mesenchyme EMAPA:36438 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas EFO:0002557 EMAPA:26220 uberon UBERON:0009752 pancreas mesenchyme The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas MP:0011265 A ganglion that is part of a abdominal segment of trunk. uberon UBERON:0009758 abdominal ganglion A ganglion that is part of a abdominal segment of trunk. OBOL:automatic An inter-phalangeal joint that connects a proximal phalanx to either a medial or distal phalanx. FMA:65022 NCIT:C101528 PIJ joint PIP joint uberon UBERON:0009767 proximal interphalangeal joint An inter-phalangeal joint that connects a proximal phalanx to either a medial or distal phalanx. PIJ joint PIP joint An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx. FMA:65024 NCIT:C101529 DIJ joint DIP joint uberon UBERON:0009768 distal interphalangeal joint An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx. DIJ joint DIP joint A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules renal tubule (generic) tubule of excretory system uberon UBERON:0009773 renal tubule A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. GO:0061333 GOC:dph GOC:mtg_kidney_jan10 renal tubule (generic) tubule of excretory system OBOL:automatic A serous sac that has the pleura and the pleural cavity as parts. despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2:0004737 FMA:9690 uberon UBERON:0009778 pleural sac FMA FMA-abduced-lr A serous sac that has the pleura and the pleural cavity as parts. despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2 The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. acinar acinus FMA:55588 uberon acini UBERON:0009842 glandular acinus http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. acinus FMA:55588 acini A solid cord of prostate epithelium. cord of prostate epithelium epithelial cord of prostate uberon UBERON:0009843 Complexity is conferred on the prostate during a postnatal development phase known as branching morphogenesis. Solid cords of prostate epithelium formed in utero elongate postnatally and their tips are bifurcated into primary, secondary, and tertiary branches in a pattern that is unique for each prostate lobe. Branching morphogenesis proceeds differentially for each of the three mouse prostate lobes (ventral, dorsolateral, and anterior) and is completed by about postnatal day 20 in mice, providing each lobe with unique glandular architecture [5]. It is important to note that the developing human prostate undergoes a similar series of morphogenetic events especially during prostatic bud formation, but gives rise to a mature glandular prostate that is unique from the rodent and features peripheral, central, and transitional zones[PMID:18977204] prostate epithelial cord A solid cord of prostate epithelium. GO:0060527 OBOL:automatic cord of prostate epithelium An anatomical space that surrounded_by a primitive urogenital sinus. EHDAA2:0002142 uberon UBERON:0009844 urogenital sinus lumen EHDAA2 An anatomical space that surrounded_by a primitive urogenital sinus. OBOL:automatic Mesenchyme that surrounds primitive urogenital sinus. Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth EMAPA:31500 UGM uberon UBERON:0009845 urogenital sinus mesenchyme Mesenchyme that surrounds primitive urogenital sinus. OBOL:automatic UGM An epithelium that is part of a embryonic cloaca. cloacal epithelium EHDAA2:0004585 uberon UBERON:0009846 embryonic cloacal epithelium EHDAA2 An epithelium that is part of a embryonic cloaca. OBOL:automatic cloacal epithelium EHDAA2:0004585 A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop. uberon prostate primordium UBERON:0009847 prostate field A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop. GO:0060515 GOC:dph The part of the uterus above the isthmus and below the orifices of the uterine tubes. CALOHA:TS-1265 EFO:0000382 FMA:17739 NCIT:C12316 UMLS:C0227813 corpus uteri uterine body uterine corpus uberon UBERON:0009853 body of uterus FMA The part of the uterus above the isthmus and below the orifices of the uterine tubes. UMLS:C0227813 ncithesaurus:Corpus_Uteri corpus uteri uterine body FMA:17739 uterine corpus FMA:17739 Branch or outpocketing of the digestive tract. FBbt:00100316 uberon diverticulum of gut intestinal pouch UBERON:0009854 digestive tract diverticulum Branch or outpocketing of the digestive tract. diverticulum of gut FBbt:00100316 galen:Diverticulum pouch uberon diverticulum UBERON:0009856 sac A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach UBERON:0009034 EMAPA:35821 FMA:14558 MA:0002561 gastric zone region of stomach section of stomach uberon UBERON:0009870 zone of stomach http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. ISBN:0073040584 gastric zone FMA:14558 outer portion of the renal cortex. Site of formation of medullary and cortical elements. see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish. EMAPA:27721 MA:0002996 uberon nephrogenic tissue UBERON:0009871 nephrogenic zone outer portion of the renal cortex. Site of formation of medullary and cortical elements. Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region considering adding 'acropodial region' Naming conventions for pod terms under discussion within phenoscape group metacarpal or metatarsal part of limb metacarpus/metatarsus region metapodial segment cannon region equine cannon region uberon metacarpus/metatarsus metapodium UBERON:0009877 metapodium region PHENOSCAPE:ni Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region MA:th cannon region NCBITaxon:9788 equine cannon region NCBITaxon:9788 The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] VSAO:0005022 basipodium skeleton carpal/tarsal skeleton mesopodial skeleton mesopodium skeleton skeletal parts of mesopodium uberon basipodium mesopodium UBERON:0009878 mesopodial skeleton The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO] 2012-08-14 VSAO:0005022 VSAO VSAO:NI relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0005022 VSAO basipodium skeleton VSAO:0005022 VSAO:NI mesopodial skeleton VSAO:0005022 mesopodium skeleton skeletal parts of mesopodium basipodium VSAO:0005022 VSAO:NI mesopodium VSAO:0005022 VSAO:NI Subdivision of skeleton that consists of endochondral elements distal to the zeugopodial skeletal elements which constitute the proximal region of the posterior autopod skeleton[PHENOSCAPE:ad]. Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO] The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG] Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent. AAO:0000220 EMAPA:19133 FMA:71339 GAID:1223 MA:0000050 VHOG:0001160 VSAO:0005024 XAO:0003211 hind mesopodial skeleton hind mesopodium hind mesopodium skeleton set of tarsal bones skeletal parts of hind mesopodium tarsal bones set tarsalia uberon basipodium mesopodium tarsal bones tarsus UBERON:0009879 tarsal skeleton Subdivision of skeleton that consists of endochondral elements distal to the zeugopodial skeletal elements which constitute the proximal region of the posterior autopod skeleton[PHENOSCAPE:ad]. PHENOSCAPE:ad VSAO:0005024 Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO] 2012-06-20 AAO:0000220 AAO AAO:LAP The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG] 2012-09-17 VHOG:0001160 VHOG DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001) Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present PHENOSCAPE:ad we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent. MA set of tarsal bones FMA:71339 tarsal bones set FMA:71339 tarsalia XAO:0003211 basipodium VSAO:0005024 mesopodium VSAO:0005024 tarsus XAO:0003211 Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad]. Segment of the forearm corresponding to the carpus. It consists of several elements that articulate with the radius and ulna at one end and the metacarpals at the other end.[AAO] The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG] Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad]. The structure of the carpus varies widely between different groups of tetrapods, even among those that retain the full set of five digits. In primitive fossil amphibians, such as Eryops, the carpus consists of three rows of bones; a proximal row of three carpals, a second row of four bones, and a distal row of five bones. The proximal carpals are referred to as the radiale, intermediale, and ulnare, after their proximal articulations, and are homologous with the scaphoid, lunate, and triquetal bones respectively. The remaining bones are simply numbered, as the first to fourth centralia (singular: centrale), and the first to fifth distal carpals. Primitively, each of the distal bones appears to have articulated with a single metacarpal. However, the vast majority of later vertebrates, including modern amphibians, have undergone varying degrees of loss and fusion of these primitive bones, resulting in a smaller number of carpals. Almost all mammals and reptiles, for example, have lost the fifth distal carpal, and have only a single centrale - and even this is missing in humans. The pisiform bone is somewhat unusual, in that it first appears in primitive reptiles, and is never found in amphibians. Because many tetrapods have less than five digits on the forelimb, even greater degrees of fusion are common, and a huge array of different possible combinations are found. The wing of a modern bird, for example, has only two remaining carpals; the radiale (the scaphoid of mammals) and a bone formed from the fusion of four of the distal carpals. In some macropods, the scaphoid and lunar bones are fused into the scaphollunar bone we assume MA:carpus belongs here, as there is a distinct class MA:wrist, with the carpal bone being part of the former. XAO:carpus is part of the forelimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent. AAO:0000201 FMA:71335 MA:0000040 VHOG:0001161 VSAO:0005023 XAO:0003207 carpal bones carpal bones set fore mesopodial skeleton fore mesopodium skeleton ossa carpi skeletal parts of fore mesopodium skeleton of carpus uberon carpus fore mesopodium ossa carpi set of carpal bones UBERON:0009880 carpal skeleton http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad]. PHENOSCAPE:ad Segment of the forearm corresponding to the carpus. It consists of several elements that articulate with the radius and ulna at one end and the metacarpals at the other end.[AAO] 2012-06-20 AAO:0000201 AAO AAO:LAP The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG] 2012-09-17 VHOG:0001161 VHOG DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001) Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad]. we assume MA:carpus belongs here, as there is a distinct class MA:wrist, with the carpal bone being part of the former. XAO:carpus is part of the forelimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent. MA carpal bones EMAPA:25056 FMA:71335 carpal bones set FMA:71335 carpus MA:0000040 XAO:0003207 fore mesopodium AAO:0000201 ossa carpi set of carpal bones FMA:71335 EFO:0003704 TAO:0005041 ZFA:0005041 ALPM uberon UBERON:0009881 anterior lateral plate mesoderm ZFA ALPM ZFA:0005041 A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla. FMA says parenchyma, MP says cortex Their name is potentially misleading -- the 'medullary' refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla BTO:0001155 EMAPA:37906 FMA:74299 Ferrein's pyramid kidney medullary ray renal medullary ray uberon UBERON:0009883 medullary ray FMA MP A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla. MP:0011347 FMA says parenchyma, MP says cortex FMA EMAPA:37906 MA:th Ferrein's pyramid MP:0011347 kidney medullary ray MP:0011347 renal medullary ray MP:0011347 An artery that supplies a renal lobe. FMA only has the set term EMAPA:37091 FMA:71637 arteriae interlobares renis interlobar artery of kidney kidney interlobar artery renal interlobar artery uberon arteriae interlobares renis interlobar arteries of kidney set of interlobar arteries of kidney UBERON:0009885 interlobar artery Kidney:PioM.png An artery that supplies a renal lobe. FMA only has the set term FMA EMAPA:37091 MA:th arteriae interlobares renis FMA:TA interlobar artery of kidney FMA:71637 renal interlobar artery MP:0011355 arteriae interlobares renis interlobar arteries of kidney FMA:71637 set of interlobar arteries of kidney FMA:71637 The interlobar veins are veins of the renal circulation which drain the renal lobes. FMA only has the set term FMA:71631 interlobar vein of kidney venae interlobares renis uberon interlobar veins of kidney set of interlobar veins of kidney venae interlobares renis UBERON:0009887 interlobar vein Kidney:PioM.png The interlobar veins are veins of the renal circulation which drain the renal lobes. FMA only has the set term FMA interlobar vein of kidney FMA:71631 venae interlobares renis FMA:TA interlobar veins of kidney FMA:71631 set of interlobar veins of kidney FMA:71631 venae interlobares renis A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested in mouse has left ventricular identity[PMID:22855565] XAO:0004186 anterior heart field anterior/second heart field second heart field uberon SHF UBERON:0009889 secondary heart field GO:0003129 A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). GO:0003139 GOC:mtg_heart GOC:rl extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested anterior heart field anterior/second heart field Geisha:syn NCBITaxon:8782 second heart field XAO:0004186 SHF XAO:0004186 Mesenchyme that is part of a developing face. EMAPA:35337 FMA:302884 face mesenchyme mesenchyme of face uberon UBERON:0009891 facial mesenchyme Mesenchyme that is part of a developing face. OBOL:automatic todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland) FMA:45737 NCIT:C12990 UMLS:C0921005 lobulus uberon UBERON:0009911 lobule cjm UMLS:C0921005 ncithesaurus:Lobule lobulus FMA:45737 FMA:TA A portion of an organ, such as the liver, lung, breast, or brain. FMA:45728 NCIT:C13393 lobus uberon UBERON:0009912 anatomical lobe cjm A portion of an organ, such as the liver, lung, breast, or brain. ncithesaurus:Lobe lobus FMA:45728 FMA:TA The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP]. todo - add has_part relationships. human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys FMA:17881 NCIT:C32894 UMLS:C0736382 kidney lobe lobi renalis lobus renalis uberon lobi renales UBERON:0009913 renal lobe Kidney:PioM.png The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP]. MP:0011381 human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys MP UMLS:C0736382 ncithesaurus:Kidney_Lower_Lobe kidney lobe MP:0011381 lobi renalis lobus renalis lobi renales The portion of a renal lobe consisting of nephrons grouped around a single medullary ray and draining into a single collecting duct; human kidneys have multilobular, multipapillary architecture while mice and rats have unilobular, unipapillary kidneys FMA:17670 kidney lobule lobulus renalis uberon cortical lobule cortical lobule of kidney lobuli corticales renis lobulus corticalis renalis renal cortical lobule renculus reniculus renunculus UBERON:0009914 Alternate definition: One of the subdivisions of the kidney, consisting of a medullary ray and that portion of the convoluted port (renal corpuscles and convoluted tubules) associated with its collecting duct. -http://www.mondofacto.com/facts/dictionary?lobulus+corticalis+renalis renal lobule FMA The portion of a renal lobe consisting of nephrons grouped around a single medullary ray and draining into a single collecting duct; human kidneys have multilobular, multipapillary architecture while mice and rats have unilobular, unipapillary kidneys MP:0011382 kidney lobule MP:0011382 cortical lobule MP:0011382 cortical lobule of kidney lobuli corticales renis lobulus corticalis renalis renal cortical lobule renculus reniculus renunculus An anatomical wall that is part of a ureter. FMA:15888 ureteral wall uberon UBERON:0009916 wall of ureter An anatomical wall that is part of a ureter. OBOL:automatic ureteral wall FMA:15888 The region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary EMAPA:37886 uberon UBERON:0009917 kidney corticomedullary boundary MP The region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary MP:0011376 EMAPA:37886 MA:th The smooth muscle tissue surrounding the epithelium of the ureter EMAPA:28811 ureteral smooth muscle ureteral smooth muscle layer uberon UBERON:0009919 ureter smooth muscle The smooth muscle tissue surrounding the epithelium of the ureter MP:0011426 ureteral smooth muscle MP:0011426 ureteral smooth muscle layer EMAPA:28844 EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest EHDAA2 A multicellular organism that existence_starts_with a post-embryonic stage. MA:0002405 postnatal organism TS28 mouse post-hatching organism post-natal organism postnatal mouse uberon UBERON:0009953 post-embryonic organism https://github.com/obophenotype/uberon/issues/667 A multicellular organism that existence_starts_with a post-embryonic stage. OBOL:automatic TS28 mouse MA:0002405 post-hatching organism post-natal organism postnatal mouse MA:0002405 Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. Includes: trigeminal, otic, lateral line and epibranchial placodes. While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) EFO:0003460 TAO:0001309 XAO:0004620 ZFA:0001309 neurogenic placodes uberon placodae neurogenicae UBERON:0009955 neurogenic placode cjm Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) NCBIBook:NBK53171 neurogenic placodes ZFA:0001309 placodae neurogenicae A anatomical space that is enclosed by a urinary bladder. EHDAA2:0004058 FMA:15924 galen:UrinaryBladderCavity bladder cavity cavity of urinary bladder lumen of urinary bladder urinary bladder lumen uberon UBERON:0009958 bladder lumen FMA FMA EHDAA2 A anatomical space that is enclosed by a urinary bladder. OBOL:automatic bladder cavity FMA:15924 cavity of urinary bladder FMA:15924 lumen of urinary bladder FMA:15924 urinary bladder lumen FMA:15924 A anatomical space that is enclosed by a oropharynx. EHDAA2:0004556 FMA:55095 oropharyngeal cavity oropharynx lumen uberon UBERON:0009959 lumen of oropharynx EHDAA2 A anatomical space that is enclosed by a oropharynx. OBOL:automatic oropharyngeal cavity EHDAA2:0004556 oropharynx lumen FMA:55095 An epithelium that is part of a pancreatic duct. in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this EFO:0002556 FMA:67681 pancreatic duct epithelium pancreatic ductal epithelium uberon UBERON:0009970 epithelium of pancreatic duct An epithelium that is part of a pancreatic duct. OBOL:automatic pancreatic duct epithelium FMA:67681 pancreatic ductal epithelium FMA:67681 The junction between the ureter and the renal pelvis of the kidney EMAPA:37782 FMA:15898 MA:0003021 NCIT:C106203 pelviureteric junction pelvoureteric junction uberon UBERON:0009972 ureteropelvic junction MP The junction between the ureter and the renal pelvis of the kidney MP:0011487 EMAPA:37782 MA:th pelviureteric junction FMA:15898 The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney EMAPA:37783 FMA:15899 MA:0003020 NCIT:C106202 vesico-ureteral junction vesico-ureteric junction vesicoureteric junction uberon UBERON:0009973 ureterovesical junction MP The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney MP:0011488 EMAPA:37783 MA:th vesico-ureteral junction MA:0003020 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure CARO An anatomical structure that has more than one cell as a part. CARO:0010000 multicellular structure FBbt:00100313 A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 FBbt:00007229 uberon UBERON:0010001 Examples include arthropod sensilla. cell cluster organ CARO CARO FBbt A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 The dorsal portion of the embryonic first endodermal pharyngeal pouch; it develops into the middle ear cavity. The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[well established][VHOG] EHDAA2:0004115 EHDAA:6772 EMAPA:17002 FMA:312393 MA:0001218 NCIT:C34318 UMLS:C1284046 VHOG:0001297 uberon tubotympanic recess UBERON:0010020 tubotympanic recess epithelium EHDAA2 EHDAA2 ISBN:0073040584 The dorsal portion of the embryonic first endodermal pharyngeal pouch; it develops into the middle ear cavity. ISBN:0124020607 VHOG:0001297 The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[well established][VHOG] 2012-09-17 VHOG:0001297 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417 UMLS:C1284046 ncithesaurus:Tubotympanic_Recess tubotympanic recess VHOG:0001297 in humans, persists as the tonsillar fossa - the endodermal lining covers the mesodermal lymphatic tissue to form the palatine tonsil[ISBN:1607950324]. the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract dorsal 2nd branchial pouch dorsal pharyngeal pouch 2 uberon dorsal branchial pouch 2 endoderm dorsal elongation of second pouch endoderm dorsal pharyngeal pouch 2 endoderm UBERON:0010023 dorsal part of pharyngeal pouch 2 in humans, persists as the tonsillar fossa - the endodermal lining covers the mesodermal lymphatic tissue to form the palatine tonsil[ISBN:1607950324]. the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract MP Mesenchyme that is part of a pharyngeal arch 6. EHDAA2:0004076 EMAPA:32765 FMA:318209 6th pharyngeal arch mesenchyme uberon 6th branchial arch mesenchyme pharyngeal arch 6 mesenchyme UBERON:0010031 6th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 6. OBOL:automatic The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch. The lateral lingual swellings grow and fuse with eachother, encompassing the tuberculum impar to provide the ectodermally derived mucosa of the anterior 2/3 of the tongue check NCIT EMAPA:37437 FMA:229084 NCIT:C32130 UMLS:C0226946 uberon anterior 2/3 of the tongue anterior 2/3 of tongue anterior two thirds of the tongue apex linguae apex of the tongue buccal part of the tongue front of the tongue oral part of the tongue pars anterior dorsi linguae UBERON:0010032 anterior part of tongue Illu04:tongue.jpg ISBN:1607950324 The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch. check NCIT NCIT EMAPA:37437 MA:th UMLS:C0226946 ncithesaurus:Apex_of_the_Tongue anterior 2/3 of the tongue anterior 2/3 of tongue anterior two thirds of the tongue apex linguae apex of the tongue buccal part of the tongue front of the tongue oral part of the tongue pars anterior dorsi linguae An organ of the digestive tract that is capable of retaining and storing food This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates BSA:0000123 TADS:0000172 TGMA:0001041 uberon UBERON:0010039 food storage organ An organ of the digestive tract that is capable of retaining and storing food Mesenchyme that is part of a pharyngeal arch 1. EMAPA:16128 mesenchyme of 1st arch uberon UBERON:0010042 1st arch mesenchyme Mesenchyme that is part of a pharyngeal arch 1. OBOL:automatic mesenchyme of 1st arch EMAPA:16128 Mesenchyme that is part of a 1st arch maxillary component. EHDAA2:0000041 EMAPA:16391 mesenchyme of maxillary component uberon maxillary component mesenchyme maxillary mesenchyme UBERON:0010045 1st arch maxillary mesenchyme Mesenchyme that is part of a 1st arch maxillary component. OBOL:automatic mesenchyme of maxillary component EMAPA:16391 The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. EHDAA2:0001459 EMAPA:16550 XAO:0004524 associated mesenchyme of pharyngeal region entire branchial arch associated mesenchyme pharyngeal arch associated mesenchyme uberon UBERON:0010046 entire pharyngeal arch associated mesenchyme EHDAA2 EHDAA2 cjm The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. XAO:0004524 associated mesenchyme of pharyngeal region EMAPA:16550 entire branchial arch associated mesenchyme pharyngeal arch associated mesenchyme EHDAA2:0001459 Gland of the epithelium lining the oral cavity. The most common are the salivary glands. Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa UBERON:0003293 EHDAA2:0001327 EHDAA:2181 EMAPA:16572 EMAPA:16723 VHOG:0000652 buccal gland uberon gland of oral opening gland of oral region mouth gland oral cavity gland oral region gland UBERON:0010047 oral gland Gland of the epithelium lining the oral cavity. The most common are the salivary glands. ISBN:0073040584 Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa EHDAA2 A mucosa that is part of a dorsum of tongue. check surface terms develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN:1607950324 FMA:74871 mucosa of dorsal surface of tongue uberon UBERON:0010052 mucosa of dorsum of tongue A mucosa that is part of a dorsum of tongue. OBOL:automatic A stapes endochondral element that is composed primarily of cartilage tissue. TODO - check relationship to Recihert's The stapes is homologous to the hyomandibula. In this ontology, we use the class 'hyomandibular cartilage' generally to include the future stapes, the future hyomandibular bone of teleosts and the unossified cartilage in sharks. EMAPA:18230 uberon UBERON:0010055 stapes cartilage element A stapes endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A compound organ that has the potential to develop into a tongue. EHDAA2:0000696 EHDAA:2951 uberon UBERON:0010056 future tongue EHDAA2 A compound organ that has the potential to develop into a tongue. OBOL:automatic EHDAA2:0004610 uberon UBERON:0010059 hypoglossal cord EHDAA2 EHDAA2 EHDAA2:0004116 uberon UBERON:0010063 tympanic cavity epithelium EHDAA2 EHDAA2 An anatomical space with at least one opening to another space or the exterior. AEO:0000221 EHDAA2:0004616 uberon UBERON:0010064 open anatomical space cjm An anatomical space with at least one opening to another space or the exterior. AEO:0000221 EHDAA2:0004114 uberon UBERON:0010065 auditory meatus epithelium EHDAA2 EHDAA2 A portion of the external acoustic meatus epithelium which makes up the outer (cuticular) layer of the tympanic membrane FMA:56819 cuticular layer of tympanic membrane cuticular stratum of tympanic membrane outer cuticular layer of tympanic membrane outer layer of tympanic membrane tympanic membrane external acoustic meatus epithelial component uberon UBERON:0010069 outer epithelial layer of tympanic membrane A portion of the external acoustic meatus epithelium which makes up the outer (cuticular) layer of the tympanic membrane cuticular layer of tympanic membrane FMA:56819 cuticular stratum of tympanic membrane FMA:56819 outer cuticular layer of tympanic membrane FMA:56819 tympanic membrane external acoustic meatus epithelial component The intermediate fibrous layer of the tympanic membrane. check MA EMAPA:19063 FMA:56830 MA:0001223 connective tissue layer of tympanic membrane fibrous layer of tympanic membrane fibrous stratum of tympanic membrane intermediate fibrous layer of tympanic membrane tympanic endothelium uberon UBERON:0010070 intermediate layer of tympanic membrane FMA The intermediate fibrous layer of the tympanic membrane. check MA MA connective tissue layer of tympanic membrane FMA:56830 fibrous layer of tympanic membrane FMA:56830 fibrous stratum of tympanic membrane FMA:56830 intermediate fibrous layer of tympanic membrane FMA:56830 tympanic endothelium MA:0001223 In mammals, this class groups together the two epithelial layers plus the intermediate fibrous layer FMA:56732 tympanic membrane layer uberon UBERON:0010071 layer of tympanic membrane tympanic membrane layer FMA:56732 Organ system subdivision that consists primarily of chromaffin cells and their supporting structures. in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies FMA:79645 MESH:D002838 uberon argentaffin system chromaffin tissue UBERON:0010074 chromaffin system cjm Organ system subdivision that consists primarily of chromaffin cells and their supporting structures. argentaffin system MESH:A06.224 One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia. XAO:0004192 uberon UBERON:0010075 sacral neural crest One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia. XB:curator An epithelium consisting of cuboidal epithelial cells. TODO - coordinate with CL, add cuboidal cell in NCIT this is glandular NCIT:C32415 UMLS:C0682577 uberon UBERON:0010077 cuboidal epithelium An epithelium consisting of cuboidal epithelial cells. in NCIT this is glandular NCIT UMLS:C0682577 ncithesaurus:Cuboidal_Epithelium An extrahepatic bile duct that has the potential to develop into a common hepatic duct. EHDAA2:0000595 uberon UBERON:0010081 future common hepatic duct An extrahepatic bile duct that has the potential to develop into a common hepatic duct. OBOL:automatic Mesenchyme that has the potential to develop into a dermis. check development EHDAA2:0000598 uberon UBERON:0010083 future dermis EHDAA2 EHDAA2 XAO Mesenchyme that has the potential to develop into a dermis. OBOL:automatic A structure that will develop into a diaphragm. EHDAA2:0000599 uberon UBERON:0010084 future diaphragm EHDAA2 A structure that will develop into a diaphragm. A multi-tissue structure that has the potential to develop into a meninx of hindbrain. EHDAA2:0000610 future hindbrain meninges uberon UBERON:0010091 future hindbrain meninx A multi-tissue structure that has the potential to develop into a meninx of hindbrain. OBOL:automatic future hindbrain meninges EHDAA2:0000610 A developing anatomical structure that has the potential to develop into a metencephalon. EHDAA2:0000623 uberon UBERON:0010092 future metencephalon A developing anatomical structure that has the potential to develop into a metencephalon. OBOL:automatic A developing anatomical structure that has the potential to develop into a myelencephalon. EHDAA2:0000640 uberon UBERON:0010096 future myelencephalon A developing anatomical structure that has the potential to develop into a myelencephalon. OBOL:automatic A gray matter that has the potential to develop into a facial nucleus. EHDAA2:0004639 uberon UBERON:0010123 future facial nucleus A gray matter that has the potential to develop into a facial nucleus. OBOL:automatic A gray matter that has the potential to develop into a superior salivatory nucleus. EHDAA2:0004644 uberon UBERON:0010125 future superior salivatory nucleus A gray matter that has the potential to develop into a superior salivatory nucleus. OBOL:automatic A femur endochondral element that is composed primarily of cartilage tissue. TODO - request EHDAA2 EMAPA:17742 femoral cartilage condensation uberon UBERON:0010129 femur cartilage element A femur endochondral element that is composed primarily of cartilage tissue. OBOL:automatic femoral cartilage condensation EMAPA:17742 The distal elements of the developing limb of vertebrates that will give rise to the autopod (e.g. manus, pes, paw) autopod plate limb plate uberon UBERON:0010130 embryonic autopod plate The distal elements of the developing limb of vertebrates that will give rise to the autopod (e.g. manus, pes, paw) MP:0004576 UBERON:cjm Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. EHDAA2:0004528 FMA:83378 specialized conducting tissue of heart specialized muscle tissue of heart uberon UBERON:0010131 conducting tissue of heart Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. specialized conducting tissue of heart FMA:83378 specialized muscle tissue of heart FMA:83378 any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli MA:0000720 neuroendocrine system gland uberon UBERON:0010133 neuroendocrine gland any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli ISBN:0-683-40008-8 MP:0000631 A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid. EMAPA:35759 MA:0002943 uberon UBERON:0010134 secretory circumventricular organ MA MA A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid. A circumventricular organ that is capable of monitoring the levels of substances to the cerebrospinal fluid. EMAPA:37741 MA:0002944 uberon humerosensory circumventricular organ humerosensory system humerosensory system organ sensitive circumventricular organs sensitive organs sensory CVOs sensory circumventricular organs UBERON:0010135 sensory circumventricular organ A circumventricular organ that is capable of monitoring the levels of substances to the cerebrospinal fluid. EMAPA:37741 MA:th humerosensory system NeuroNames:2856 sensitive circumventricular organs NeuroNames:2856 sensitive organs NeuroNames:2856 sensory CVOs NeuroNames:2856 sensory circumventricular organs NeuroNames:2856 A sex cord that is part of a indifferent gonad. note that this represents the indifferent structure. EHDAA2:0004051 indifferent sex cord primitive sex cords uberon UBERON:0010141 primitive sex cord of indifferent gonad EHDAA2 EHDAA2 A sex cord that is part of a indifferent gonad. OBOL:automatic primitive sex cords EHDAA2:0004051 A bodily secretion that is produced by a seminal vesicle. constitutes 60-70 % of the ejaculate in humans[MP] important for semen coagulation, sperm motility, and stability of sperm chromatin and suppression of the immune activity in the female reproductive tract[MP] in ncit, seminal fluid is a subtype of seminal vesicle secretion vesicular fluid BTO:0002053 FMA:62969 MA:0002526 NCIT:C33529 NCIT:C52552 UMLS:C0036614 UMLS:C0227987 secretion of seminal vesicle seminal vesicle secretion uberon seminal fluid UBERON:0010143 seminal vesicle fluid FMA A bodily secretion that is produced by a seminal vesicle. in ncit, seminal fluid is a subtype of seminal vesicle secretion ncit UMLS:C0036614 ncithesaurus:Seminal_Fluid UMLS:C0227987 ncithesaurus:Seminal_Vesicle_Secretion secretion of seminal vesicle FMA:62969 seminal vesicle secretion FMA:62969 seminal fluid Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. BTO:0004798 uberon male accessory gland male accessory reproductive gland UBERON:0010147 male accessory sex gland BTO Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. BTO:0004798 male accessory gland BTO:0004798 A mucous secretion that is produced by glands in the epidermis. uberon epidermal mucus skin mucous UBERON:0010152 skin mucus A mucous secretion that is produced by glands in the epidermis. epidermal mucus BTO:0005082 An anatomical cavity that surrounded_by a lymphatic vessel. FMA:59681 lumen of lymphatic duct lymphatic vessel lumen uberon UBERON:0010160 lumen of lymphatic vessel An anatomical cavity that surrounded_by a lymphatic vessel. OBOL:automatic lumen of lymphatic duct FMA:59681 lymphatic vessel lumen FMA:59681 An anatomical cavity that surrounded_by a blood vessel. FMA:312610 blood vessel lumen uberon UBERON:0010161 lumen of blood vessel An anatomical cavity that surrounded_by a blood vessel. OBOL:automatic The distal end of the tail EMAPA:37760 MA:0002848 XAO:0004057 tail tip uberon end of tail UBERON:0010162 post-anal tail tip MA The distal end of the tail EMAPA:37760 MA:th tail tip MA:0002848 end of tail MA:0002848 An anatomical cluster that composed_primarily_of a strand of hair. FMA:70752 hairs hairs set pili set of hairs uberon UBERON:0010164 collection of hairs An anatomical cluster that composed_primarily_of a strand of hair. OBOL:automatic hairs FMA:70752 hairs set FMA:70752 pili FMA:TA set of hairs FMA:70752 A collection of hairs that is part of a face. FMA:70741 facial hairs set set of facial hairs uberon facial hair UBERON:0010165 collection of hair on face A collection of hairs that is part of a face. OBOL:automatic facial hairs set FMA:70741 set of facial hairs FMA:70741 A strand of hair that is part of a face. FMA:54360 face hair face hair strand hair of face uberon facial hair UBERON:0010171 strand of hair of face A strand of hair that is part of a face. OBOL:automatic face hair FMA:54360 hair of face FMA:54360 facial hair FMA:54360 A trabecula that is part of a liver uberon hepatic trabecula UBERON:0010183 liver trabecula A trabecula that is part of a liver GO:0060344 OBOL:automatic any of the numerous small mucous-secreting glands located in the wall of the penile urethra EMAPA:29645 FMA:21443 NCIT:C49311 UMLS:C1314737 Littre's gland gland of Littre gland of male urethra male urethra gland urethral gland (male) uberon glandulae urethrales urethrae masculinae UBERON:0010186 male urethral gland any of the numerous small mucous-secreting glands located in the wall of the penile urethra MGI:anna MP:0011794 UMLS:C1314737 ncithesaurus:Urethral_Gland Littre's gland FMA:21443 urethral gland (male) FMA:21443 glandulae urethrales urethrae masculinae An urethral gland that is part of a female urethra. EMAPA:29653 FMA:21444 female urethra gland gland of female urethra urethral gland (female) uberon UBERON:0010187 female urethral gland An urethral gland that is part of a female urethra. OBOL:automatic urethral gland (female) FMA:21444 A roughly circular bulge in a surface. requires review AEO:0000205 EHDAA2:0003250 FMA:82506 uberon UBERON:0010188 protuberance FMA A roughly circular bulge in a surface. EHDAA2:0003250 part_of in EHDAA2. Only child in MA. EHDAA2:0001762 EMAPA:17010 EMAPA:17328 MA:0001872 uberon right venous valve UBERON:0010189 right atrium venous valve part_of in EHDAA2. Only child in MA. EHDAA2 right venous valve EHDAA2:0001762 the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation EHDAA2:0000410 EMAPA:18606 MA:0000476 paired dorsal aortae uberon UBERON:0010190 pair of dorsal aortae EHDAA2 EHDAA2 the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation ISBN:0-914294-08-3 MP:0004787 paired dorsal aortae EHDAA2:0000410 EHDAA2:0004512 uberon UBERON:0010191 aortic system Wikipedia One of the laterally paired arteries that supply the gonads. gonadal artery uberon UBERON:0010192 genital artery One of the laterally paired arteries that supply the gonads. ISBN:0073040584 An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 uberon UBERON:0010199 One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) bona-fide anatomical boundary CARO An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 A vasculature that is part of a post-anal tail. isa blood vessel in XAO TAO:0005037 XAO:0004151 ZFA:0005037 post-vent vasculature uberon tail vasculature UBERON:0010204 tail vasculature A vasculature that is part of a post-anal tail. OBOL:automatic isa blood vessel in XAO XAO post-vent vasculature ZFA:0005037 tail vasculature ZFA:0005037 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton AAO:0000267 EHDAA2:0000904 laryngeal cartilage system uberon UBERON:0010212 laryngeal apparatus EHDAA2 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. AAO:0000267 laryngeal cartilage system EHDAA2:0000904 uberon UBERON:0010213 laryngeal pre-cartilage condensation EHDAA2-abstracted EHDAA2-abstracted EHDAA2:0004085 uberon UBERON:0010221 Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6? laryngeal associated mesenchyme EHDAA2 EHDAA2 Wikipedia Wikipedia Wikipedia A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified]. EHDAA2:0004469 FMA:258745 uberon UBERON:0010225 thalamic complex A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified]. Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. FMA:71005 TAO:0002228 ZFA:0001718 presumptive atrium heart tube primordial atrium primordial cardiac atrium uberon UBERON:0010227 future cardiac atrium ZFA Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. ZFA:0001718 presumptive atrium heart tube ZFA:0001718 primordial atrium FMA:71005 primordial cardiac atrium FMA:71005 The core globe-shaped component of the camera-type eye. See notes for camera-type eye FMA:12513 MIAA:0000283 VHOG:0001616 bulbus oculi eye globe eyeball uberon eye globe UBERON:0010230 eyeball of camera-type eye FMA The core globe-shaped component of the camera-type eye. UBERON:cjm eye globe VHOG:0001616 eyeball FMA:12513 eye globe HP:0100886 MIAA:0000283 The connective tissue that supports the lobules and follicles of the thyroid gland. FMA:86304 thyroid gland stroma thyroid stroma uberon UBERON:0010233 stroma of thyroid gland The connective tissue that supports the lobules and follicles of the thyroid gland. thyroid gland stroma FMA:86304 Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000037 uberon UBERON:0010252 1st arch mandibular mesenchyme from neural crest inferred Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000044 uberon UBERON:0010253 1st arch maxillary mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme. EHDAA2:0000068 EMAPA:16281 neural crest derived arch 2 mesenchyme pharyngeal arch 2 mesenchyme from neural crest uberon branchial arch 2 mesenchyme from neural crest UBERON:0010254 2nd arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000083 EMAPA:16404 VHOG:0000571 3rd pharyngeal arch mesenchyme derived from neural crest mesenchyme derived from neural crest of mesenchyme of 3rd arch neural crest derived arch 3 mesenchyme pharyngeal arch 3 mesenchyme from neural crest uberon branchial arch 3 mesenchyme from neural crest UBERON:0010255 3rd arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000571 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 3rd pharyngeal arch mesenchyme derived from neural crest VHOG:0000571 mesenchyme derived from neural crest of mesenchyme of 3rd arch EMAPA:16404 Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000098 EMAPA:16772 VHOG:0000580 4th pharyngeal arch mesenchyme derived from neural crest mesenchyme derived from neural crest of mesenchyme of 4th arch neural crest derived arch 4 mesenchyme pharyngeal arch 4 mesenchyme from neural crest uberon branchial arch 4 mesenchyme from neural crest UBERON:0010256 4th arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000580 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) 4th pharyngeal arch mesenchyme derived from neural crest VHOG:0000580 mesenchyme derived from neural crest of mesenchyme of 4th arch EMAPA:16772 Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. EHDAA2:0004077 neural crest derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from neural crest uberon branchial arch 6 mesenchyme from neural crest UBERON:0010257 6th arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a rhombencephalon neural crest. EHDAA2:0004423 uberon UBERON:0010258 mesenchyme from rhombencephalic neural crest Mesenchyme that develops_from a rhombencephalon neural crest. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. EMAPA:16129 mesenchyme derived from neural crest of mesenchyme of 1st arch neural crest derived arch 1 mesenchyme pharyngeal arch 1 mesenchyme from neural crest uberon branchial arch 1 mesenchyme from neural crest UBERON:0010259 1st arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from neural crest of mesenchyme of 1st arch EMAPA:16129 One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton's jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta. EMAPA:36493 allantoic vessel umbilical cord blood vessel umbilical vessel uberon umbilical cord blood vessels umbilical vasculature UBERON:0010260 umbilical blood vessel One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton's jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta. MP:0003230 allantoic vessel Hymans:Hymans umbilical cord blood vessels A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO] relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO] In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process). AAO:0000225 AAO:0000682 EMAPA:37600 MA:0003037 uberon apparatus hyobranchialis apparatus hyoideus hyobranchial apparatus hyolingual system UBERON:0010272 hyoid apparatus AAO A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO] 2012-06-20 AAO:0000225 AAO AAO:LAP relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO] 2012-06-20 AAO:0000225 AAO EMAPA:37600 MA:th apparatus hyobranchialis apparatus hyoideus hyobranchial apparatus AAO:0000225 hyolingual system AAO:0000225 A zone of bone organ that is part of a hyoid bone. FMA:59494 hyoid bone zone uberon UBERON:0010273 zone of hyoid bone A zone of bone organ that is part of a hyoid bone. OBOL:automatic hyoid bone zone FMA:59494 Any anatomical space that is part of a vertebral column. AAO:0000700 vertebral column opening vertebral conduit uberon UBERON:0010276 space in vertebral column Any anatomical space that is part of a vertebral column. OBOL:automatic vertebral column opening AAO:0000700 A minute orifice on the summit of the papillae lacrimales, which is the commencement point of the lacrimal canaliculi. collect tears produced by the lacrimal glands FMA:59365 uberon lacrimal point lacrimal puncta puncta lacrimalia UBERON:0010284 lacrimal punctum http://upload.wikimedia.org/wikipedia/commons/5/53/Gray895.png FMA A minute orifice on the summit of the papillae lacrimales, which is the commencement point of the lacrimal canaliculi. lacrimal point lacrimal puncta puncta lacrimalia Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 EHDAA2:0004375 TAO:0000761 ZFA:0000761 basal plate midbrain basal plate midbrain region uberon UBERON:0010285 midbrain basal plate EHDAA2 EHDAA2 ZFA Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. ZFA:0000761 basal plate midbrain TAO:0000761 basal plate midbrain region ZFA:0000761 Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 ZFA:0007039 uberon UBERON:0010286 midbrain neural tube ZFA Portion of neural tube that gives rise to the midbrain. ZFA:0007039 . uberon UBERON:0010291 layer of sclera cjm . An endothelium that is part of a sclera. uberon UBERON:0010294 scleral endothelium Wikipedia An endothelium that is part of a sclera. OBOL:automatic A stroma that is part of a sclera. subsantia propria FMA:58365 NCIT:C33652 UMLS:C1704397 scleral stroma stroma of sclera subsantia propria sclerae substantia propria sclerae uberon UBERON:0010295 substantia propria of sclera Wikipedia A stroma that is part of a sclera. OBOL:automatic UMLS:C1704397 ncithesaurus:Substantia_Propria scleral stroma FMA:58365 stroma of sclera FMA:58365 subsantia propria sclerae FMA:58365 substantia propria sclerae FMA:58365 FMA:TA Mesenchyme surrounding the developing optic cup which develops into the sclera. The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288 uberon UBERON:0010299 scleral mesenchyme Mesenchyme surrounding the developing optic cup which develops into the sclera. An epithelium that is part of a extraembryonic structure. extra-embryonic epithelium uberon UBERON:0010303 extraembryonic epithelium An epithelium that is part of a extraembryonic structure. OBOL:automatic Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus. FMA:45569 epithelium stratificatum squamosum noncornificatum nonkeratinizing stratified squamous epithelium stratified squamous non-keratinized epithelium stratified squamous nonkeratinizing epithelium uberon UBERON:0010304 non-keratinized stratified squamous epithelium FMA Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus. FMA:45569 epithelium stratificatum squamosum noncornificatum FMA:45569 nonkeratinizing stratified squamous epithelium FMA:45569 stratified squamous non-keratinized epithelium stratified squamous nonkeratinizing epithelium Developing anatomical structure that develops into the eyeball and associated structures. Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] TAO:0002201 ZFA:0001678 future eye uberon UBERON:0010312 immature eye definitional Developing anatomical structure that develops into the eyeball and associated structures. ZFA:0001678 Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] 2012-08-14 TAO:0002201 TAO ZFIN:curator An anatomical structure that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010313 neural crest-derived structure An anatomical structure that develops from the neural crest. An anatomical structure that has some part that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010314 structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. uberon UBERON:0010316 germ layer / neural crest A skeletal element that is part of a orbital region. uberon eye skeleton ocular skeleton skeletal element of orbital region UBERON:0010321 skeletal element of eye region A skeletal element that is part of a orbital region. OBOL:automatic Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints) that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] AAO:0000109 AAO:0000971 AAO:0010185 TAO:0000737 VSAO:0000049 XAO:0003075 ZFA:0000737 cranial skeleton osteocranium uberon cranium UBERON:0010323 cranial skeletal system Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. GO_REF:0000034 PSPUB:0000170 VSAO:0000049 Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] 2012-06-20 AAO:0000109 AAO AAO:LAP Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] 2012-08-14 TAO:0000737 TAO ZFIN:curator cranium ZFA:0000737 Mesenchyme that is part of a limb bud. uberon UBERON:0010328 limb bud mesenchyme Mesenchyme that is part of a limb bud. OBOL:automatic Mesenchyme that is part of a limb/fin bud. uberon UBERON:0010329 paired limb/fin bud mesenchyme Mesenchyme that is part of a limb/fin bud. OBOL:automatic An epithelium that is part of a handplate. EHDAA2:0000730 EMAPA:32630 handplate epithelium uberon UBERON:0010332 epithelium of handplate EHDAA2 EHDAA2 An epithelium that is part of a handplate. OBOL:automatic handplate epithelium EHDAA2:0000730 Mesenchyme that is part of a extraembryonic membrane. uberon UBERON:0010333 extraembryonic membrane mesenchyme EHDAA2-abduced Mesenchyme that is part of a extraembryonic membrane. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme. EHDAA2:0004601 uberon UBERON:0010334 maxillary process mesenchyme from neural crest EHDAA2 Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme. EHDAA2:0004602 uberon UBERON:0010335 maxillary process mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. EHDAA2:0004603 uberon UBERON:0010336 mandibular process mesenchyme from neural crest EHDAA2 Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. EHDAA2:0004604 uberon UBERON:0010337 mandibular process mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme. EHDAA2:0000043 uberon UBERON:0010338 1st arch maxillary mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000036 uberon UBERON:0010339 1st arch mandibular mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. EMAPA:16130 mesenchyme derived from head mesoderm of mesenchyme of 1st arch uberon UBERON:0010341 1st arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 1st arch EMAPA:16130 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme. EHDAA2:0000067 EMAPA:16280 head mesenchyme derived arch 2 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 2nd arch pharyngeal arch 2 mesenchyme from head mesenchyme uberon branchial arch 2 mesenchyme from head mesenchyme UBERON:0010343 2nd arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 2nd arch EMAPA:16280 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme. EHDAA2:0000082 EMAPA:16403 head mesenchyme derived arch 3 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 3rd arch pharyngeal arch 3 mesenchyme from head mesenchyme uberon branchial arch 3 mesenchyme from head mesenchyme UBERON:0010344 3rd arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 3rd arch EMAPA:16403 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. EHDAA2:0000097 EMAPA:16771 head mesenchyme derived arch 4 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 4th arch pharyngeal arch 4 mesenchyme from head mesenchyme uberon branchial arch 4 mesenchyme from head mesenchyme UBERON:0010345 4th arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 4th arch EMAPA:16771 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. EHDAA2:0004078 head mesenchyme derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from head mesenchyme uberon branchial arch 6 mesenchyme from head mesenchyme UBERON:0010347 6th arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. OBOL:automatic EMAPA:17351 future Reichert's cartilage hyoid cartilage pre-cartilage condensation uberon UBERON:0010354 Reichert's cartilage pre-cartilage condensation EHDAA2 hyoid cartilage pre-cartilage condensation EMAPA:17351 The first step in ossification of the cartilage is that the cartilage cells, at the point where ossification is commencing and which is termed a ossification center, enlarge and arrange themselves in rows. The matrix in which they are imbedded increases in quantity, so that the cells become further separated from each other. A deposit of calcareous material now takes place in this matrix, between the rows of cells, so that they become separated from each other by longitudinal columns of calcified matrix, presenting a granular and opaque appearance. Here and there the matrix between two cells of the same row also becomes calcified, and transverse bars of calcified substance stretch across from one calcareous column to another. Thus there are longitudinal groups of the cartilage cells enclosed in oblong cavities, the walls of which are formed of calcified matrix which cuts off all nutrition from the cells; the cells, in consequence, atrophy, leaving spaces called the primary areolC&. currently classified as a zone of a bone organ, but exists prior to bone ossifying FMA:75436 centrum ossificationis ossification centre uberon center of ossification centrum ossificationis UBERON:0010355 ossification center http://upload.wikimedia.org/wikipedia/commons/f/fd/Gray79.png FMA The first step in ossification of the cartilage is that the cartilage cells, at the point where ossification is commencing and which is termed a ossification center, enlarge and arrange themselves in rows. The matrix in which they are imbedded increases in quantity, so that the cells become further separated from each other. A deposit of calcareous material now takes place in this matrix, between the rows of cells, so that they become separated from each other by longitudinal columns of calcified matrix, presenting a granular and opaque appearance. Here and there the matrix between two cells of the same row also becomes calcified, and transverse bars of calcified substance stretch across from one calcareous column to another. Thus there are longitudinal groups of the cartilage cells enclosed in oblong cavities, the walls of which are formed of calcified matrix which cuts off all nutrition from the cells; the cells, in consequence, atrophy, leaving spaces called the primary areolC&. centrum ossificationis FMA:TA ossification centre FMA:75436 center of ossification centrum ossificationis Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from neural crest branchial arch mesenchyme from neural crest neural crest derived arch mesenchyme uberon UBERON:0010359 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from head mesenchyme branchial arch mesenchyme from head mesenchyme head mesenchyme derived arch mesenchyme uberon UBERON:0010360 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t VSAO:0000037 XAO:0004026 replacement skeleton uberon UBERON:0010362 endoskeleton VSAO Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. GO_REF:0000034 PSPUB:0000170 VSAO:0000037 An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t replacement skeleton VSAO:curator A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. VSAO:0000139 XAO:0004017 ZFA:0005620 endochondral replacement element uberon UBERON:0010363 endochondral element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern VSAO A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. GO_REF:0000034 PSPUB:0000170 VSAO:0000139 endochondral replacement element VSAO:0000139 Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. exoskeleton VSAO:0000035 XAO:0004025 uberon dermal skeletal system dermoskeleton desmoskeleton UBERON:0010364 This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO dermal skeleton VSAO Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. GO_REF:0000034 PSPUB:0000170 VSAO:0000035 exoskeleton VSAO:curator dermal skeletal system VSAO:curator dermoskeleton VSAO:curator desmoskeleton VSAO:curator Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla. in many vertebrates, odontoid tissue is not restricted to the teeth Classified as a portion of organism substance in FMA UBERON:0001973 EMAPA:35872 FMA:63001 MA:0002540 NCIT:C33794 UMLS:C1519551 VSAO:0000063 XAO:0004046 ZFA:0005623 odontogenic tissue portion of substance of tooth substance of tooth tooth substance uberon dental tissue tooth hard tissue tooth tissue UBERON:0010365 odontoid tissue Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla. GO_REF:0000034 PSPUB:0000170 VSAO:0000063 Classified as a portion of organism substance in FMA FMA UMLS:C1519551 ncithesaurus:Tooth_Tissue odontogenic tissue VSAO:curator portion of substance of tooth FMA:63001 substance of tooth FMA:63001 tooth substance MA:0002540 dental tissue VSAO:curator tooth hard tissue VT:0003930 The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa. FMA:75739 NCIT:C33428 lobulus pulmonis uberon UBERON:0010368 pulmonary lobule The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa. ncithesaurus:Pulmonary_Lobule lobulus pulmonis FMA:75739 FMA:TA Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 ectoderm-derived epithelium uberon UBERON:0010371 ecto-epithelium Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen') EHDAA2:0001384 FMA:79793 uberon dorsal pancreas UBERON:0010375 pancreas dorsal primordium EHDAA2 dorsal pancreas FMA:79793 Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen') EHDAA2:0001387 FMA:79794 uberon ventral pancreas UBERON:0010376 pancreas ventral primordium EHDAA2 ventral pancreas FMA:79794 Mesenchyme that develops_from a somatopleure. the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives EHDAA2:0001120 uberon UBERON:0010377 mesenchyme from somatopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a somatopleure. OBOL:automatic Mesenchyme that develops_from a splanchnopleure. EHDAA2:0001122 uberon UBERON:0010378 mesenchyme from splanchnopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a splanchnopleure. OBOL:automatic A anatomical space that is enclosed by a hypopharynx. FMA:55096 laryngopharynx lumen uberon UBERON:0010384 lumen of laryngopharynx FMA A anatomical space that is enclosed by a hypopharynx. OBOL:automatic laryngopharynx lumen FMA:55096 The segment of the rib that connects to a vertebra[MP]. a small part of the rib composed of the head, neck, tuberculum and a short proximal part of the body[PMID] EMAPA:37495 MA:0001400 MA:0001414 proximal part of rib proximal rib proximal rib segment uberon costal part of rib vertebral part of rib UBERON:0010388 The proximal rib derives from the caudal half of somite[PMID:15906248] proximal segment of rib MA The segment of the rib that connects to a vertebra[MP]. a small part of the rib composed of the head, neck, tuberculum and a short proximal part of the body[PMID] MP:0000152 EMAPA:37495 MA:th proximal part of rib proximal rib MA:0001400 An organ cavity that is part of a urethra. FMA:19709 urethral lumen uberon UBERON:0010390 lumen of urethra An organ cavity that is part of a urethra. OBOL:automatic urethral lumen FMA:19709 one of the branches of the splenic artery[MP] When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia] MA:0000759 NCIT:C49775 UMLS:C1710159 uberon trabecular artery UBERON:0010399 spleen trabecular artery MP one of the branches of the splenic artery[MP] MP:0002354 When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia] Wikipedia UMLS:C1710159 ncithesaurus:Splenic_Trabecular_Artery one of the veins that feed the splenic vein The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia] MA:0000760 NCIT:C49779 UMLS:C1710160 uberon trabecular vein UBERON:0010400 spleen trabecular vein one of the veins that feed the splenic vein MP:0002228 The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia] Wikipedia UMLS:C1710160 ncithesaurus:Splenic_Trabecular_Vein trabecular vein The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. EMAPA:35336 MA:0002486 eye surface eye surface region ocular surface uberon UBERON:0010409 ocular surface region The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. MP:0013754 eye surface MA:0002486 An orifice that is part of a lower urinary tract. EMAPA:35965 MA:0002867 urethral orifice uberon UBERON:0010418 urethral opening An orifice that is part of a lower urinary tract. OBOL:automatic urethral orifice OBOL:automatic A naris that is located inside the nasal cavity and connects to the pharynx. choanal In humans the only internal naris is the posterior nasal aperture, which connects to the nasopharynx NCIT:C32856 choana internal choana uberon choanae internal nares internal nostril UBERON:0010425 internal naris A naris that is located inside the nasal cavity and connects to the pharynx. choanae internal nares The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. FMA:76551 ciliary processes ciliary processes set processus ciliares set of ciliary processes uberon ciliary process processus ciliares UBERON:0010427 ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. ciliary processes FMA:76551 ciliary processes set FMA:76551 processus ciliares FMA:TA set of ciliary processes FMA:76551 ciliary process processus ciliares A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. In an adult mammal, most red blood cells are formed in flat bones Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment FMA:7476 NCIT:C32616 UMLS:C0222649 galen:FlatBone uberon os planum UBERON:0010428 Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs flat bone FMA A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. UMLS:C0222649 ncithesaurus:Flat_Bone os planum A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia. glandular in NCIT; we consider the two NCIT terms synonymous FMA:45572 NCIT:C33419 NCIT:C49316 UMLS:C0836138 UMLS:C1514590 uberon UBERON:0010498 pseudostratified columnar epithelium FMA A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. glandular in NCIT; we consider the two NCIT terms synonymous NCIT UMLS:C0836138 ncithesaurus:Pseudostratified_Columnar_Epithelium UMLS:C1514590 ncithesaurus:Pseudostratified_Epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. FMA:13146 NCIT:C13181 UMLS:C0506992 epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) uberon UBERON:0010499 pseudostratified ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. NCIT:NCIT UMLS:C0506992 ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) FMA:13146 Skeletal element that forms as a replacement or substitution of another element or tissue. VSAO:0000135 XAO:0004016 ZFA:0005624 uberon UBERON:0010522 replacement element VSAO cjm Skeletal element that forms as a replacement or substitution of another element or tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000135 A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 TAO:0005251 ZFA:0005251 uberon microcirculatory vessels UBERON:0010523 microcirculatory vessel ZFA A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 ZFA:0005251 microcirculatory vessels TAO:0005251 An organ cavity that surrounded_by a bone. FMA:24021 bone organ cavity uberon UBERON:0010527 cavity of bone organ An organ cavity that surrounded_by a bone. OBOL:automatic bone organ cavity FMA:24021 FMA:24028 air space of bone uberon UBERON:0010528 pneumatic cavity of bone FMA air space of bone FMA:24028 . different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic. EHDAA2:0001143 EHDAA:7007 EHDAA:8105 EMAPA:17953 EMAPA:27621 MA:0002998 VHOG:0001241 induced blastemal cells nephrogenic interstitium of nephrogenic zone uberon cap mesenchyme of metanephros of urinary system nephrogenic interstitium peripheral blastema UBERON:0010531 metanephros induced blastemal cells EHDAA2 . different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic. EMAPA induced blastemal cells VHOG:0001241 nephrogenic interstitium of nephrogenic zone EMAPA:17953 cap mesenchyme of metanephros of urinary system EMAPA:17645 peripheral blastema EMAPA:17953 An epithelial tube that is fated to become a nephron. EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells developing nephron primitive nephron future nephron presumptive nephron uberon UBERON:0010532 primitive nephron EHDAA2-inferred EHDAA2 An epithelial tube that is fated to become a nephron. EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells EHDAA2 The metanephric cortex is the outer region of the metanephros[GO]. VHOG:0000714 uberon UBERON:0010533 metanephros cortex VHOG The metanephric cortex is the outer region of the metanephros[GO]. GO:0072214 Anatomical cluster which give rise to mature mesonephric nephrons. Zebrafish continously generate new mesonephric nephrons. ZFA:0005584 developing mesonephric nephron primitive mesonephric nephron uberon UBERON:0010534 primitive mesonephric nephron Anatomical cluster which give rise to mature mesonephric nephrons. Zebrafish continously generate new mesonephric nephrons. GOC:cvs ORCiD:0000-0002-2244-7917 ZFA:0005584 developing mesonephric nephron ZFA:0005584 A primitive nephron that is part of a metanephros. primitive nephron EHDAA2:0001516 developing metanephric nephron primitive metanephric nephron uberon UBERON:0010535 primitive metanephric nephron EHDAA2 A primitive nephron that is part of a metanephros. OBOL:automatic primitive nephron EHDAA2:0001516 uberon UBERON:0010536 nephron progenitor ZFA cjm Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells. ZFA:0005587 uberon UBERON:0010537 mesonephric nephron progenitor Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells. ZFA:0005587 An appendage segment that is part of a limb/fin. limb/fin segment uberon UBERON:0010538 paired limb/fin segment An appendage segment that is part of a limb/fin. OBOL:automatic A pre-cartilage condensation that has the potential to develop into a tarsal bone. EHDAA2:0001978 uberon UBERON:0010540 tarsus pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a tarsal bone. OBOL:automatic A cartilaginous condensation that has the potential to develop into a tarsal bone. EHDAA2:0001977 uberon UBERON:0010541 tarsus cartilage element EHDAA2 A cartilaginous condensation that has the potential to develop into a tarsal bone. OBOL:automatic The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified]. FMA:231315 VSAO:0005028 acropodial skeleton acropodium skeleton set of phalanges skeletal parts of acropodial region uberon acropodium digital skeleton digits skeleton phalangeal skeleton skeletal parts of acropodium skeleton of digits UBERON:0010543 acropodial skeleton PHENOSCAPE:ni The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified]. VSAO:0005028 VSAO:NI set of phalanges FMA:231315 acropodium VSAO:0005028 VSAO:NI The metacarpus is the intermediate part of the manus skeleton that is located between the phalanges (bones of the fingers) distally and the carpus which forms the connection to the forearm. The metacarpus consists of metacarpal bones. The metacarpals form a transverse arch to which the rigid row of distal carpal bones are fixed. The peripheral metacarpals (those of the thumb and little finger) form the sides of the cup of the palmar gutter and as they are brought together they deepen this concavity. The index metacarpal is the most firmly fixed, while the thumb metacarpal articulates with the trapezium and acts independently from the others. The middle metacarpals are tightly united to the carpus by intrinsic interlocking bone elements at their bases. The ring metacarpal forms a transitional element of the semi-independent last metacarpal. [WP,unvetted]. Segment of the forearm corresponding to the metacarpus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO] AAO:0000946 EMAPA:36158 FMA:71336 MESH:A02.835.232.087.535 VSAO:0005026 XAO:0003208 anterior metapodial skeleton metacarpal bones metacarpal skeleton metacarpals [I-V] metacarpals set ossa metacarpalia [I-V] ossa metacarpi [I-V] set of metacarpal bones set of metacarpals set of metacarpals [I-V] skeleton of metacarpus uberon anterior metapodium fore metapodial skeleton fore metapodium metacarpalia UBERON:0010544 metacarpus skeleton Metacarpals:numbered-en.svg many to one lexical The metacarpus is the intermediate part of the manus skeleton that is located between the phalanges (bones of the fingers) distally and the carpus which forms the connection to the forearm. The metacarpus consists of metacarpal bones. The metacarpals form a transverse arch to which the rigid row of distal carpal bones are fixed. The peripheral metacarpals (those of the thumb and little finger) form the sides of the cup of the palmar gutter and as they are brought together they deepen this concavity. The index metacarpal is the most firmly fixed, while the thumb metacarpal articulates with the trapezium and acts independently from the others. The middle metacarpals are tightly united to the carpus by intrinsic interlocking bone elements at their bases. The ring metacarpal forms a transitional element of the semi-independent last metacarpal. [WP,unvetted]. Segment of the forearm corresponding to the metacarpus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO] 2012-06-20 AAO:0000946 AAO AAO:LAP metacarpal bones FMA:71336 metacarpals [I-V] FMA:71336 metacarpals set FMA:71336 ossa metacarpalia [I-V] FMA:71336 FMA:TA ossa metacarpi [I-V] FMA:71336 FMA:TA set of metacarpal bones FMA:71336 set of metacarpals FMA:71336 set of metacarpals [I-V] FMA:71336 anterior metapodium VSAO:0005026 VSAO:NI fore metapodium AAO:0000946 MA:th metacarpalia Limb segment that consists of the long bones of the pes. The metatarsals are analogous to the metacarpal bones of the manus. Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO] AAO:0000221 FMA:71340 MESH:D008684 OpenCyc:Mx4rva_rBJwpEbGdrcN5Y29ycA VSAO:0005027 XAO:0003212 metatarsal bones set metatarsal skeleton metatarsals [I-V] ossa metatarsalia [I-V] ossa metatarsi[I-V] posterior metapodial skeleton set of metatarsal bones set of metatarsals [I-V] skeleton of metatarsus uberon metatarsalia ossa metatarsalia posterior metapodium UBERON:0010545 metatarsus skeleton http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png many to one lexical Limb segment that consists of the long bones of the pes. The metatarsals are analogous to the metacarpal bones of the manus. Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO] 2012-06-20 AAO:0000221 AAO AAO:LAP metatarsal bones set FMA:71340 metatarsals [I-V] FMA:71340 ossa metatarsalia [I-V] FMA:71340 FMA:TA ossa metatarsi[I-V] FMA:71340 FMA:TA set of metatarsal bones FMA:71340 set of metatarsals [I-V] FMA:71340 ossa metatarsalia posterior metapodium VSAO:0005027 VSAO:NI Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton. Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] VSAO:0005025 metacarpal/metatarsal skeleton metapodial skeleton metapodium skeleton skeletal parts of metapodium skeleton of metapodium uberon metapodium UBERON:0010546 metapodial skeleton PHENOSCAPE:ni Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton. Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO] 2012-08-14 VSAO:0005025 VSAO VSAO:NI relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0005025 VSAO relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0005025 VSAO metapodial skeleton VSAO:0005025 metapodium skeleton skeletal parts of metapodium metapodium VSAO:0005025 VSAO:NI A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 1 mesenchyme. EHDAA2:0002040 EMAPA:17725 hind limb digit 1 metatarsal pre-cartilage condensation pedal digit I metatarsal pre-cartilage condensation toe 1 metatarsal pre-cartilage condensation foot digit 1 metatarsal pre-cartilage condensation uberon UBERON:0010547 pedal digit 1 metatarsal pre-cartilage condensation A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 1 mesenchyme. OBOL:automatic hind limb digit 1 metatarsal pre-cartilage condensation OBOL:accepted pedal digit I metatarsal pre-cartilage condensation toe 1 metatarsal pre-cartilage condensation EHDAA2:0002040 foot digit 1 metatarsal pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 5 mesenchyme. EHDAA2:0002060 EMAPA:17733 hind limb digit 5 metatarsal pre-cartilage condensation pedal digit V metatarsal pre-cartilage condensation toe 5 metatarsal pre-cartilage condensation foot digit 5 metatarsal pre-cartilage condensation uberon UBERON:0010551 pedal digit 5 metatarsal pre-cartilage condensation A pedal digit metatarsal pre-cartilage condensation that is part of a pedal digit 5 mesenchyme. OBOL:automatic hind limb digit 5 metatarsal pre-cartilage condensation OBOL:accepted pedal digit V metatarsal pre-cartilage condensation toe 5 metatarsal pre-cartilage condensation EHDAA2:0002060 foot digit 5 metatarsal pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pedal digit metatarsal cartilage condensation that is part of a pedal digit 1 mesenchyme. EMAPA:18106 hind limb digit 1 metatarsal cartilage condensation pedal digit I metatarsal cartilage element toe 1 metatarsal cartilage condensation foot digit 1 metatarsal cartilage element uberon UBERON:0010557 pedal digit 1 metatarsal cartilage element A pedal digit metatarsal cartilage condensation that is part of a pedal digit 1 mesenchyme. OBOL:automatic hind limb digit 1 metatarsal cartilage condensation OBOL:accepted pedal digit I metatarsal cartilage element foot digit 1 metatarsal cartilage element NCBITaxon:9606 OBOL:accepted A pedal digit metatarsal cartilage element that is part of a pedal digit 5 mesenchyme. EMAPA:18126 hind limb digit 5 metatarsal cartilage element pedal digit V metatarsal cartilage element toe 5 metatarsal cartilage element foot digit 5 metatarsal cartilage element uberon UBERON:0010561 pedal digit 5 metatarsal cartilage element A pedal digit metatarsal cartilage element that is part of a pedal digit 5 mesenchyme. OBOL:automatic hind limb digit 5 metatarsal cartilage element OBOL:accepted pedal digit V metatarsal cartilage element foot digit 5 metatarsal cartilage element NCBITaxon:9606 OBOL:accepted Mesenchyme that is part of a developing pedal digit 1. EHDAA2:0002039 EMAPA:17462 hind limb digit 1 mesenchyme pedal digit I mesenchyme foot digit 1 mesenchyme uberon UBERON:0010562 pedal digit 1 mesenchyme Mesenchyme that is part of a developing pedal digit 1. OBOL:automatic hind limb digit 1 mesenchyme OBOL:accepted pedal digit I mesenchyme foot digit 1 mesenchyme NCBITaxon:9606 OBOL:accepted Mesenchyme that is part of a developing manual digit 1. EHDAA2:0000513 EMAPA:17431 fore limb digit 1 mesenchyme manual digit I mesenchyme hand digit 1 mesenchyme uberon UBERON:0010564 manual digit 1 mesenchyme Mesenchyme that is part of a developing manual digit 1. OBOL:automatic fore limb digit 1 mesenchyme OBOL:accepted manual digit I mesenchyme hand digit 1 mesenchyme NCBITaxon:9606 OBOL:accepted A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 1 mesenchyme. EHDAA2:0000515 EMAPA:17714 finger 1 metacarpus pre-cartilage condensation fore limb digit 1 metacarpus pre-cartilage condensation manual digit I metacarpus pre-cartilage condensation metacarpal 1 pre-cartilage condensation hand digit 1 metacarpus pre-cartilage condensation uberon UBERON:0010565 manual digit 1 metacarpus pre-cartilage condensation A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 1 mesenchyme. OBOL:automatic finger 1 metacarpus pre-cartilage condensation EHDAA2:0000515 fore limb digit 1 metacarpus pre-cartilage condensation OBOL:accepted manual digit I metacarpus pre-cartilage condensation hand digit 1 metacarpus pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 5 mesenchyme. EHDAA2:0000539 EMAPA:17722 finger 5 metacarpus pre-cartilage condensation fore limb digit 5 metacarpus pre-cartilage condensation manual digit V metacarpus pre-cartilage condensation metacarpal 5 pre-cartilage condensation hand digit 5 metacarpus pre-cartilage condensation uberon UBERON:0010569 manual digit 5 metacarpus pre-cartilage condensation A manual digit metacarpus pre-cartilage condensation that is part of a manual digit 5 mesenchyme. OBOL:automatic finger 5 metacarpus pre-cartilage condensation EHDAA2:0000539 fore limb digit 5 metacarpus pre-cartilage condensation OBOL:accepted manual digit V metacarpus pre-cartilage condensation hand digit 5 metacarpus pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A manual digit metacarpus cartilage element that is part of a manual digit 1 mesenchyme. EHDAA2:0000514 EMAPA:18065 finger 1 metacarpus cartilage element fore limb digit 1 metacarpus cartilage element manual digit I metacarpus cartilage element metacarpus 1 cartilage element hand digit 1 metacarpus cartilage element uberon UBERON:0010570 manual digit 1 metacarpus cartilage element A manual digit metacarpus cartilage element that is part of a manual digit 1 mesenchyme. OBOL:automatic finger 1 metacarpus cartilage element EHDAA2:0000514 fore limb digit 1 metacarpus cartilage element OBOL:accepted manual digit I metacarpus cartilage element hand digit 1 metacarpus cartilage element NCBITaxon:9606 OBOL:accepted A manual digit metacarpus cartilage element that is part of a manual digit 5 mesenchyme. EHDAA2:0000538 EMAPA:18085 finger 5 metacarpus cartilage condensation fore limb digit 5 metacarpus cartilage element manual digit V metacarpus cartilage element metacarpus 5 cartilage element hand digit 5 metacarpus cartilage element uberon UBERON:0010574 manual digit 5 metacarpus cartilage element A manual digit metacarpus cartilage element that is part of a manual digit 5 mesenchyme. OBOL:automatic finger 5 metacarpus cartilage condensation EHDAA2:0000538 fore limb digit 5 metacarpus cartilage element OBOL:accepted manual digit V metacarpus cartilage element hand digit 5 metacarpus cartilage element NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a manual digit 1 mesenchyme. EHDAA2:0000516 EMAPA:17715 fore limb digit 1 phalanx pre-cartilage condensation manual digit I phalanx pre-cartilage condensation hand digit 1 phalanx pre-cartilage condensation uberon UBERON:0010575 manual digit 1 phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a manual digit 1 mesenchyme. OBOL:automatic fore limb digit 1 phalanx pre-cartilage condensation OBOL:accepted manual digit I phalanx pre-cartilage condensation hand digit 1 phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a manual digit 5 mesenchyme. EHDAA2:0000540 EMAPA:17723 fore limb digit 5 phalanx pre-cartilage condensation manual digit V phalanx pre-cartilage condensation hand digit 5 phalanx pre-cartilage condensation uberon UBERON:0010579 manual digit 5 phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a manual digit 5 mesenchyme. OBOL:automatic fore limb digit 5 phalanx pre-cartilage condensation OBOL:accepted manual digit V phalanx pre-cartilage condensation hand digit 5 phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a pedal digit 1 mesenchyme. EHDAA2:0002041 EMAPA:17726 hind limb digit 1 phalanx pre-cartilage condensation pedal digit I phalanx pre-cartilage condensation foot digit 1 phalanx pre-cartilage condensation uberon UBERON:0010580 pedal digit 1 phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a pedal digit 1 mesenchyme. OBOL:automatic hind limb digit 1 phalanx pre-cartilage condensation OBOL:accepted pedal digit I phalanx pre-cartilage condensation foot digit 1 phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a pedal digit 5 mesenchyme. EHDAA2:0002061 EMAPA:17734 hind limb digit 5 phalanx pre-cartilage condensation pedal digit V phalanx pre-cartilage condensation foot digit 5 phalanx pre-cartilage condensation uberon UBERON:0010584 pedal digit 5 phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a pedal digit 5 mesenchyme. OBOL:automatic hind limb digit 5 phalanx pre-cartilage condensation OBOL:accepted pedal digit V phalanx pre-cartilage condensation foot digit 5 phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a pedal digit mesenchyme. EMAPA:32950 VHOG:0000952 foot phalanx pre-cartilage condensation hind limb digit phalanx pre-cartilage condensation hindlimb phalanx pre-cartilage condensation pes phalanx pre-cartilage condensation foot digit phalanx pre-cartilage condensation uberon UBERON:0010585 pedal digit phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a pedal digit mesenchyme. OBOL:automatic foot phalanx pre-cartilage condensation VHOG:0000952 hind limb digit phalanx pre-cartilage condensation OBOL:accepted foot digit phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A pre-cartilage condensation that is part of a manual digit mesenchyme. EMAPA:32639 VHOG:0000954 fore limb digit phalanx pre-cartilage condensation forelimb phalanx pre-cartilage condensation hand phalanx pre-cartilage condensation manus phalanx pre-cartilage condensation hand digit phalanx pre-cartilage condensation uberon UBERON:0010586 manual digit phalanx pre-cartilage condensation A pre-cartilage condensation that is part of a manual digit mesenchyme. OBOL:automatic fore limb digit phalanx pre-cartilage condensation OBOL:accepted hand phalanx pre-cartilage condensation VHOG:0000954 hand digit phalanx pre-cartilage condensation NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a manual digit 1 mesenchyme. EMAPA:18066 fore limb digit 1 phalanx cartilage condensation manual digit I phalanx cartilage element hand digit 1 phalanx cartilage element uberon UBERON:0010675 manual digit 1 phalanx cartilage element A cartilage element that is part of a manual digit 1 mesenchyme. OBOL:automatic fore limb digit 1 phalanx cartilage condensation OBOL:accepted manual digit I phalanx cartilage element hand digit 1 phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a manual digit 5 mesenchyme. EMAPA:18086 fore limb digit 5 phalanx cartilage condensation manual digit V phalanx cartilage element hand digit 5 phalanx cartilage element uberon UBERON:0010679 manual digit 5 phalanx cartilage element A cartilage element that is part of a manual digit 5 mesenchyme. OBOL:automatic fore limb digit 5 phalanx cartilage condensation OBOL:accepted manual digit V phalanx cartilage element hand digit 5 phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a pedal digit 1 mesenchyme. EMAPA:18107 hind limb digit 1 phalanx cartilage condensation pedal digit I phalanx cartilage element foot digit 1 phalanx cartilage element uberon UBERON:0010680 pedal digit 1 phalanx cartilage element A cartilage element that is part of a pedal digit 1 mesenchyme. OBOL:automatic hind limb digit 1 phalanx cartilage condensation OBOL:accepted pedal digit I phalanx cartilage element foot digit 1 phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a pedal digit 5 mesenchyme. EMAPA:18127 hind limb digit 5 phalanx cartilage condensation pedal digit V phalanx cartilage element foot digit 5 phalanx cartilage element uberon UBERON:0010684 pedal digit 5 phalanx cartilage element A cartilage element that is part of a pedal digit 5 mesenchyme. OBOL:automatic hind limb digit 5 phalanx cartilage condensation OBOL:accepted pedal digit V phalanx cartilage element foot digit 5 phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a pedal digit mesenchyme. EMAPA:32948 hind limb digit phalanx cartilage condensation foot digit phalanx cartilage element uberon UBERON:0010685 pedal digit phalanx cartilage element A cartilage element that is part of a pedal digit mesenchyme. OBOL:automatic hind limb digit phalanx cartilage condensation OBOL:accepted foot digit phalanx cartilage element NCBITaxon:9606 OBOL:accepted A cartilage element that is part of a manual digit mesenchyme. EMAPA:32658 fore limb digit phalanx cartilage condensation hand digit phalanx cartilage condensation uberon UBERON:0010686 manual digit phalanx cartilage element A cartilage element that is part of a manual digit mesenchyme. OBOL:automatic fore limb digit phalanx cartilage condensation OBOL:accepted hand digit phalanx cartilage condensation NCBITaxon:9606 OBOL:accepted EMAPA:32956 EMAPA:35568 VHOG:0000948 hind limb digit metatarsal pre-cartilage condensation metatarsal bone pre-cartilage condensation metatarsus pre-cartilage condensation foot digit metatarsal pre-cartilage condensation uberon metatarsal pre-cartilage condensation UBERON:0010687 pedal digit metatarsal pre-cartilage condensation hind limb digit metatarsal pre-cartilage condensation OBOL:accepted metatarsus pre-cartilage condensation VHOG:0000948 foot digit metatarsal pre-cartilage condensation NCBITaxon:9606 OBOL:accepted metatarsal pre-cartilage condensation EMAPA:32956 The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the manual autopodium - i.e. the bones of the hands or their cartilaginous precursors[VSAO,modified]. FMA:71337 VSAO:0005029 all phalanges in forelimb autopod anterior acropodium skeleton fore acropodium skeleton hand digit skeleton manual digit skeleton manual phalanges phalanges of hand phalanges of manus set of manual phalanges set of phalanges of hand set of phalanges of manus uberon anterior acropodium UBERON:0010688 skeleton of manual acropodium PHENOSCAPE:ni lexical The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the manual autopodium - i.e. the bones of the hands or their cartilaginous precursors[VSAO,modified]. VSAO:0005029 VSAO:NI manual phalanges VSAO:0005029 VSAO:NI phalanges of hand FMA:71337 set of phalanges of hand FMA:71337 anterior acropodium VSAO:0005029 VSAO:NI An epithelium that is part of a manual digit 1. EHDAA2:0000512 EMAPA:17430 fore limb digit 1 epithelium manual digit I epithelium hand digit 1 epithelium uberon UBERON:0010690 manual digit 1 epithelium An epithelium that is part of a manual digit 1. OBOL:automatic fore limb digit 1 epithelium OBOL:accepted manual digit I epithelium hand digit 1 epithelium NCBITaxon:9606 OBOL:accepted An epithelium that is part of a pedal digit 1. EHDAA2:0002038 EMAPA:17461 hind limb digit 1 epithelium pedal digit I epithelium foot digit 1 epithelium uberon UBERON:0010693 pedal digit 1 epithelium An epithelium that is part of a pedal digit 1. OBOL:automatic hind limb digit 1 epithelium OBOL:accepted pedal digit I epithelium foot digit 1 epithelium NCBITaxon:9606 OBOL:accepted Mesenchyme of the carpal region that contributes to the tarsal skeleton. EMAPA:18502 uberon UBERON:0010695 mesenchyme of tarsal region Mesenchyme of the carpal region that contributes to the tarsal skeleton. The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the pedal autopodium - i.e. the bones of the foot or their cartilaginous precursors[cjm]. FMA:78512 VSAO:0005030 all phalanges in hindlimb autopod foot digit skeleton hind acropodium skeleton pedal phalanges phalanges of foot phalanges of pes posterior acropodium skeleton set of pedal phalanges set of phalanges of foot set of phalanges of pes uberon posterior acropodium UBERON:0010696 skeleton of pedal acropodium PHENOSCAPE:ni lexical The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the pedal autopodium - i.e. the bones of the foot or their cartilaginous precursors[cjm]. pedal phalanges VSAO:0005030 VSAO:NI phalanges of foot FMA:78512 set of phalanges of foot FMA:78512 posterior acropodium VSAO:0005030 VSAO:NI EMAPA represents the specific child classes as being part of the digit mesenchyme - we follow this although for the fully formed structure we represent the metatarsals as adjoining rather than being part of the digit skeleton EMAPA:32951 hind limb digit metatarsal cartilage condensation foot digit metatarsal cartilage condensation uberon metatarsal cartilage condensation UBERON:0010697 pedal digit metatarsal cartilage element hind limb digit metatarsal cartilage condensation OBOL:accepted foot digit metatarsal cartilage condensation NCBITaxon:9606 OBOL:accepted metatarsal cartilage condensation EMAPA:32951 EMAPA:32850 VHOG:0000953 fore limb digit metacarpus pre-cartilage condensation metacarpal bone pre-cartilage condensation metacarpal pre-cartilage condensation metacarpus pre-cartilage condensation hand digit metacarpus pre-cartilage condensation uberon UBERON:0010698 manual digit metacarpus pre-cartilage condensation fore limb digit metacarpus pre-cartilage condensation OBOL:accepted metacarpal bone pre-cartilage condensation VHOG:0000953 metacarpus pre-cartilage condensation VHOG:0000953 hand digit metacarpus pre-cartilage condensation NCBITaxon:9606 OBOL:accepted EMAPA:32849 finger metacarpus cartilage element fore limb digit metacarpus cartilage element metacarpal cartilage element metacarpus cartilage element hand digit metacarpus cartilage element uberon metacarpal cartilage condensation UBERON:0010699 manual digit metacarpus cartilage element fore limb digit metacarpus cartilage element OBOL:accepted hand digit metacarpus cartilage element NCBITaxon:9606 OBOL:accepted metacarpal cartilage condensation EMAPA:32849 EMAPA:32720 uberon UBERON:0010700 phalanx pre-cartilage condensation EMAPA EMAPA:32721 phalanx cartilage condensation uberon UBERON:0010701 phalanx cartilage element phalanx cartilage condensation EMAPA:32721 Mesenchyme of the digit region. EMAPA:32719 NCIT:C34141 uberon digital ray UBERON:0010702 digit mesenchyme Mesenchyme of the digit region. digital ray NCIT:C34141 The collection of all skeletal elements in an forelimb zeugopod region. adding proxinally_connected_to humerus causes inconsistencies - requires investigation Segment of the forearm corresponding to the radius and ulna.[AAO] AAO:0000200 FMA:71199 VSAO:0005011 antebrachial skeleton antebrachium skeleton anterior zeugopodium skeleton fore epipodium skeleton forearm skeleton skeleton of forearm wing zeugopod skeleton uberon anterior zeugopodium fore epipodium forelimb epipodium forelimb epipodium skeleton mesomere 2 of pectoral appendage radius and ulna UBERON:0010703 forelimb zeugopod skeleton lexical The collection of all skeletal elements in an forelimb zeugopod region. Segment of the forearm corresponding to the radius and ulna.[AAO] 2012-06-20 AAO:0000200 AAO AAO:LAP antebrachium skeleton PHENOSCAPE:ni anterior zeugopodium skeleton VSAO:0005011 VSAO:NI forearm skeleton FMA:71199 skeleton of forearm FMA:71199 wing zeugopod skeleton NCBITaxon:8782 OBOL:automatic anterior zeugopodium VSAO:0005011 VSAO:NI fore epipodium AAO:0000200 forelimb epipodium VSAO:0005011 VSAO:NI mesomere 2 of pectoral appendage ISBN:0226313409 An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) haendel 2012-04-23T10:46:51Z EMAPA:37858 FMA:7182 VSAO:0000214 appendage complex appendage-girdle complex appendage/girdle complex girdle plus limb or fin uberon limb UBERON:0010707 appendage girdle complex An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] 2012-08-14 VSAO:0000214 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] 2012-09-06 VSAO:0000214 VSAO Curator note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) FMA EMAPA:37858 MA:th appendage complex appendage-girdle complex appendage/girdle complex VSAO:0000214 girdle plus limb or fin limb FMA:7182 Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle. Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO] note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region) EMAPA:37860 FMA:7183 VSAO:0000213 pectoral appendage/girdle complex pectoral girdle plus anterior limb or fin pectoral girdle plus pectoral limb or fin uberon upper limb upper limb and pectoral girdle upper limb and shoulder UBERON:0010708 pectoral complex Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle. VSAO:0000213 Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO] 2012-08-14 VSAO:0000213 VSAO VSAO:MAH note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region) FMA EMAPA:37860 MA:th pectoral appendage/girdle complex VSAO:0000213 pectoral girdle plus anterior limb or fin pectoral girdle plus pectoral limb or fin upper limb FMA:7183 upper limb and pectoral girdle upper limb and shoulder Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here EMAPA:37863 FMA:7184 VSAO:0000215 pelvic appendage/girdle complex pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin uberon lower limb lower limb and pelvic girdle lower limb and pelvis UBERON:0010709 pelvic complex Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. VSAO:0000215 Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] 2012-08-14 VSAO:0000215 VSAO VSAO:MAH note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here FMA EMAPA:37863 MA:th pelvic appendage/girdle complex VSAO:0000215 pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin lower limb FMA:7184 lower limb and pelvic girdle lower limb and pelvis Skeletal subdivision that is a segment of the limb skeleton. note the distinction between this and skeleton of limb VSAO:0005018 uberon UBERON:0010712 limb skeleton subdivision VSAO Skeletal subdivision that is a segment of the limb skeleton. VSAO:0005018 VSAO:NI A iliac endochondral element that is composed primarily of cartilage tissue. EHDAA2:0000808 EMAPA:18347 VHOG:0001126 uberon iliac cartilage condensation UBERON:0010714 iliac cartilage element EHDAA2 EHDAA2 A iliac endochondral element that is composed primarily of cartilage tissue. OBOL:automatic iliac cartilage condensation EMAPA:18347 The subdivision of the skeleton of either the pectoral or pelvic girdle. Skeletal subdivision that is part of the appendage girdle region.[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] AAO:0010686 VSAO:0000302 skeleton of girdle uberon UBERON:0010719 girdle skeleton The subdivision of the skeleton of either the pectoral or pelvic girdle. Skeletal subdivision that is part of the appendage girdle region.[VSAO] 2012-08-14 VSAO:0000302 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region. Typically consists of the tibia and the fibula. Segment of the leg corresponding to the tibia and fibula.[AAO] AAO:0000216 VSAO:0005014 crural skeleton crus skeleton hindlimb zygopod skeleton posterior zeugopodium skeleton skeleton cruris uberon hind epipodium hindlimb epipodium mesomere 2 of pelvic appendage posterior zeugopodium UBERON:0010720 hindlimb zeugopod skeleton lexical Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region. Typically consists of the tibia and the fibula. Segment of the leg corresponding to the tibia and fibula.[AAO] 2012-06-20 AAO:0000216 AAO AAO:LAP crural skeleton crus skeleton PHENOSCAPE:ni skeleton cruris NominaAnatomicaVeterinaria:2005 hind epipodium AAO:0000216 hindlimb epipodium VSAO:0005014 VSAO:NI mesomere 2 of pelvic appendage ISBN:0226313409 posterior zeugopodium VSAO:0005014 A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). EMAPA:35494 MA:0000688 uberon bone of extended limb/fin region limb bone UBERON:0010740 bone of appendage girdle complex UBERONREF:0000003 A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). UBERONREF:0000003 bone of extended limb/fin region UBERONREF:0000003 limb bone MA:0000688 UBERONREF:0000003 A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin. considering adding pectoral and pelvic complex skeleton classes note that the MA class includes girdle parts so it belongs here; EMAPA:32623 EMAPA:35933 MA:0000612 wing bone uberon bone of forelimb or pectoral fin or pectoral girdle forelimb bone UBERON:0010741 bone of pectoral complex A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin. UBERONREF:0000003 note that the MA class includes girdle parts so it belongs here; MA wing bone UBERONREF:0000003 bone of forelimb or pectoral fin or pectoral girdle UBERONREF:0000003 forelimb bone MA:0000612 UBERONREF:0000003 A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle EMAPA:32633 EMAPA:35934 MA:0000660 uberon hindlimb bone UBERON:0010742 bone of pelvic complex MA A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. UBERONREF:0000003 the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle MA hindlimb bone MA:0000660 UBERONREF:0000003 The collection of all meningeal layers that line a central nervous system. meningeal In some primitive organisms, the meningeal cluster includes only the primitive meninx EHDAA2:0004661 EMAPA:32660 FMA:231572 NCIT:C12349 cerebral meninges cluster of meninges meninges uberon UBERON:0010743 meningeal cluster The collection of all meningeal layers that line a central nervous system. cluster of meninges FMA:231572 meninges FMA:231572 A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg. FBbt:00007018 appendage segment appendicular segment uberon UBERON:0010758 subdivision of organism along appendicular axis A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg. appendage segment FBbt:00007018 A skin of neck that is part of a throat. FMA:23023 skin of anterior neck skin of anterior part of neck skin of anterior portion of neck skin of throat uberon UBERON:0010854 skin of front of neck A skin of neck that is part of a throat. OBOL:automatic skin of anterior neck FMA:23023 skin of anterior part of neck FMA:23023 skin of anterior portion of neck FMA:23023 A skeletal element that is part of a limb and composed of cartilage tissue. uberon UBERON:0010881 limb cartilage element A skeletal element that is part of a limb and composed of cartilage tissue. A skeletal element that is part of a limb and composed of pre-cartilage tissue. uberon UBERON:0010882 limb bone pre-cartilage condensation A skeletal element that is part of a limb and composed of pre-cartilage tissue. A cartilaginous condensation that has the potential to develop into a forelimb bone. EMAPA:32626 forelimb wing cartilaginous condensation wing cartilaginous condensation uberon UBERON:0010883 forelimb cartilage element A cartilaginous condensation that has the potential to develop into a forelimb bone. OBOL:automatic forelimb wing cartilaginous condensation NCBITaxon:8782 OBOL:automatic wing cartilaginous condensation NCBITaxon:8782 OBOL:automatic A pre-cartilage condensation that has the potential to develop into a forelimb bone. EMAPA:32625 wing bone pre-cartilage condensation uberon UBERON:0010884 forelimb bone pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a forelimb bone. OBOL:automatic wing bone pre-cartilage condensation NCBITaxon:8782 OBOL:automatic A cartilaginous condensation that has the potential to develop into a hindlimb bone. EMAPA:32632 hindlimb cartilage condensation uberon UBERON:0010885 hindlimb cartilage element A cartilaginous condensation that has the potential to develop into a hindlimb bone. OBOL:automatic hindlimb cartilage condensation EMAPA:32632 A pre-cartilage condensation that has the potential to develop into a hindlimb bone. EMAPA:32638 hindlimb pre-cartilage condensation uberon UBERON:0010886 hindlimb pre-cartilage condensation A pre-cartilage condensation that has the potential to develop into a hindlimb bone. OBOL:automatic hindlimb pre-cartilage condensation EMAPA:32638 Muscles of the pelvic girdle, hindlimb or pelvic fin. Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] AAO:0000218 EMAPA:32634 FMA:9622 MA:0000663 pelvic girdle and hind limb muscles pelvic girdle or hind limb muscle pelvic girdle or posterior limb muscle uberon lower limb muscle muscle of lower limb muscle of pelvic girdle and leg UBERON:0010890 pelvic complex muscle prolog Muscles of the pelvic girdle, hindlimb or pelvic fin. Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] 2012-06-20 AAO:0000218 AAO AAO:EJS pelvic girdle and hind limb muscles AAO:0000218 pelvic girdle or hind limb muscle pelvic girdle or posterior limb muscle lower limb muscle FMA:9622 muscle of lower limb FMA:9622 A muscle of a pectoral girdle, pectoral fin or anterior limb. the MA class belongs here, based on its current child classes Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] AAO:0010687 EMAPA:32624 FMA:9621 MA:0000615 pectoral girdle and fore limb muscles muscle of pectoral girdle and wing muscle of upper limb upper limb muscle uberon muscle of pectoral girdle and limb UBERON:0010891 pectoral complex muscle prolog A muscle of a pectoral girdle, pectoral fin or anterior limb. Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO] 2012-06-20 AAO:0010687 AAO AAO:EJS pectoral girdle and fore limb muscles AAO:0010687 muscle of pectoral girdle and wing NCBITaxon:8782 muscle of upper limb FMA:9621 upper limb muscle FMA:9621 Am unpaired external naris that lies in the midline of the head. UBERON:0012123 median anterior naris median nostril nasohypophysial opening uberon UBERON:0010893 median external naris Am unpaired external naris that lies in the midline of the head. OBOL:automatic nasohypophysial opening Hermaphroditic organism that produces both male and female gametes at the same time. AAO:0010046 BILA:0000046 CARO:0000046 HAO:0000046 TADS:0000609 uberon serially hermaphroditic organism simultaneous hermaphroditic organism UBERON:0010899 synchronous hermaphroditic organism CARO Hermaphroditic organism that produces both male and female gametes at the same time. CARO:0000046 serially hermaphroditic organism CARO:0000046 simultaneous hermaphroditic organism Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 VSAO:0000042 skeletal subdivision uberon subdivision of skeleton (in vivo) UBERON:0010912 subdivision of skeleton cjm UBERONREF:0000003 VSAO Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. UBERONREF:0000003 Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] 2012-08-14 VSAO:0000042 incorrect VSAO VSAO:curator skeletal subdivision VSAO:0000042 subdivision of skeleton (in vivo) FMA:23879 Skeletal element that forms around the notochord and is part of the vertebral column. we include a distinct subclass for bony vertebra In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] vertebral Typically an endochondral element, in salamanders there is an argument that vertebral development is perichondral and not preformed in cartilage UBERON:0015005 vertebra skeletal element VHOG:0001143 VSAO:0000184 vertebra element vertebra endochondral element vertebral endochondral element uberon UBERON:0010913 vertebral element VSAO VSAO cjm Skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001143 VHOG DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011) vertebra skeletal element vertebra element vertebra endochondral element vertebral endochondral element EHDAA2:0001909 uberon UBERON:0010929 stapedius pre-muscle condensation EHDAA2 Any muscle organ that is part of either the head or the neck. NCIT:C32716 UMLS:C0448281 muscle of head or neck uberon muscle of head and neck UBERON:0010959 craniocervical muscle prolog Any muscle organ that is part of either the head or the neck. UMLS:C0448281 ncithesaurus:Head_and_Neck_Muscle EHDAA2:0003425 uberon UBERON:0010963 isa row in EHDAA2 trunk and cervical myotome group EHDAA2 EHDAA2:0000993 uberon UBERON:0010983 levator scapulae pre-muscle mass EHDAA2 EHDAA2 EHDAA2 A cartilage element that is part of a splanchnocranium. EFO:0003689 TAO:0001460 ZFA:0001460 pharyngeal arch cartilages splanchnocranium cartilage uberon UBERON:0011004 pharyngeal arch cartilage ZFA ZFA A cartilage element that is part of a splanchnocranium. OBOL:automatic pharyngeal arch cartilages ZFA:0001460 splanchnocranium cartilage ZFA:0001460 A skeleton of pelvic girdle that is part of a right pelvic girdle region. FMA:87593 uberon UBERON:0011090 skeleton of right pelvic girdle A skeleton of pelvic girdle that is part of a right pelvic girdle region. OBOL:automatic A skeleton of pelvic girdle that is part of a left pelvic girdle region. FMA:87594 uberon UBERON:0011091 skeleton of left pelvic girdle A skeleton of pelvic girdle that is part of a left pelvic girdle region. OBOL:automatic A pelvic girdle region that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16582 right pelvic girdle uberon UBERON:0011092 right pelvic girdle region A pelvic girdle region that is in the right side of a multicellular organism. OBOL:automatic right pelvic girdle FMA:16582 A pelvic girdle region that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16583 left pelvic girdle uberon UBERON:0011093 left pelvic girdle region A pelvic girdle region that is in the left side of a multicellular organism. OBOL:automatic left pelvic girdle FMA:16583 The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups EMAPA:32669 VHOG:0000584 vertebral cartilage condensation uberon UBERON:0011094 vertebra cartilage element The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist PMC3157150 This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups EHDAA2 vertebral cartilage condensation VHOG:0000584 The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. EMAPA:32671 VHOG:0000582 vertebral pre-cartilage condensation uberon UBERON:0011095 vertebra pre-cartilage condensation The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 vertebral pre-cartilage condensation VHOG:0000582 The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve. FMA:52628 NCIT:C32908 nervus lacrimalis uberon UBERON:0011096 lacrimal nerve FMA The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve. nervus lacrimalis An epiphysis that is part of a metacarpal bone of digit 5. FMA:86330 fifth metacarpal bone epiphysis metacarpal 5 epiphysis uberon UBERON:0011104 epiphysis of fifth metacarpal bone An epiphysis that is part of a metacarpal bone of digit 5. OBOL:automatic fifth metacarpal bone epiphysis FMA:86330 A synovial joint that is part of a pelvic girdle region. FMA:35173 NCIT:C32890 UMLS:C0827002 joint of pelvic girdle pelvic girdle joint uberon UBERON:0011107 synovial joint of pelvic girdle A synovial joint that is part of a pelvic girdle region. OBOL:automatic UMLS:C0827002 ncithesaurus:Joint_of_the_Pelvic_Girdle pelvic girdle joint FMA:35173 A synovial joint that is part of a pectoral girdle region. in FMA, these are part of the bony pectoral girdle FMA:35243 joint of shoulder girdle pectoral girdle joint uberon UBERON:0011108 synovial joint of pectoral girdle A synovial joint that is part of a pectoral girdle region. OBOL:automatic in FMA, these are part of the bony pectoral girdle FMA pectoral girdle joint FMA:35243 The tarsometatarsal articulations are arthrodial joints in the pes. FMA:35216 tarso-metatarsal join uberon Lisfranc joint articulationes tarsometatarsales cuboideometatarsal tarsometatarsal tarsometatarsal articulation UBERON:0011118 tarsometatarsal joint http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray355.png http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png The tarsometatarsal articulations are arthrodial joints in the pes. Lisfranc joint articulationes tarsometatarsales cuboideometatarsal tarsometatarsal tarsometatarsal articulation The carpometacarpal joints (CMC) are joints in the wrist that articulates the distal row of carpal bones and the proximal bases of the metacarpal bones. CMJ carpometacarpal FMA:35287 NCIT:C32265 UMLS:C0224620 articulationes carpometacarpeæ uberon carpometacarpal articulation UBERON:0011119 carpometacarpal joint http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray335.png The carpometacarpal joints (CMC) are joints in the wrist that articulates the distal row of carpal bones and the proximal bases of the metacarpal bones. CMJ carpometacarpal UMLS:C0224620 ncithesaurus:Carpometacarpal_Joint articulationes carpometacarpeæ carpometacarpal articulation A skeletal joint that connects a laryngeal cartilage. FMA:55100 joint of larynx laryngeal articulation uberon UBERON:0011120 laryngeal joint FMA A skeletal joint that connects a laryngeal cartilage. OBOL:automatic joint of larynx FMA:55100 laryngeal articulation FMA:55100 2 2 A skeletal joint that connects two adjacent metacarpals[FMA,modified]. FMA:35288 uberon intermetacarpal intermetacarpal articulation UBERON:0011131 intermetacarpal joint two adjacent metacarpals A skeletal joint that connects two adjacent metacarpals[FMA,modified]. FMA:35288 intermetacarpal intermetacarpal articulation 2 2 A skeletal joint that connects two carpal bones. FMA:35292 NCIT:C32264 UMLS:C1262468 carpal joint uberon intercarpal intercarpal articulation midcarpal articulation UBERON:0011132 intercarpal joint http://upload.wikimedia.org/wikipedia/commons/3/37/Gray336.png FMA two adjacent carpals A skeletal joint that connects two carpal bones. UMLS:C1262468 ncithesaurus:Carpal_Joint carpal joint FMA:35292 intercarpal intercarpal articulation midcarpal articulation 2 2 A joint that connects two adjacent metatarsals In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb FMA:35219 uberon UBERON:0011133 intermetatarsal joint http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png two adjacent metatarsals A joint that connects two adjacent metatarsals In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb WP Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint uberon UBERON:0011134 nonsynovial joint FMA Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint FMA:7491 2 2 A cartilage element that lies between two successive vertebral centra. Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO] AAO:0000795 uberon UBERON:0011135 intervertebral cartilage FMA MA between two centra A cartilage element that lies between two successive vertebral centra. ISBN:0073040584 Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO] 2012-06-20 AAO:0000795 AAO AAO:Trueb_1973 ligament that joins successive centra. Important in controlling the stiffness of the vertebral column when it flexes. intervertebral ligament vertebral centrum ligament FMA:31892 vertebral column ligament uberon UBERON:0011136 ligament of vertebral column ligament that joins successive centra. Important in controlling the stiffness of the vertebral column when it flexes. ISBN:0073040584 vertebral column ligament FMA:31892 Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. FMA:7483 uberon UBERON:0011137 axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 post-cranial axial skeletal system uberon UBERON:0011138 postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA cjm Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system Any synovial joint that is part of a (free) limb. FMA:258776 synovial joint of free limb segment uberon UBERON:0011139 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. synovial limb joint Any synovial joint that is part of a (free) limb. synovial joint of free limb segment FMA:258776 Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 NCIT:C61107 galen:UpperUrinaryTract uberon UBERON:0011143 upper urinary tract FMA FMA-abduced-lr Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 EMAPA:37970 uberon UBERON:0011148 submucosal gland perforates Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue. BTO:0003751 EMAPA:37970 MA:th AAO:0010371 TAO:0001401 XAO:0003178 ZFA:0001401 dorsal hyoid arch dorsal pharyngeal arch 2 skeleton dorsal visceral arch 2 uberon UBERON:0011152 dorsal hyoid arch skeleton AAO dorsal hyoid arch ZFA:0001401 dorsal visceral arch 2 ZFA:0001401 Surface structure that extends from the chin covering pharynx and larynx. Surface structure that is the region between the chin and the isthmus. (from http://www.briancoad.com/Dictionary/introduction.htm).[TAO] TAO:0002286 uberon UBERON:0011154 gular region TAO Surface structure that extends from the chin covering pharynx and larynx. Surface structure that is the region between the chin and the isthmus. (from http://www.briancoad.com/Dictionary/introduction.htm).[TAO] 2012-08-14 TAO:0002286 TAO TAO:wd Subdivision of skull that consists of the facial bones. EHDAA2:0002206 EHDAA:8361 EMAPA:18022 FMA:53673 MA:0000318 facial skeleton uberon facial bone ossa facialia ossa faciei viscerocranium UBERON:0011156 facial skeleton http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg FMA FMA Subdivision of skull that consists of the facial bones. MP:0005274 facial skeleton FMA:53673 facial bone MA:0000318 ossa facialia ossa faciei viscerocranium MA:0000318 The skull can be divided into two: the neurocranium and the facial skeleton FMA:54964 skull subdivision subdivision of skull uberon UBERON:0011158 primary subdivision of skull FMA The skull can be divided into two: the neurocranium and the facial skeleton skull subdivision FMA:54964 subdivision of skull FMA:54964 uberon UBERON:0011159 primary subdivision of cranial skeletal system FMA A bone that is part of a neurocranium [Automatically generated definition]. EMAPA:35238 MA:0001478 chondrocranium bone uberon UBERON:0011164 neurocranium bone A bone that is part of a neurocranium [Automatically generated definition]. OBOL:automatic chondrocranium bone MA:0001478 A sphincter muscle that is part of the gastrointestinal system NCIT:C32669 UMLS:C1517464 uberon UBERON:0011185 gastrointestinal sphincter A sphincter muscle that is part of the gastrointestinal system OBOL:automatic UMLS:C1517464 ncithesaurus:Gastrointestinal_Sphincter A lamina propria that is part of a large intestine. FMA:15654 NCIT:C49298 UMLS:C1708644 lamina propria of mucosa of large intestine large intestinal lamina propria large intestine lamina propria uberon UBERON:0011189 lamina propria of large intestine FMA A lamina propria that is part of a large intestine. OBOL:automatic UMLS:C1708644 ncithesaurus:Large_Intestinal_Lamina_Propria lamina propria of mucosa of large intestine FMA:15654 large intestine lamina propria FMA:15654 An epithelium that is part of a parathyroid gland. CALOHA:TS-2141 NCIT:C48258 UMLS:C1709466 uberon UBERON:0011197 parathyroid epithelium EHDAA2-abduced An epithelium that is part of a parathyroid gland. OBOL:automatic UMLS:C1709466 ncithesaurus:Parathyroid_Gland_Epithelial_Tissue A muscle layer that is part of a large intestine. FMA:14971 NCIT:C32927 UMLS:C0734205 muscular coat of large intestine muscular layer of large intestine muscularis externa of large intestine tunica muscularis intestini crassi uberon UBERON:0011198 muscle layer of large intestine FMA A muscle layer that is part of a large intestine. OBOL:automatic UMLS:C0734205 ncithesaurus:Large_Intestinal_Muscular_Coat muscular coat of large intestine FMA:14971 muscular layer of large intestine FMA:14971 muscularis externa of large intestine FMA:14971 tunica muscularis intestini crassi FMA:TA A muscle layer that is part of a small intestine. FMA:14932 NCIT:C33569 UMLS:C0227269 muscular coat of small intestine muscular layer of small intestine muscularis externa of small intestine small intestine muscularis propria tunica muscularis (intestinum tenue) tunica muscularis intestini tenuis uberon UBERON:0011201 muscle layer of small intestine FMA A muscle layer that is part of a small intestine. OBOL:automatic UMLS:C0227269 ncithesaurus:Small_Intestinal_Muscular_Coat muscular coat of small intestine FMA:14932 muscular layer of small intestine FMA:14932 muscularis externa of small intestine FMA:14932 small intestine muscularis propria FMA:14932 tunica muscularis (intestinum tenue) FMA:14932 tunica muscularis intestini tenuis FMA:TA A multi cell part structure that is part of a central nervous system. FMA:83143 cell part cluster of neuraxis neuraxis layer uberon UBERON:0011215 central nervous system cell part cluster A multi cell part structure that is part of a central nervous system. OBOL:automatic cell part cluster of neuraxis FMA:83143 neuraxis layer FMA:83143 A subdivision of an anatomical system. FBbt:00007330 FMA:67509 uberon UBERON:0011216 organ system subdivision FBbt FBbt A subdivision of an anatomical system. Muscles within the eye (bulbus oculi).[AAO] AAO:0010038 EMAPA:18808 FMA:49150 intrinsic muscle of eyeball intrinsic ocular muscle uberon UBERON:0011222 intra-ocular muscle EMAPA Muscles within the eye (bulbus oculi).[AAO] 2012-06-20 AAO:0010038 AAO AAO:EJS intrinsic ocular muscle EMAPA:18808 Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. synovium BTO:0001823 FMA:40878 uberon UBERON:0011233 Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath] synovial membrane of synovial tendon sheath Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. FMA:45087 synovium BTO:0001823 FMA:40877 uberon UBERON:0011234 fibrous membrane of synovial tendon sheath The most anterior region of the braincase. Provides structural support for peripheral olfactory organ. currently this is not restricted to skeletal elements, unlike UBERONREF:0000007 AAO:0000986 uberon UBERON:0011241 ethmoid region The most anterior region of the braincase. Provides structural support for peripheral olfactory organ. UBERONREF:0000007 Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] FMA:7484 VHOG:0001666 VSAO:0000306 uberon UBERON:0011249 appendicular skeletal system https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] 2012-08-14 VSAO:0000306 VSAO A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones. https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern uberon UBERON:0011250 autopod bone A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones. Scent glands are exocrine glands found in most mammals. They produce semi-viscous secretions which contain pheromones and other semiochemical compounds. These odor-messengers indicate information such as status, territory marking, mood, and sexual power. The odor may be subliminal-not consciously detectable. Though it is not their primary function, the salivary glands may also function as scent glands in some animals. Exocrine glands in animals which secrete scents which either repel or attract other animals, e.g. perianal glands of skunks, anal glands of weasels, musk glands of foxes, ventral glands of wood rats, and dorsal glands of peccaries[MESH:A13.820]. BTO:0002068 MESH:D012543 uberon UBERON:0011252 scent gland http://upload.wikimedia.org/wikipedia/commons/8/85/Civetglands.png Scent glands are exocrine glands found in most mammals. They produce semi-viscous secretions which contain pheromones and other semiochemical compounds. These odor-messengers indicate information such as status, territory marking, mood, and sexual power. The odor may be subliminal-not consciously detectable. Though it is not their primary function, the salivary glands may also function as scent glands in some animals. Exocrine glands in animals which secrete scents which either repel or attract other animals, e.g. perianal glands of skunks, anal glands of weasels, musk glands of foxes, ventral glands of wood rats, and dorsal glands of peccaries[MESH:A13.820]. MESH:A13.820 A carpometacarpal joint that connects to metacarpal 1. In humans it connects the trapezium to the first metacarpal bone, plays an irreplaceable role in the normal functioning of the thumb. The most important joint connecting the wrist to the metacarpus, osteoarthritis of the TMC is a severely disabling condition; up to twenty times more common among old women than in average FMA:35421 carpometacarpal joint of digit I carpometacarpal joint of pollex carpometacarpal joint of thumb uberon TMJ carpometacarpal joint of the thumb trapeziometacarpal joint UBERON:0011265 carpometacarpal joint of digit 1 A carpometacarpal joint that connects to metacarpal 1. In humans it connects the trapezium to the first metacarpal bone, plays an irreplaceable role in the normal functioning of the thumb. The most important joint connecting the wrist to the metacarpus, osteoarthritis of the TMC is a severely disabling condition; up to twenty times more common among old women than in average WP carpometacarpal joint of digit I carpometacarpal joint of pollex FMA:35421 carpometacarpal joint of thumb FMA:35421 TMJ carpometacarpal joint of the thumb trapeziometacarpal joint The part of the trunk that is in the dorsum[cjm]. In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA] EMAPA:35162 FMA:25056 MA:0000020 back of trunk dorsal part of trunk dorsum of trunk trunk back uberon UBERON:0011270 dorsal trunk FMA FMA The part of the trunk that is in the dorsum[cjm]. UBERONREF:0000006 back of trunk FMA:25056 dorsum of trunk FMA:25056 trunk back FMA:25056 compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' EHDAA2:0001845 uberon basal cell layer of skin outer epithelium of body UBERON:0011272 embryonic skin basal layer EHDAA2 EHDAA2 EHDAA2 outer epithelium of body Wikipathways:WP2062 The submucous layer of the wall of the uterine tube. BTO:0002116 submucosa of fallopian tube tela submucosa tubae uterinae uberon submucous layer of uterine tube uterine submucosa UBERON:0011298 submucosa of uterine tube The submucous layer of the wall of the uterine tube. BTO:0002116 tela submucosa tubae uterinae BTO:0002116 submucous layer of uterine tube BTO:0002116 A portion of gray matter that is part of a telencephalon. UBERON:0024186 BIRNLEX:1067 FMA:83911 predominantly gray regional part of telencephalon uberon UBERON:0011300 gray matter of telencephalon A portion of gray matter that is part of a telencephalon. OBOL:automatic predominantly gray regional part of telencephalon BIRNLEX:1067 EMAPA:17884 uberon UBERON:0011332 extrinsic tongue pre-muscle mass A blood vasculature that is part of a head. Blood vessel part of cranial vasculature.[TAO] TAO:0005297 ZFA:0005297 cranial blood vessel set of blood vessels of head uberon cranial blood vessels UBERON:0011362 cranial blood vasculature A blood vasculature that is part of a head. OBOL:automatic Blood vessel part of cranial vasculature.[TAO] 2012-08-14 TAO:0005297 TAO ZFIN:curator cranial blood vessel ZFA:0005297 cranial blood vessels TAO:0005297 A lymph vasculature that is part of a head. FMA:224562 TAO:0005298 ZFA:0005298 cranial lymph vessel cranial lymphatics set of lymphatic vessels of head uberon cranial lymph vessels set of cranial lymphatic vessels UBERON:0011363 cranial lymph vasculature A lymph vasculature that is part of a head. OBOL:automatic cranial lymph vessel ZFA:0005298 cranial lymphatics UBERON:cjm set of lymphatic vessels of head FMA:224562 cranial lymph vessels TAO:0005298 set of cranial lymphatic vessels FMA:224562 A retractable double-layered fold of skin and mucous membrane that covers the glans penis or clitoris. Glands may also be present. this is a generic sex-neutral grouping class for the male and female prepuce. Note that this structure is a combination of skin and other tissue preputial NCIT:C12323 uberon UBERON:0011374 prepuce A retractable double-layered fold of skin and mucous membrane that covers the glans penis or clitoris. Glands may also be present. A zone of skin that is part of a prepuce of clitoris. FMA:27886 preputial skin of clitoris uberon UBERON:0011375 skin of prepuce of clitoris A zone of skin that is part of a prepuce of clitoris. OBOL:automatic preputial skin of clitoris FMA:27886 FMA:54364 cavity of digestive tract cavity of gastrointestinal tract gastrointestinal tract lumen lumen of gastrointestinal tract uberon UBERON:0011565 lumen of gastrointestinal system gastrointestinal tract lumen FMA:54364 lumen of gastrointestinal tract FMA:54364 An anatomical cavity that is part of a esophagus. EMAPA:18380 FMA:9398 cavity of eosophagus cavity of esophagus eosophageal cavity eosophageal lumen eosophagus lumen esophageal cavity esophageal lumen esophagus lumen uberon UBERON:0011566 lumen of esophagus FMA An anatomical cavity that is part of a esophagus. OBOL:automatic cavity of esophagus FMA:9398 esophageal cavity FMA:9398 esophageal lumen FMA:9398 esophagus lumen FMA:9398 A tube lumen that is part of a mesonephric duct. EHDAA2:0001244 nephric duct lumen uberon cavity of nephric duct UBERON:0011574 mesonephric duct lumen A tube lumen that is part of a mesonephric duct. OBOL:automatic nephric duct lumen EHDAA2:0001244 The collection of all skeletal elements in an individual limb or fin. Skeletal subdivision that is part of the paired limb/fin.[VSAO] VSAO:0000301 limb/fin skeleton skeletal parts of limb/fin skeleton of limb/fin uberon UBERON:0011582 paired limb/fin skeleton ISBN:9780878932504 The collection of all skeletal elements in an individual limb or fin. Skeletal subdivision that is part of the paired limb/fin.[VSAO] 2012-08-14 VSAO:0000301 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 limb/fin skeleton VSAO:0000301 Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified]. Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO] propodial stylopodial VSAO:0005007 stylopodium skeleton uberon mesomere 1 propodial skeleton propodium proximal metapterygial mesomere stylopod stylopodium UBERON:0011583 stylopodial skeleton VSAO Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified]. VSAO:0005007 Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO] 2012-08-14 VSAO:0005007 VSAO VSAO:NI mesomere 1 ISBN:0226313409 propodium VSAO:0005007 proximal metapterygial mesomere ISBN:0226313409 stylopod VSAO:0005007 Section of the forelimb skeleton located between the stylopodium and the autopodium. zeugopodial zygopodial VSAO:0005010 epipodial skeleton skeleton of zeugopod zeugopod skeleton uberon epipodium mesomere 2 mesomere 2 skeleton zygopodium UBERON:0011584 zeugopodial skeleton VSAO Section of the forelimb skeleton located between the stylopodium and the autopodium. VSAO:0005010 skeleton of zeugopod zeugopod skeleton epipodium VSAO:0005010 mesomere 2 ISBN:0226313409 mesomere 2 skeleton ISBN:0226313409 zygopodium VSAO:0005010 Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). consider obsoleting, coordinate with VSAO VSAO:0000006 XAO:0004021 uberon UBERON:0011585 cell condensation VSAO Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). GO_REF:0000034 PSPUB:0000170 VSAO:0000006 Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix. EMAPA:36439 VSAO:0000071 XAO:0004052 pre-dentine tissue predentin predentine tissue uberon UBERON:0011587 pre-dentine VSAO Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix. GO_REF:0000034 PSPUB:0000170 VSAO:0000071 pre-dentine tissue VSAO:curator predentin PMCID:PMC3360947 predentine tissue VSAO:curator Cartilage tissue that is not mineralized. add developmental relationships; add disjointness axiom VSAO:0000089 XAO:0004044 uberon UBERON:0011589 non-mineralized cartilage tissue VSAO Cartilage tissue that is not mineralized. GO_REF:0000034 PSPUB:0000170 VSAO:0000089 Tooth that is attached to a dentary/mandible[TAO,modified]. Note that we treat dentary tooth and mandibular tooth as equivalent Tooth that is attached to the dentary.[TAO] relationship loss: part_of dentary tooth row (TAO:0001952)[TAO] AAO:0000125 AAO:0000641 FMA:321647 TAO:0001628 uberon mandibular teeth mandibular tooth tooth of dentary UBERON:0011594 dentary tooth Tooth that is attached to a dentary/mandible[TAO,modified]. TAO:0001628 Tooth that is attached to the dentary.[TAO] 2012-08-14 TAO:0001628 TAO TAO:wd relationship loss: part_of dentary tooth row (TAO:0001952)[TAO] 2012-08-14 TAO:0001628 TAO mandibular teeth AAO:0000641 A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. EMAPA:32905 NCIT:C114916 uberon UBERON:0011595 jaw region http://eol.org/collections/11578 EMAPA FMA-abduced ZFA-abduced A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. EHDAA2:0001020 lower jaw future lip uberon UBERON:0011596 future lower lip EHDAA2 lower jaw future lip EHDAA2:0001020 Replacement bone that is bilaterally paired and (in teleosts) articulates with the neurocranium dorsally and the opercle posteriorly[TAO,modified]. Replacement bone that is bilaterally paired and articulates with the neurocranium dorsally and the opercle posteriorly.[TAO] relationship loss: overlaps hyomandibula-metapterygoid joint (TAO:0001979)[TAO] relationship loss: overlaps hyomandibula-opercle joint (TAO:0005265)[TAO] relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO] relationship loss: overlaps preopercle vertical limb-hyomandibula joint (TAO:0005278)[TAO] relationship loss: overlaps quadrate-hyomandibula joint (TAO:0001801)[TAO] This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG] In most teleosts, there is a symplectic, and the hyomandibula articulates with it anteroventrally. hyomandibula hyomandibular EFO:0003556 TAO:0000672 VHOG:0000688 ZFA:0000672 uberon UBERON:0011606 hyomandibular bone TAO TAO Replacement bone that is bilaterally paired and (in teleosts) articulates with the neurocranium dorsally and the opercle posteriorly[TAO,modified]. TAO:0000672 Replacement bone that is bilaterally paired and articulates with the neurocranium dorsally and the opercle posteriorly.[TAO] 2012-08-14 TAO:0000672 TAO ZFIN:curator relationship loss: overlaps hyomandibula-metapterygoid joint (TAO:0001979)[TAO] 2012-08-14 TAO:0000672 TAO relationship loss: overlaps hyomandibula-opercle joint (TAO:0005265)[TAO] 2012-08-14 TAO:0000672 TAO relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO] 2012-08-14 TAO:0000672 TAO relationship loss: overlaps preopercle vertical limb-hyomandibula joint (TAO:0005278)[TAO] 2012-08-14 TAO:0000672 TAO relationship loss: overlaps quadrate-hyomandibula joint (TAO:0001801)[TAO] 2012-08-14 TAO:0000672 TAO This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG] 2012-09-17 VHOG:0000688 VHOG DOI:10.1017/S0022215100009087 Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) hyomandibula TAO:0000672 hyomandibular TAO:0000672 Cartilage form of the hyomandibular element. Pharyngeal arch cartilage that is bilaterally paired and articulates with the chondrocranium dorsally, the opercle bone posteriorly, and the palatoquadrate cartilage anteriorly.[TAO] This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG] The stapes is homologous to the hyomandibula. In this ontology, we use the class 'hyomandibular cartilage' generally to include the future stapes, the future hyomandibular bone of teleosts and the unossified cartilage in sharks. EFO:0003686 TAO:0001422 VHOG:0000688 ZFA:0001422 hyosymplectic cartilage symplectic cartilage uberon UBERON:0011607 hyomandibular cartilage TAO Cartilage form of the hyomandibular element. Pharyngeal arch cartilage that is bilaterally paired and articulates with the chondrocranium dorsally, the opercle bone posteriorly, and the palatoquadrate cartilage anteriorly.[TAO] 2012-08-14 TAO:0001422 TAO ZFIN:curator This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG] 2012-09-17 VHOG:0000688 VHOG DOI:10.1017/S0022215100009087 Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) hyosymplectic cartilage ZFA:0001422 symplectic cartilage TAO:0001422 The upper paired deep bone or cartilage of the hyoid region, sometimes taking part in jaw suspension and which supports the opercle. Dorsally it articulates with the otic capsule at the hyomandibular fossa, ventrally with the quadrate and symplectic. In most Teleostei it has a foramen for the hyomandibular branch of the facial nerve (VII). Replacement bone that is bilaterally paired and articulates with the neurocranium dorsally and the opercle posteriorly.[TAO] relationship loss: overlaps hyomandibula-metapterygoid joint (TAO:0001979)[TAO] relationship loss: overlaps hyomandibula-opercle joint (TAO:0005265)[TAO] relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO] relationship loss: overlaps preopercle vertical limb-hyomandibula joint (TAO:0005278)[TAO] relationship loss: overlaps quadrate-hyomandibula joint (TAO:0001801)[TAO] This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG] In most teleosts, there is a symplectic, and the hyomandibula articulates with it anteroventrally.[TAO] TAO:0000672 VHOG:0000688 hyomandibula - stapes hyomandibula element uberon epihyal hyomandibula UBERON:0011608 hyomandibular element The upper paired deep bone or cartilage of the hyoid region, sometimes taking part in jaw suspension and which supports the opercle. Dorsally it articulates with the otic capsule at the hyomandibular fossa, ventrally with the quadrate and symplectic. In most Teleostei it has a foramen for the hyomandibular branch of the facial nerve (VII). Replacement bone that is bilaterally paired and articulates with the neurocranium dorsally and the opercle posteriorly.[TAO] 2012-08-14 TAO:0000672 TAO ZFIN:curator relationship loss: overlaps hyomandibula-metapterygoid joint (TAO:0001979)[TAO] 2012-08-14 TAO:0000672 TAO relationship loss: overlaps hyomandibula-opercle joint (TAO:0005265)[TAO] 2012-08-14 TAO:0000672 TAO relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO] 2012-08-14 TAO:0000672 TAO relationship loss: overlaps preopercle vertical limb-hyomandibula joint (TAO:0005278)[TAO] 2012-08-14 TAO:0000672 TAO relationship loss: overlaps quadrate-hyomandibula joint (TAO:0001801)[TAO] 2012-08-14 TAO:0000672 TAO This structure (the hyomandibular), on ontogenic grounds alone, can be considered homologous with the amphibian and reptilian columella and the mammalian stapes.[well established][VHOG] 2012-09-17 VHOG:0000688 VHOG DOI:10.1017/S0022215100009087 Gerrie J, The phylogeny of the mammalian tympanic cavity and auditory ossicles. The Journal of Laryngology and Otology (1948) In most teleosts, there is a symplectic, and the hyomandibula articulates with it anteroventrally.[TAO] 2012-09-06 TAO:0000672 TAO Curator hyomandibula - stapes VHOG:0000688 epihyal An epithelium that develops_from a ectoderm and is part of a oral epithelium. EHDAA2:0004137 uberon UBERON:0011642 oral epithelium from ectoderm EHDAA2 EHDAA2 An epithelium that develops_from a ectoderm and is part of a oral epithelium. OBOL:automatic Limb extensor that runs from ilium to femur. iliofemoralis uberon UBERON:0011645 iliofemoralis muscle Limb extensor that runs from ilium to femur. ISBN:0073040584 AAO:0000247 EFO:0003511 TAO:0000236 XAO:0003269 ZFA:0000236 mandibular muscle mandibular muscles uberon UBERON:0011648 jaw muscle mandibular muscle TAO:0000236 mandibular muscles TAO:0000236 A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem axial subdivision of organism uberon body segment main body segment UBERON:0011676 subdivision of organism along main body axis A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly. thoracolumbar vertebra uberon presacral vertebra UBERON:0011677 trunk vertebra true A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly. UBERONREF:0000006 presacral vertebra A tarsal bone that connected_to a hindlimb zeugopod skeleton. uberon UBERON:0011679 proximal tarsal bone A tarsal bone that connected_to a hindlimb zeugopod skeleton. OBOL:automatic A cardiovascular system that is part of a conceptus. EHDAA2:0000216 FMA:305965 NCIT:C34148 conceptus cardiovascular system uberon embryonic circulatory system fetal circulatory system UBERON:0011695 embryonic cardiovascular system A cardiovascular system that is part of a conceptus. OBOL:automatic Paired structures in the embryo that represent the final stage of development of the caudal end of the external genitals before sexual differentiation. In both males and females the two swellings merge: in the female, they become the posterior labial commissure; In the male, they become the scrotum todo - add parthood relationships to tubercles EMAPA:30074 EMAPA:35377 VHOG:0000976 labioscrotal swelling uberon tuberculum labioscrotale UBERON:0011754 genital swelling EHDAA2 Paired structures in the embryo that represent the final stage of development of the caudal end of the external genitals before sexual differentiation. In both males and females the two swellings merge: in the female, they become the posterior labial commissure; In the male, they become the scrotum tuberculum labioscrotale A genital swelling that is part of a female reproductive system. labial swelling EHDAA2:0000501 EHDAA:9363 EMAPA:18329 EMAPA:30423 labioscrotal swelling of female uberon labial primordium UBERON:0011755 female labial swelling A genital swelling that is part of a female reproductive system. OBOL:automatic labial swelling EMAPA:18329 labioscrotal swelling of female EMAPA:30423 A genital swelling that is part of a male reproductive organ. EHDAA2:0001049 EMAPA:30509 labioscrotal swelling of male scrotal bulge scrotal primordium uberon UBERON:0011756 male genital swelling A genital swelling that is part of a male reproductive organ. OBOL:automatic labioscrotal swelling of male EMAPA:30509 . NCIT:C34274 UMLS:C1514448 uberon phallus phallus primordialis primordial phallus UBERON:0011757 differentiated genital tubercle . UMLS:C1514448 ncithesaurus:Primordial_Phallus phallus phallus primordialis primordial phallus The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP] EMAPA:25350 FMA:14469 MA:0001107 left recurrent laryngeal branch left recurrent laryngeal nerve vagus X nerve left recurrent laryngeal branch uberon UBERON:0011766 left recurrent laryngeal nerve https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg left recurrent laryngeal branch EMAPA:25350 left recurrent laryngeal nerve FMA:14469 vagus X nerve left recurrent laryngeal branch MA:0001107 EMAPA:17275 FMA:14468 MA:0001108 right recurrent laryngeal branch right recurrent laryngeal nerve vagus X nerve right recurrent laryngeal branch uberon UBERON:0011767 right recurrent laryngeal nerve right recurrent laryngeal branch EMAPA:17275 right recurrent laryngeal nerve FMA:14468 vagus X nerve right recurrent laryngeal branch MA:0001108 Anatomical projection that is composed of cartilage tissue. FMA:284626 cartilage process cartilaginous process uberon UBERON:0011769 cartilaginous projection Anatomical projection that is composed of cartilage tissue. VSAO:wd An anatomical space that is part of a bone of lower jaw. AAO:0000273 uberon UBERON:0011772 lower jaw opening An anatomical space that is part of a bone of lower jaw. OBOL:automatic A cranial nerve nucleus that is associated with a vagus nerve. FMA:54573 nucleus of Xth nerve nucleus of vagal X nerve nucleus of vagal nerve nucleus of vagus nerve tenth cranial nerve nucleus vagal X nucleus vagal nucleus vagus nucleus uberon nodosal nucleus UBERON:0011775 vagus nerve nucleus A cranial nerve nucleus that is associated with a vagus nerve. OBOL:automatic nucleus of vagus nerve FMA:54573 tenth cranial nerve nucleus FMA:54573 vagal X nucleus vagal nucleus vagus nucleus nodosal nucleus A neural nucleus that is part of the spinal cord. FMA:77011 spinal cord nucleus uberon UBERON:0011777 nucleus of spinal cord A neural nucleus that is part of the spinal cord. spinal cord nucleus FMA:77011 A nerve that is part of a head. uberon cephalic nerve head nerve UBERON:0011779 nerve of head region A nerve that is part of a head. OBOL:automatic Ectodermal placode that does not develop into a component of the nervous system. uberon UBERON:0011814 non-neurogenic ectodermal placode cjm Ectodermal placode that does not develop into a component of the nervous system. An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales). cutaneous appendage follicle placode skin follicle placode uberon UBERON:0011817 skin appendage placode NCBIBook:NBK53175 An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales). An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. EHDAA2:0004149 FMA:85125 uberon AV region AV segment atrial ventricular junction atrioventricular junction atrioventricular segment UBERON:0011820 atrioventricular region An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. AV region AV segment atrial ventricular junction GO:0003294 atrioventricular junction FMA:85125 GO:0003294 atrioventricular segment Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 uberon UBERON:0011821 irregular connective tissue FMA Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] FMA:20109 NCIT:C32882 UMLS:C0738366 irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) uberon UBERON:0011822 dense irregular connective tissue FMA Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20109 Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] 2012-08-29 ncithesaurus:Irregular_Dense_Connective_Tissue NCIT UMLS:C0738366 ncithesaurus:Irregular_Dense_Connective_Tissue typus irregularis (textus connectivus collagenosus compactus) FMA:20109 Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid. Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] AAO:0000121 NCIT:C32450 UMLS:C1511770 uberon UBERON:0011823 dense connective tissue Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] 2012-08-29 ncithesaurus:Dense_Connective_Tissue NCIT UMLS:C1511770 ncithesaurus:Dense_Connective_Tissue FMA:75634 uberon UBERON:0011824 fibrous connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 NCIT:C33007 UMLS:C1253917 textus connectivus collagenosus laxus textus connectivus laxus uberon UBERON:0011825 loose connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 UMLS:C1253917 ncithesaurus:Loose_Connective_Tissue textus connectivus collagenosus laxus FMA:19783 FMA:TA textus connectivus laxus FMA:19783 FMA:TA A duct that is part of a sebaceous gland. FMA:70947 NCIT:C33520 sebaceous gland duct uberon UBERON:0011845 duct of sebaceous gland A duct that is part of a sebaceous gland. OBOL:automatic sebaceous gland duct FMA:70947 An acinus that is part of a sebaceous gland. FMA:59657 sebaceous gland acinus uberon UBERON:0011846 acinus of sebaceous gland An acinus that is part of a sebaceous gland. OBOL:automatic sebaceous gland acinus FMA:59657 An acinus that is part of a salivary gland. FMA:59870 salivary gland acinus uberon UBERON:0011850 acinus of salivary gland An acinus that is part of a salivary gland. OBOL:automatic salivary gland acinus FMA:59870 An acinus that is part of a lacrimal gland. FMA:85250 lacrimal gland acinus uberon UBERON:0011857 acinus of lacrimal gland An acinus that is part of a lacrimal gland. OBOL:automatic lacrimal gland acinus FMA:85250 An acinus that is part of a exocrine gland. exocrine gland acinus uberon UBERON:0011858 acinus of exocrine gland An acinus that is part of a exocrine gland. OBOL:automatic the FMA class specifically refers to ureter FMA:63212 MESH:D024022 NCIT:C32339 NIF_Subcellular:sao7547390221 uberon UBERON:0011860 collection of collagen fibrils ZFA the FMA class specifically refers to ureter FMA The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011861 aorta collagen fibril The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011640 The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011862 pulmonary collagen fibril The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011641 The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011863 bone collagen fibril The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011642 The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011864 tendon collagen fibril The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011643 The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011865 corneal stroma collagen fibril The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity MP:0011650 A muscle layer that is part of a wall of esophagus. In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle FMA:62998 muscle coat of esophagus muscular coat of oesophagus muscular layer of oesophagus tela muscularis (oesophagus) tunica muscularis esophagi tunica muscularis oesophageae uberon UBERON:0011878 muscle layer of esophagus upper part A muscle layer that is part of a wall of esophagus. OBOL:automatic In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle WP muscle coat of esophagus FMA:62998 muscular coat of oesophagus FMA:62998 muscular layer of oesophagus FMA:62998 tela muscularis (oesophagus) FMA:62998 FMA:TA tunica muscularis esophagi tunica muscularis oesophageae FMA:TA Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. EMAPA:37417 Haller tunica vascula anterior part of uveal tract anterior uveal tract anterior vascular layer of the eyeball anterior vascular tunic of the eye tunica vasculosa bulbosa ventral uveal tract uberon ciliary body and iris vasculosa oculi UBERON:0011892 anterior uvea ZFA MP lexical Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. MP:0005194 EMAPA:37417 MA:th Haller tunica vascula MP:0005194 tunica vasculosa bulbosa MP:0005194 vasculosa oculi MP:0005194 A organ cavity that is part of a vagina. FMA:19982 vaginal lumen uberon UBERON:0011894 lumen of vagina A organ cavity that is part of a vagina. OBOL:automatic vaginal lumen FMA:19982 Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. The Epimysium also protects muscles from friction against other muscles and bones FMA:9726 NCIT:C32527 UMLS:C0504096 fascia of muscle organ uberon epimysia UBERON:0011899 epimysium FMA FMA Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. UMLS:C0504096 ncithesaurus:Epimysium fascia of muscle organ FMA:9726 epimysia masses of developing blood cells attached to endothelium in the yolk sac EHDAA2:0000177 EMAPA:16115 visceral yolk sac blood island yolk sac blood islands uberon UBERON:0011919 yolk sac blood island EHDAA2 masses of developing blood cells attached to endothelium in the yolk sac MP:0011204 visceral yolk sac blood island MP:0011204 yolk sac blood islands EHDAA2:0000177 in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels EHDAA2:0003242 blood island of umbilical vesicle insula sanguinea vesiculae umbilicalis uberon UBERON:0011921 connecting stalk blood islands EHDAA2 EHDAA2 EHDAA2 in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels EHDAA2 blood island of umbilical vesicle insula sanguinea vesiculae umbilicalis Hair in the nose FMA:53670 hair of nose hair of vestibular part of nose nose hair uberon UBERON:0011931 nasal hair Hair in the nose hair of nose FMA:53670 hair of vestibular part of nose FMA:53670 nose hair FMA:53670 An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle EMAPA:36582 FMA:70661 fabrica pilosebacea pilo-sebaceous apparatus pilo-sebaceous unit pilosebaceous apparatus uberon pilosebaceous gland UBERON:0011932 pilosebaceous unit ISBN:0123813611 An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle ISBN:0123813611 PMCID:PMC3130146 fabrica pilosebacea pilo-sebaceous apparatus FMA:70661 pilosebaceous gland FMA:70661 A region of the stomach that is lined with glandular epithelium. as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus EMAPA:17623 MA:0001613 NCIT:C77661 UMLS:C0227197 uberon glandular stomach UBERON:0011953 stomach glandular region A region of the stomach that is lined with glandular epithelium. UMLS:C0227197 ncithesaurus:Glandular_Stomach A hepatic vein that is part of a left lobe of liver. EMAPA:37164 FMA:14339 MA:0003032 uberon UBERON:0011955 left hepatic vein A hepatic vein that is part of a left lobe of liver. OBOL:automatic EMAPA:37164 MA:th A hepatic vein that is part of a right lobe of liver. EMAPA:37377 FMA:14338 MA:0003034 uberon UBERON:0011956 right hepatic vein A hepatic vein that is part of a right lobe of liver. OBOL:automatic EMAPA:37377 MA:th An articular capsule that is part of the glenohumeral joint. FMA:34944 articular capsule of humerus articular capsule of shoulder joint capsule of shoulder joint fibrous capsule of glenohumeral joint uberon glenohumeral joint capsule UBERON:0011960 articular capsule of glenohumeral joint An articular capsule that is part of the glenohumeral joint. articular capsule of humerus capsule of shoulder joint FMA:34944 fibrous capsule of glenohumeral joint FMA:34944 glenohumeral joint capsule FMA:34944 An articular capsule that is part of the hip joint. FMA:42821 capsula articularis coxae capsule of hip joint fibrous capsule of hip joint uberon UBERON:0011961 articular capsule of hip joint An articular capsule that is part of the hip joint. capsula articularis coxae capsule of hip joint fibrous capsule of hip joint FMA:42821 An epiphysis that is part of a phalanx of a pes [Automatically generated definition]. epiphysis of phalanx of toe uberon UBERON:0011973 epiphysis of phalanx of pes An epiphysis that is part of a phalanx of a pes [Automatically generated definition]. OBOL:automatic An epiphysis that is part of a proximal phalanx of pes. epiphysis of proximal phalanx of toe uberon UBERON:0011974 epiphysis of proximal phalanx of pes An epiphysis that is part of a proximal phalanx of pes. OBOL:automatic An epiphysis that is part of a middle phalanx of pes. epiphysis of middle phalanx of toe uberon UBERON:0011975 epiphysis of middle phalanx of pes An epiphysis that is part of a middle phalanx of pes. OBOL:automatic An epiphysis that is part of a distal phalanx of pes. epiphysis of distal phalanx of toe uberon UBERON:0011976 epiphysis of distal phalanx of pes An epiphysis that is part of a distal phalanx of pes. OBOL:automatic An epiphysis that is part of a proximal phalanx of manus. epiphysis of proximal phalanx of finger uberon UBERON:0011977 epiphysis of proximal phalanx of manus An epiphysis that is part of a proximal phalanx of manus. OBOL:automatic An epiphysis that is part of a middle phalanx of manus. epiphysis of middle phalanx of finger uberon UBERON:0011978 epiphysis of middle phalanx of manus An epiphysis that is part of a middle phalanx of manus. OBOL:automatic An epiphysis that is part of a distal phalanx of manus. FMA:321561 epiphysis of distal phalanx of finger uberon UBERON:0011979 epiphysis of distal phalanx of manus An epiphysis that is part of a distal phalanx of manus. OBOL:automatic A joint that connects the bones of the crus to the proximal tarsal bones an ankle joint that passes between the astragalus and calcaneum[Palaeos]. uberon crurotarsal UBERON:0011980 line of flexion between calcaneus and astragalus crurotarsal joint A joint that connects the bones of the crus to the proximal tarsal bones an ankle joint that passes between the astragalus and calcaneum[Palaeos]. The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. coelomic EHDAA2:0004731 enterocoelom haemocoelom schizocoelom uberon coelem coelomic cavity UBERON:0011997 coelom EHDAA2 The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. UBERON:cjm enterocoelom NCBITaxon:33511 coelomic cavity EHDAA2:0004731 The cavity within a myotome The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] EMAPA:31134 VHOG:0001283 uberon UBERON:0012054 myocoele The cavity within a myotome The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001283 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6 FMA:62811 uberon UBERON:0012069 epithelium-associated lymphoid tissue FMA Bone that forms as a replacement of another structural tissue. Bone that forms as a replacement of another structural tissue.[TAO] This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. AAO:0010768 TAO:0001637 ZFA:0001628 replacement bones uberon UBERON:0012075 replacement bone ZFA ZFA Bone that forms as a replacement of another structural tissue. ZFA:0001628 Bone that forms as a replacement of another structural tissue.[TAO] 2012-08-14 TAO:0001637 TAO TAO:wd This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. ZFA replacement bones ZFA:0001628 An anatomical cavity that is part of a bronchus. FMA:62646 bronchial lumen lumen of bronchus uberon UBERON:0012082 bronchial lumen FMA FMA An anatomical cavity that is part of a bronchus. OBOL:automatic bronchial lumen FMA:62646 lumen of bronchus FMA:62646 A salivary gland that is part of a cheek. FMA:59793 NCIT:C32237 uberon UBERON:0012102 buccal salivary gland A salivary gland that is part of a cheek. OBOL:automatic Anatomical system that consists of the integumental system plus all mucosae and submucosae. uberon dermatological system UBERON:0012125 dermatological-muscosal system Anatomical system that consists of the integumental system plus all mucosae and submucosae. dermatological system OBI:MC Outermost point on an external nose or snout EMAPA:37915 FMA:59518 apex nasi apex of nose nasal tip tip of nose uberon pirula snout tip tip of snout UBERON:0012128 nose tip FMA Outermost point on an external nose or snout EMAPA:37915 MA:th apex nasi FMA:TA apex of nose FMA:59518 nasal tip FMA:59518 tip of nose FMA:59518 pirula uberon UBERON:0012139 segment of autopod may be revised A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon acropodium (Wagner) UBERON:0012140 digitopodium region https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region. PHENOSCAPE:ni A digitopodium region that is part of a manus[Obol]. This includes the fingers and metacarpal region, but excludes the carpal region. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon UBERON:0012141 manual digitopodium region https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A digitopodium region that is part of a manus[Obol]. This includes the fingers and metacarpal region, but excludes the carpal region. A digitopodium region that is part of a pes[Obol]. This includes the toes and metatarsal region, but excludes the tarsals region. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon UBERON:0012142 pedal digitopodium region https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A digitopodium region that is part of a pes[Obol]. This includes the toes and metatarsal region, but excludes the tarsals region. A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon digitopodium skeleton of digits UBERON:0012150 skeleton of digitopodium https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton. PHENOSCAPE:ni digitopodium PHENOSCAPE:ni skeleton of digits A subdivision of the manus skeleton consisting of both manual acropodial skeleton and metacarpal skeleton, but excluding the carpal skeleton. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon manual digitopodium UBERON:0012151 skeleton of manual digitopodium https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod FMA A subdivision of the manus skeleton consisting of both manual acropodial skeleton and metacarpal skeleton, but excluding the carpal skeleton. PHENOSCAPE:ni A subdivision of the pes skeleton consisting of both pedal acropodial skeleton and metatarsal skeleton, but excluding the tarsal skeleton. some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon pedal digitopodium UBERON:0012152 skeleton of pedal digitopodium https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod A subdivision of the pes skeleton consisting of both pedal acropodial skeleton and metatarsal skeleton, but excluding the tarsal skeleton. PHENOSCAPE:ni umbilical cord blood blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. BTO:0004053 CALOHA:TS-1079 EFO:0001942 MESH:D005312 uberon cord blood fetal blood umbilical cord blood UBERON:0012168 Cord blood is collected because it contains stem cells, which can be used to treat hematopoietic and genetic disorders.[WP] umbilical cord blood blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. cord blood BTO:0004053 fetal blood MESH:A12.207.152.200 umbilical cord blood MESH:A12.207.152.200 A primordium that has the potential to develop into a stomach. EFO:0002580 NCIT:C34305 UMLS:C1514976 uberon stomach endoderm UBERON:0012172 stomach primordium A primordium that has the potential to develop into a stomach. OBOL:automatic UMLS:C1514976 ncithesaurus:Stomach_Primordium stomach endoderm EFO:0002580 EHDAA2:0000494 EMAPA:16794 VHOG:0000715 acousticofacial ganglion facio-acoustic ganglion facio-acoustic ganglion complex VII-VIII uberon facio-acoustic VII-VIII ganglion complex facio-acoustic ganglion complex UBERON:0012175 acoustico-facial VII-VIII ganglion complex cjm EHDAA2 cjm facio-acoustic ganglion complex VII-VIII EMAPA:16794 facio-acoustic VII-VIII ganglion complex VHOG:0000715 facio-acoustic ganglion complex EMAPA:16794 A zone of skin that is part of a craniocervical region. EMAPA:37276 MA:0000574 NCIT:C12294 UMLS:C1522650 uberon UBERON:0012180 head or neck skin A zone of skin that is part of a craniocervical region. OBOL:automatic EMAPA:37276 MA:th UMLS:C1522650 ncithesaurus:Skin_of_the_Scalp_and_Neck The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. EMAPA:37180 MA:0002194 NCIT:C53062 UMLS:C1709532 uberon UBERON:0012193 phrenic vein The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. ncithesaurus:Phrenic_Vein EMAPA:37180 MA:th UMLS:C1709532 ncithesaurus:Phrenic_Vein network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP] EMAPA:28679 bladder vasculature blood vessels of bladder set of urinary bladder blood vessels uberon blood vessel of bladder UBERON:0012239 urinary bladder vasculature EMAPA network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP] MP:MP blood vessels of bladder EMAPA:28679 blood vessel of bladder EMAPA:28679 external opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP]. EMAPA:37977 FMA:19650 external meatus of urethra external urethral orifice external urethral ostium external urinary meatus meatus urinarius orificium urethrae externum orificium urethræ externum urethral meatus uberon urinary meatus UBERON:0012240 urethral meatus external opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP]. MP:MP EMAPA:37977 MA:th external meatus of urethra FMA:19650 external urethral orifice FMA:19650 external urethral ostium FMA:19650 external urinary meatus FMA:19650 meatus urinarius orificium urethrae externum orificium urethræ externum urethral meatus FMA:19650 A urethral meatus that is part of a male urethra[Automatically generated definition]. The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis. EMAPA:36434 FMA:85265 MA:0002642 external orifice of male urethra external urethral orifice (male) male urethra ostium ostium urethrae externum (urethra masculina) urethral meatus of penile urethra uberon distal urethral opening of male urethral opening of penile urethra UBERON:0012241 male urethral meatus A urethral meatus that is part of a male urethra[Automatically generated definition]. OBOL:automatic The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis. external orifice of male urethra FMA:85265 external urethral orifice (male) FMA:85265 male urethra ostium MA:0002642 ostium urethrae externum (urethra masculina) FMA:TA urethral meatus of penile urethra EMAPA:36434 distal urethral opening of male EMAPA:36434 urethral opening of penile urethra EMAPA:36434 the usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone FMA:85263 internal meatus of urethra internal urethral orifice of urinary bladder internal urethral ostium orificium urethrae internum ostium orificium internum ostium urethrae internum vesicourethral orifice uberon internal urethral ostium internal urinary meatus UBERON:0012242 internal urethral orifice the usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone MGI:anna MP:0011782 internal meatus of urethra FMA:85263 internal urethral orifice of urinary bladder FMA:85263 internal urethral ostium FMA:85263 orificium urethrae internum MP:0011782 ostium orificium internum ostium urethrae internum vesicourethral orifice FMA:85263 internal urethral ostium MP:0011782 internal urinary meatus MP:0011782 mucus-secreting glands in the mucosa of the uterine cervix NCIT:C32296 UMLS:C2724437 glandulae cervicales uberon UBERON:0012247 cervical gland mucus-secreting glands in the mucosa of the uterine cervix UMLS:C2724437 ncithesaurus:Cervical_Gland glandulae cervicales FMA:TA Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing. BTO:0000411 uberon UBERON:0012248 cervical mucosa Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing. BTO:0000411 The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium. distinction between two FMA classes not clear - we merge them here UBERON:0010182 BTO:0001850 CALOHA:TS-1098 FMA:77056 FMA:86484 NCIT:C12310 UMLS:C0227829 ectocervix portio vaginalis portio vaginalis cervicis uterine ectocervix vaginal part of cervix uberon exocervix UBERON:0012249 ectocervix BTO The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium. BTO:0001850 distinction between two FMA classes not clear - we merge them here FMA UMLS:C0227829 ncithesaurus:Ectocervix ectocervix BTO:0001850 ectocervix FMA:86484 portio vaginalis portio vaginalis cervicis BTO:0001850 uterine ectocervix CALOHA:TS-1098 vaginal part of cervix FMA:77056 exocervix BTO:0001850 A glandular epithelium that is part of a uterine cervix. The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. NCIT:C54414 UMLS:C1707350 uberon cervix columnar epithelium UBERON:0012250 cervix glandular epithelium A glandular epithelium that is part of a uterine cervix. OBOL:automatic The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium. UMLS:C1707350 ncithesaurus:Cervix_Columnar_Epithelium A epithelium that is part of a ectocervix. exocervical epithelium uberon UBERON:0012251 ectocervical epithelium A epithelium that is part of a ectocervix. OBOL:automatic The glandular epithelium that lines the endocervix. NCIT:C96180 endocervical glandular epithelium uberon UBERON:0012252 endocervical epithelium The glandular epithelium that lines the endocervix. ncithesaurus:Endocervical_Glandular_Epithelium Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet squamocolumnar junction NCIT:C97148 squamo-columnar junction of uterine cervix squamocolumnar junction of uterine cervix uberon UBERON:0012253 Site of 90% of lower genital tract neoplasia. This junction is presumed, but not proven, to be the embryologic junction of the Müllerian and urogenital sinus epithelia. cervical squamo-columnar junction Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet An artery that originates from the abdominal aorta abdominal artery artery of abdomen uberon UBERON:0012254 abdominal aorta artery An artery that originates from the abdominal aorta An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] uberon UBERON:0012274 columnar epithelium An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] Epithelium that derives from the mesoderm. [Automatically generated definition]. FMA:86452 mesoderm-derived epithelium mesoepithelium uberon UBERON:0012275 meso-epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. OBOL:automatic EMAPA:35308 FMA:86488 MA:0002732 glandular part of endometrium uterine glands uterine glands set uberon UBERON:0012276 endometrium glandular epithelium glandular part of endometrium FMA:86488 The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands. nasal gland EMAPA:37871 FMA:321518 NCIT:C22725 UMLS:C1522269 glandula nasalis glandulae nasales uberon UBERON:0012278 gland of nasal mucosa The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands. EMAPA:37871 MA:th UMLS:C1522269 ncithesaurus:Nose_Nasal_Cavity_Nasal_Gland_MMHCC glandula nasalis glandulae nasales A holocrine gland that is part of the pilosebaceous unit of a hair located in the area around the anus. EMAPA:37936 MESH:D010481 NCIT:C77620 uberon circumanal gland perianal gland UBERON:0012281 perianal sebaceous gland ISBN:0123813611 A holocrine gland that is part of the pilosebaceous unit of a hair located in the area around the anus. ISBN:0123813611 EMAPA:37936 MA:th circumanal gland MESH:A13.734 perianal gland MESH:A13.734 One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly cloacal fold EHDAA2:0004009 uberon UBERON:0012292 We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold EHDAA2 One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly MP:0011836 MP:anna cloacal fold EHDAA2:0004009 A mucosa that is part of a urethra. EMAPA:37912 FMA:76904 mucous membrane of urethra tunica mucosa urethrae urethral mucosa uberon UBERON:0012299 mucosa of urethra A mucosa that is part of a urethra. OBOL:automatic EMAPA:37912 MA:th mucous membrane of urethra FMA:76904 tunica mucosa urethrae FMA:TA urethral mucosa FMA:76904 EHDAA2:0000039 EMAPA:16389 ectoderm of maxillary component uberon UBERON:0012313 1st arch maxillary ectoderm EHDAA2 EHDAA2 EHDAA2 EHDAA2 ectoderm of maxillary component EMAPA:16389 One of five swellings formed during the development of the face FMA:293103 uberon embryonic facial process facial primordium primordium of face UBERON:0012314 embryonic facial prominence One of five swellings formed during the development of the face The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice introitus EMAPA:37983 FMA:19984 opening of vagina orifice of vagina ostium vaginae vagina opening vaginal orifice uberon introitus introitus of vagina vaginal introitus UBERON:0012317 vagina orifice The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice MGI:anna MGI:csmith MP:0001142 introitus FMA:19984 EMAPA:37983 MA:th orifice of vagina FMA:19984 ostium vaginae FMA:TA vagina opening MP:0001142 vaginal orifice FMA:19984 introitus FMA:19984 introitus of vagina MP:0001142 An artery of the neck EMAPA:37075 NCIT:C52850 UMLS:C1707349 uberon UBERON:0012320 cervical artery An artery of the neck EMAPA:37075 MA:th UMLS:C1707349 ncithesaurus:Cervical_Artery The deep cervical artery (Profunda cervicalis) is an artery of the neck. FMA:10659 uberon profunda cervicalis UBERON:0012321 deep cervical artery FMA The deep cervical artery (Profunda cervicalis) is an artery of the neck. profunda cervicalis Keratinized stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesize and accumulate keratin. FMA:45568 epithelium stratificatum squamosum cornificatum uberon UBERON:0012329 keratinized stratified squamous epithelium Keratinized stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesize and accumulate keratin. FMA:45568 epithelium stratificatum squamosum cornificatum FMA:45568 The lymphocytic cell population present in the mucosa of the nasopharyngeal duct of some animals. FMA:79771 MA:0003030 NCIT:C77659 UMLS:C2698431 NALT naso-pharyngeal lymphoid tissue uberon UBERON:0012330 nasal-associated lymphoid tissue The lymphocytic cell population present in the mucosa of the nasopharyngeal duct of some animals. ncithesaurus:Nasal-Associated_Lymphoid_Tissue UMLS:C2698431 ncithesaurus:Nasal-Associated_Lymphoid_Tissue NALT naso-pharyngeal lymphoid tissue FMA:79771 A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis. FMA:16516 MESH:D001956 NCIT:C12318 UMLS:C0006205 broad uterine ligament uberon broad ligament ligamentum latum uteri UBERON:0012332 broad ligament of uterus MESH A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis. MESH:A02.513.170 UMLS:C0006205 ncithesaurus:Broad_Ligament broad uterine ligament FMA:16516 broad ligament MESH:A02.513.170 ligamentum latum uteri A zone of skin that is part of the area surrounding the anus. EMAPA:37715 FMA:29350 MA:0003046 skin of perianal area uberon UBERON:0012336 perianal skin A zone of skin that is part of the area surrounding the anus. EMAPA:37715 MA:th any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen. BTO:0002325 MA:0003042 uberon UBERON:0012344 holocrine gland MA MP any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen. MP:0013543 The segment of the autopod that is distal to the metapodial region and consists of the digits. class refers to an entire limb segment, not just the bones acropodial limb segment acropodial region acropodial segment of autopod set of digits uberon UBERON:0012354 acropodium region The segment of the autopod that is distal to the metapodial region and consists of the digits. The segment of the manus that is distal to the metacarpal region and consists of the manual digits (fingers). class refers to an entire limb segment, not just the bones FMA:75592 acropodial hindlimb segment acropodial region of manus acropodial segment of manus all fingers anterior acropodium region anterior acropodium segment of limb digiti manus digits of hand fingers including thumb fingers set manual acropodium region manual acropodium segment of limb set of digits of hand set of fingers uberon anterior acropodium manual acropodium UBERON:0012355 manual acropodium region The segment of the manus that is distal to the metacarpal region and consists of the manual digits (fingers). digiti manus FMA:TA digits of hand FMA:75592 fingers including thumb FMA:75592 fingers set FMA:75592 set of digits of hand FMA:75592 set of fingers FMA:75592 The segment of the pes that is distal to the metatarsal region and consists of the pedal digits (toes). class refers to an entire limb segment, not just the bones FMA:70664 acropodial forelimb segment acropodial region of pes acropodial segment of pes all toes digits of foot pedal acropodium region set of toes toes set uberon toes UBERON:0012356 pedal acropodium region The segment of the pes that is distal to the metatarsal region and consists of the pedal digits (toes). digits of foot FMA:70664 set of toes FMA:70664 toes set FMA:70664 toes FMA:70664 A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton. uberon digit bone UBERON:0012357 digitopodium bone A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton. digit bone A bone that is part of a the manual digitopodium skeleton - i.e. the fingers or the metacarpal skeleton. bone of forelimb digitopodium uberon UBERON:0012358 manual digitopodium bone A bone that is part of a the manual digitopodium skeleton - i.e. the fingers or the metacarpal skeleton. A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton. bone of hindlimb digitopodium uberon UBERON:0012359 pedal digitopodium bone A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton. A bone element that is part of a jaw region. Do not manually classify under here - bones are automatically classified EMAPA:35453 MA:0003130 jaw bone uberon UBERON:0012360 bone of jaw A bone element that is part of a jaw region. OBOL:automatic EHDAA2:0004588 uberon UBERON:0012361 internal anal region EHDAA2 A muscle layer that is part of an intestine. FMA:15697 intestinal muscularis propria muscularis externa of intestine uberon smooth muscle of intestine UBERON:0012367 muscle layer of intestine FMA A muscle layer that is part of an intestine. OBOL:automatic intestinal muscularis propria FMA:15697 muscularis externa of intestine FMA:15697 A layer of tissue between the muscularis and serosa. FMA:45636 NCIT:C94494 UMLS:C0225334 uberon UBERON:0012375 Contains nerves, blood vessels, lymphatics and lymph nodes subserosa A layer of tissue between the muscularis and serosa. UMLS:C0225334 ncithesaurus:Subserosa A muscular coat that is part of a urinary bladder. FMA:15930 NCIT:C32206 UMLS:C1288327 bladder muscular coat muscle layer of urinary bladder muscular coat of bladder muscular coat of urinary bladder muscular layer of bladder muscular layer of urinary bladder tunica musculari vesicae tunica muscularis (vesica urinaria) uberon UBERON:0012378 muscle layer of urinary bladder FMA A muscular coat that is part of a urinary bladder. OBOL:automatic UMLS:C1288327 ncithesaurus:Bladder_Muscular_Coat muscle layer of urinary bladder FMA:15930 muscular coat of bladder FMA:15930 muscular coat of urinary bladder FMA:15930 muscular layer of bladder FMA:15930 muscular layer of urinary bladder FMA:15930 tunica musculari vesicae FMA:TA tunica muscularis (vesica urinaria) FMA:TA EMAPA:37567 MA:0001802 uberon UBERON:0012416 respiratory system arterial smooth muscle EMAPA:37567 MA:th A smooth muscle tissue that is part of a respiratory system venous blood vessel. EMAPA:37586 MA:0001812 uberon UBERON:0012418 respiratory system venous smooth muscle A smooth muscle tissue that is part of a respiratory system venous blood vessel. OBOL:automatic EMAPA:37586 MA:th A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified] a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction increases the surface area of a cell lining whilst minimizing increase in volume FMA class represents an individual microvillus. FMA:67296 MESH:D008871 NCIT:C33112 UMLS:C0026049 uberon microvilli microvillus UBERON:0012423 layer of microvilli A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified] GO:0005902 FMA class represents an individual microvillus. FMA UMLS:C0026049 ncithesaurus:Microvillus microvilli MESH:A11.284.180.565 microvillus FMA:67296 A microvillus layer that is striated and found in the intestine. FMA class represents an individual microvillus FMA:70978 NCIT:C33634 uberon striated border UBERON:0012425 striated border microvillus layer A microvillus layer that is striated and found in the intestine. FMA class represents an individual microvillus FMA striated border FMA:70978 Blood-forming tissue, consisting of reticular fibers and cells. Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 NCIT:C13051 UMLS:C0229619 haemopoietic tissue hematopoietic tissue hemopoietic tissue textus haemopoieticus bone marrow tissue uberon UBERON:0012429 hematopoietic tissue FMA defitional Blood-forming tissue, consisting of reticular fibers and cells. UMLS:C0229619 ncithesaurus:Hematopoietic_Tissue haemopoietic tissue FMA:14073 hematopoietic tissue FMA:14073 hemopoietic tissue FMA:14073 textus haemopoieticus FMA:14073 bone marrow tissue NCBITaxon:9606 The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. tunica fibrosa FMA:58102 fibrous layer of eyeball uberon corneosclera fibrous tunic UBERON:0012430 tunica fibrosa of eyeball FMA The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. fibrous layer of eyeball FMA:58102 corneosclera fibrous tunic A anatomical space that is enclosed by a cloaca. the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ TAO:0000330 ZFA:0000330 cloaca lumen cloacal chamber uberon UBERON:0012463 cloacal lumen cjm A anatomical space that is enclosed by a cloaca. OBOL:automatic the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ ZFA cloaca lumen ZFA:0000330 cloacal chamber ZFA:0000330 The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. cloacal opening uberon cloacal orifice vent UBERON:0012464 cloacal vent The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. A anatomical space that is enclosed by a terminal part of digestive tract. includes the cloacal lumen, in species where this is present uberon UBERON:0012465 lumen of terminal part of digestive tract A anatomical space that is enclosed by a terminal part of digestive tract. OBOL:automatic EHDAA2:0000472 EMAPA:16054 VHOG:0000767 uberon extraembryonic cavities UBERON:0012466 extraembryonic cavity extraembryonic cavities EHDAA2:0000472 An anatomical space with no opening to another space or to the exterior. AEO:0000222 closed anatomical space uberon UBERON:0012467 enclosed anatomical space An anatomical space with no opening to another space or to the exterior. AEO:0000222 Triangular calcified papillae (often five) placed radially around the anus of some Holothuriidae anal teeth uberon calcified anal papilla cloacal tooth perianal tooth UBERON:0012468 anal tooth Triangular calcified papillae (often five) placed radially around the anus of some Holothuriidae anal teeth EHDAA2:0004589 uberon UBERON:0012469 external anal region EHDAA2 The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle. FMA:24139 uberon bones of upper limb ossa membri superioris pectoral complex skeleton set of bones of upper limb skeleton of anterior limb/fin and girdle upper limb skeleton UBERON:0012475 skeleton of pectoral complex FMA The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle. bones of upper limb FMA:24139 ossa membri superioris FMA:TA pectoral complex skeleton set of bones of upper limb FMA:24139 skeleton of anterior limb/fin and girdle upper limb skeleton FMA:24139 The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. FMA:24140 uberon bones of lower limb lower limb skeleton ossa membri inferioris pelvic complex skeleton set of bones of lower limb skeleton of posterior limb/fin and girdle UBERON:0012476 skeleton of pelvic complex FMA The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. bones of lower limb FMA:24140 lower limb skeleton FMA:24140 ossa membri inferioris FMA:TA pelvic complex skeleton set of bones of lower limb FMA:24140 skeleton of posterior limb/fin and girdle The posterior region of the neck, including the suboccipital region. nuchal nape BTO:0000957 FMA:24189 back of neck nape of neck neck back nucha nuchal region posterior cervical region posterior neck region posterior part of neck regio cervicalis posterior uberon hindneck UBERON:0012477 dorsal part of neck FMA FMA FMA The posterior region of the neck, including the suboccipital region. MP:0012723 nape BTO:0000957 back of neck FMA:24189 neck back FMA:24189 nucha FMA:24189 nuchal region FMA:24189 posterior cervical region FMA:24189 posterior neck region FMA:24189 posterior part of neck FMA:24189 regio cervicalis posterior FMA:TA A gland that is part of a cloaca. uberon UBERON:0012478 cloacal gland A gland that is part of a cloaca. OBOL:automatic A mucosa that is part of a cloaca [Automatically generated definition]. UBERON:0003349 cloaca mucosa cloaca mucosa of organ cloaca mucous membrane cloaca organ mucosa cloacal mucous membrane mucosa of cloaca mucosa of organ of cloaca mucous membrane of cloaca organ mucosa of cloaca uberon UBERON:0012480 cloacal mucosa A mucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic An epithelium that is part of a cloaca. cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 EMAPA:36070 ZFA:0005783 uberon cloacal endoderm UBERON:0012481 cloacal epithelium An epithelium that is part of a cloaca. cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 cloacal endoderm EMAPA:27577 A submucosa that is part of a cloaca [Automatically generated definition]. cloaca submucosa cloacal submucosa uberon UBERON:0012482 submucosa of cloaca A submucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic A serous membrane that is part of a cloaca [Automatically generated definition]. cloaca serosa cloaca serous membrane cloacal serosa serous membrane of cloaca visceral peritoneum of cloaca uberon UBERON:0012483 serosa of cloaca A serous membrane that is part of a cloaca [Automatically generated definition]. OBOL:automatic cloacal villi uberon UBERON:0012485 cloacal villus cloacal villi A muscular coat that is part of a cloaca. muscularis externa of cloaca uberon smooth muscle of cloaca UBERON:0012486 muscle layer of cloaca A muscular coat that is part of a cloaca. OBOL:automatic A sphincter muscle that is part of a vagina. sphincter of vagina uberon UBERON:0012487 vaginal sphincter A sphincter muscle that is part of a vagina. OBOL:automatic A muscular coat that is part of a duodenum. FMA:14944 duodenal muscularis propria muscularis externa of duodenum uberon muscularis propria of duodenum smooth muscle of duodenum UBERON:0012488 muscle layer of duodenum A muscular coat that is part of a duodenum. OBOL:automatic duodenal muscularis propria FMA:14944 muscularis externa of duodenum FMA:14944 muscularis propria of duodenum smooth muscle of duodenum A muscular coat that is part of a colon. EMAPA:27383 FMA:14986 MA:0003198 colonic muscularis propria muscular coat of colon muscular layer of colon muscularis externa of colon tunica muscularis coli uberon colon muscularis UBERON:0012489 muscle layer of colon A muscular coat that is part of a colon. OBOL:automatic colonic muscularis propria FMA:14986 muscular coat of colon FMA:14986 muscular layer of colon FMA:14986 muscularis externa of colon FMA:14986 tunica muscularis coli FMA:TA colon muscularis MA:0003198 A muscular coat that is part of a anal canal. FMA:15708 anal canal muscularis propria anal muscularis propria muscular coat of anal canal muscular layer of anal canal muscularis externa of anal canal muscularis propria of anal canal uberon UBERON:0012490 muscle layer of anal canal A muscular coat that is part of a anal canal. OBOL:automatic anal muscularis propria FMA:15708 muscularis propria of anal canal FMA:15708 A serous membrane that is part of a vermiform appendix. FMA:14997 appendiceal serosa appendix serosa serosa of vermiform appendix visceral peritoneum of vermiform appendix uberon UBERON:0012498 serosa of appendix A serous membrane that is part of a vermiform appendix. OBOL:automatic appendiceal serosa FMA:14997 appendix serosa FMA:14997 serosa of vermiform appendix FMA:14997 visceral peritoneum of vermiform appendix FMA:14997 A serous membrane that is part of a fallopian tube. FMA:18316 serosa of fallopian tube serosa of oviduct serous coat of uterine tube tunica serosa (tuba uterina) tunica serosa tubae uterinae uterine tubal serosa uterine tube serosa uberon UBERON:0012499 serosa of uterine tube A serous membrane that is part of a fallopian tube. OBOL:automatic serosa of fallopian tube FMA:18316 serosa of oviduct FMA:18316 serous coat of uterine tube FMA:18316 tunica serosa (tuba uterina) FMA:18316 tunica serosa tubae uterinae FMA:TA uterine tubal serosa FMA:18316 uterine tube serosa FMA:18316 A adventitia that is part of a esophagus. FMA:63006 adventitia of oesophagus adventitious layer of esophagus esophageal adventitia esophagus adventitia tunica adventitia (esophagus) tunica adventitia oesophageae uberon UBERON:0012504 adventitia of esophagus A adventitia that is part of a esophagus. OBOL:automatic adventitia of oesophagus FMA:63006 adventitious layer of esophagus FMA:63006 esophageal adventitia FMA:63006 esophagus adventitia FMA:63006 tunica adventitia (esophagus) FMA:63006 tunica adventitia oesophageae FMA:TA A smooth muscle tissue that is part of a umbilical cord. BTO:0001847 uberon UBERON:0012615 umbilical smooth muscle A smooth muscle tissue that is part of a umbilical cord. OBOL:automatic A anatomical junction that connects a stomach and connects a duodenum. FMA:17046 uberon UBERON:0012650 gastroduodenal junction A anatomical junction that connects a stomach and connects a duodenum. OBOL:automatic A mucosa that is part of a gastroduodenal junction. BTO:0005415 gastroduodenal mucosa uberon UBERON:0012651 mucosa of gastroduodenal junction A mucosa that is part of a gastroduodenal junction. OBOL:automatic gastroduodenal mucosa BTO:0005415 The subdivision of the digestive tract that consists of the colon and the rectum. colorectal BTO:0001613 CALOHA:TS-1298 NCIT:C54189 UMLS:C1711309 uberon UBERON:0012652 colorectum non-canonical cjm The subdivision of the digestive tract that consists of the colon and the rectum. UMLS:C1711309 ncithesaurus:Colorectal_Region A mucosa that is part of a colorectum. UBERON:0019041 BTO:0002435 uberon UBERON:0013067 colorectal mucosa A mucosa that is part of a colorectum. OBOL:automatic FMA:32888 basal epiphysis of phalanx of foot base of phalanx of foot basis phalangis (pedis) basis phalangis pedis proximal epiphysis of phalanx of toe uberon UBERON:0013121 proximal epiphysis of phalanx of pes basal epiphysis of phalanx of foot FMA:32888 base of phalanx of foot FMA:32888 basis phalangis (pedis) FMA:32888 basis phalangis pedis FMA:TA proximal epiphysis of phalanx of toe FMA:32888 FMA:32890 caput phalangis (pedis) caput phalangis pedis distal end of phalanx of foot distal epiphysis of phalanx of toe head of phalanx of foot uberon ungual tuberosity of distal phalanx of toe UBERON:0013122 distal epiphysis of phalanx of pes caput phalangis (pedis) FMA:32890 caput phalangis pedis FMA:TA distal end of phalanx of foot FMA:32890 distal epiphysis of phalanx of toe FMA:32890 head of phalanx of foot FMA:32890 ungual tuberosity of distal phalanx of toe FMA:32890 A vein that is part of a abdomen. TODO mirror representation of abdominal aorta this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein abdominal vein uberon UBERON:0013126 vein of abdomen A vein that is part of a abdomen. OBOL:automatic A vein that drains a lip. labial vein of face lip vein vena labialis uberon labial vein UBERON:0013136 vein of lip FMA A vein that drains a lip. OBOL:automatic lip vein OBOL:automatic vena labialis A nonskeletal ligament that is part of a liver. FMA:15820 NCIT:C32997 UMLS:C0230238 hepatic ligament liver ligament uberon UBERON:0013139 ligament of liver A nonskeletal ligament that is part of a liver. OBOL:automatic UMLS:C0230238 ncithesaurus:Liver_Ligament hepatic ligament FMA:15820 Any vein within the general circulation that transports blood back to the right atrium of the heart. FMA:66644 NCIT:C33719 UMLS:C0447117 systemic venous tree organ part uberon UBERON:0013140 systemic vein Any vein within the general circulation that transports blood back to the right atrium of the heart. ncithesaurus:Systemic_Vein UMLS:C0447117 ncithesaurus:Systemic_Vein systemic venous tree organ part FMA:66644 EHDAA2:0000101 EMAPA:16917 rhombencephalic vesicle uberon UBERON:0013149 gives rise of 4th ventricle hindbrain vesicle EHDAA2 rhombencephalic vesicle EHDAA2:0000101 consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html). Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle' NCIT:C34259 early brain vesicle primitive brain vesicle primary brain vesicle secondary brain vesicle uberon brain vesicle UBERON:0013150 future brain vesicle EHDAA2 EHDAA2 One of two arteries (anterior and posterior choroidal artery) that supply blood to the choroid plexus, optic tract, hippocampus, globus pallidus, and other various brain regions. NCIT:C32310 UMLS:C0226164 artery of choroid plexus choroid artery uberon UBERON:0013151 choroidal artery One of two arteries (anterior and posterior choroidal artery) that supply blood to the choroid plexus, optic tract, hippocampus, globus pallidus, and other various brain regions. ncithesaurus:Choroidal_Artery UMLS:C0226164 ncithesaurus:Choroidal_Artery EHDAA2:0000033 EMAPA:16384 endoderm of mandibular component uberon UBERON:0013156 1st arch mandibular endoderm EHDAA2 EHDAA2 EHDAA2 endoderm of mandibular component EMAPA:16384 A gland that is part of a foregut-midgut junction. EHDAA2:0000574 EMAPA:17065 gland of foregut-midgut junction uberon UBERON:0013158 foregut-midgut junction gland A gland that is part of a foregut-midgut junction. OBOL:automatic gland of foregut-midgut junction EMAPA:17065 EHDAA2:0000449 EHDAA:5435 EMAPA:17533 VHOG:0000913 mantle layer epithalamus mantle layer of epithalamus uberon UBERON:0013159 epithalamus mantle layer mantle layer epithalamus VHOG:0000913 EHDAA2:0000450 EHDAA:5437 EMAPA:17535 VHOG:0000884 ventricular layer epithalamus ventricular layer of epithalamus uberon UBERON:0013160 epithalamus ventricular layer ventricular layer epithalamus VHOG:0000884 A telencephalic ventricle that is in_the_left_side_of a telencephalon. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:78450 left telencephalic ventricle uberon UBERON:0013161 left lateral ventricle FMA A telencephalic ventricle that is in_the_left_side_of a telencephalon. OBOL:automatic A telencephalic ventricle that is in_the_right_side_of a telencephalon. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:78449 right telencephalic ventricle uberon UBERON:0013162 right lateral ventricle FMA A telencephalic ventricle that is in_the_right_side_of a telencephalon. OBOL:automatic the layer of the ovarian stroma lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles. EMAPA:37927 FMA:18613 NCIT:C33243 UMLS:C0227878 cortex of ovary cortex ovarii (zona parenchymatosa) uberon UBERON:0013191 ovarian cortex the layer of the ovarian stroma lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles. MGI:anna EMAPA:37927 MA:th UMLS:C0227878 ncithesaurus:Ovarian_Cortex cortex of ovary FMA:18613 cortex ovarii (zona parenchymatosa) FMA:18613 highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles. composed of loose connective tissue that contains blood vessels, lymph vessels and nerves EMAPA:37928 FMA:18616 NCIT:C33245 UMLS:C0227879 medulla of ovary medulla ovarii (zona vasculosa) uberon zona vasculosa of Waldeyer UBERON:0013192 ovarian medulla highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles. MGI:anna composed of loose connective tissue that contains blood vessels, lymph vessels and nerves NCIT EMAPA:37928 MA:th UMLS:C0227879 ncithesaurus:Ovarian_Medulla medulla of ovary FMA:18616 medulla ovarii (zona vasculosa) FMA:18616 zona vasculosa of Waldeyer The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. FMA:86279 acinus of serous gland uberon UBERON:0013232 serous acinus The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. uberon UBERON:0013238 future glans A future glans that is part of a male genital tubercle. EMAPA:29252 glans of male genital tubercle uberon UBERON:0013239 future glans penis EMAPA A future glans that is part of a male genital tubercle. OBOL:automatic A future glans that is part of a female genital tubercle. EMAPA:19170 glans of female genital tubercle uberon UBERON:0013240 future glans clitoris EMAPA A future glans that is part of a female genital tubercle. OBOL:automatic The precursor of the urethra In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week sulcus urethralis primarius urethral groove urethral sulcus uberon UBERON:0013241 embryonic urethral groove Wikipedia The precursor of the urethra In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week sulcus urethralis primarius A epithelial tube that develops from a Mullerian duct in a male. Later degenerates. consider separating the duct from the degenerating portion, as in EMAPA EHDAA2:0001052 EMAPA:29161 EMAPA:35661 uberon degenerating mesonephric portion of male paramesonephric duct UBERON:0013247 male paramesonephric duct EHDAA2 EHDAA2 A epithelial tube that develops from a Mullerian duct in a male. Later degenerates. degenerating mesonephric portion of male paramesonephric duct EMAPA:29161 Anatomical cavity that is the lumen of the skull and contains the brain. EMAPA:37497 FMA:9644 MA:0003061 NCIT:C77638 UMLS:C0230041 cavitas cranii uberon intracranial cavity intracranial space UBERON:0013411 cranial cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg Wikipedia Anatomical cavity that is the lumen of the skull and contains the brain. UBERON:cjm EMAPA:37497 MA:th UMLS:C0230041 ncithesaurus:Cranial_Cavity cavitas cranii FMA:9644 FMA:TA intracranial cavity intracranial space The upper one third of esophagus in which the muscle layer is composed of muscle cells of the striated type. NCIT:C12253 UMLS:C0227187 uberon proximal part of esophagus upper third of esophagus UBERON:0013472 upper esophagus The upper one third of esophagus in which the muscle layer is composed of muscle cells of the striated type. ncithesaurus:Upper_Third_of_the_Esophagus UMLS:C0227187 ncithesaurus:Upper_Third_of_the_Esophagus A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus. In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil caecal tonsil uberon cecal GALT UBERON:0013478 cecal tonsil A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus. ISBN:0824754077 A blood vessel endothelium that is part of a lung [Automatically generated definition]. BTO:0004128 CALOHA:TS-0573 uberon respiratory endothelium UBERON:0013479 lung endothelium A blood vessel endothelium that is part of a lung [Automatically generated definition]. OBOL:automatic respiratory endothelium BTO:0004128 The panniculus adiposus is the fatty layer of the subcutaneous tissues, superficial to a deeper vestigial layer of muscle, the panniculus carnosus. An example is the Fascia of Camper. Another example is the superficial cervical fascia[WP] It includes structures that are considered fascia by some sources but not by others. Consider merging with subcutaneous adipose tissue panniculus adiposus group uberon subcutaneous fat UBERON:0013488 panniculus adiposus The panniculus adiposus is the fatty layer of the subcutaneous tissues, superficial to a deeper vestigial layer of muscle, the panniculus carnosus. An example is the Fascia of Camper. Another example is the superficial cervical fascia[WP] subcutaneous fat A sphincter muscle that is part of a cloaca. NCIT:C34129 UMLS:C1516658 sphincter cloacae uberon UBERON:0013501 the muscles of the cloacal sphincter specialise into the perineal muscles in mammals (Gegenbaur, 1883; Popowsky, 1899; Nishi, 1938). cloacal sphincter A sphincter muscle that is part of a cloaca. OBOL:automatic UMLS:C1516658 ncithesaurus:Cloacal_Sphincter sphincter cloacae A caudal vertebra endochondral element that is composed primarily of cartilage tissue. UBERON:0013517 EHDAA2:0000260 EMAPA:18044 coccygeal vertebra cartilage element coccygeal vertebral cartilage condensation group tail vertebral cartilage condensation uberon UBERON:0013503 caudal vertebra cartilage element A caudal vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic coccygeal vertebra cartilage element coccygeal vertebral cartilage condensation group EHDAA2:0000260 tail vertebral cartilage condensation EMAPA:18044 A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation. UBERON:0013518 EMAPA:18045 coccygeal vertebra pre-cartilage condensation tail vertebral pre-cartilage condensation uberon UBERON:0013504 caudal vertebra pre-cartilage condensation A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic coccygeal vertebra pre-cartilage condensation tail vertebral pre-cartilage condensation EMAPA:18045 A cervical vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0000240 cervical vertebral cartilage condensation group uberon UBERON:0013505 cervical vertebra cartilage element A cervical vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic cervical vertebral cartilage condensation group EHDAA2:0000240 A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013506 cervical vertebra pre-cartilage condensation A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0002014 thoracic vertebral cartilage condensation group uberon UBERON:0013507 thoracic vertebra cartilage element A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic thoracic vertebral cartilage condensation group EHDAA2:0002014 A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013508 thoracic vertebra pre-cartilage condensation A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A lumbar vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0001038 lumbar vertebral cartilage condensation group uberon UBERON:0013509 lumbar vertebra cartilage element A lumbar vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic lumbar vertebral cartilage condensation group EHDAA2:0001038 A lumbar vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013510 lumbar vertebra pre-cartilage condensation A lumbar vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic The space that surrounds an organism. external to organism outside of body uberon UBERON:0013514 space surrounding organism The space that surrounds an organism. A section through the tube or network of tubes that connects the ovaries to the outside of the body. FMA class may only represent the uterine portion FMA:18302 subdivision of oviduct subdivision of uterine tube uterine tube zone zone of uterine tube subdivision of fallopian tube uberon UBERON:0013515 subdivision of oviduct A section through the tube or network of tubes that connects the ovaries to the outside of the body. FMA class may only represent the uterine portion FMA subdivision of oviduct FMA:18302 uterine tube zone FMA:18302 zone of uterine tube FMA:18302 subdivision of fallopian tube FMA:18302 uberon UBERON:0013522 subdivision of tube The anatomical space that is enclosed by a stomach. Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. EMAPA:18395 FMA:14585 cavity of stomach uberon gastric cavity UBERON:0013525 stomach lumen FMA The anatomical space that is enclosed by a stomach. Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. FMA:14585 cavity of stomach FMA:14585 gastric cavity FMA:14585 A anatomical cavity that is part of a ear vesicle. EHDAA2:0004121 EMAPA:25363 lumen of otocyst uberon UBERON:0013526 otocyst lumen EHDAA2 EHDAA2 EHDAA2 A anatomical cavity that is part of a ear vesicle. OBOL:automatic lumen of otocyst EMAPA:25363 A metapodium bone that is part of a digit 1 plus metapodial segment. metapodium 1 metapodium I uberon UBERON:0013581 metapodium bone 1 A metapodium bone that is part of a digit 1 plus metapodial segment. OBOL:automatic A metapodium bone that is part of a digit 5 plus metapodial segment. metapodium 5 metapodium V uberon UBERON:0013585 metapodium bone 5 A metapodium bone that is part of a digit 5 plus metapodial segment. OBOL:automatic Short bones are designated as those bones that are as wide as they are long. Their primary function is to provide support and stability with little to no movement. They are one of five types of bones: long, short, flat, irregular and sesamoid. Examples of these bones include the tarsals in the foot and the carpals in the hand. TODO - make subclass links FMA:7475 NCIT:C33545 uberon UBERON:0013630 short bone NCIT Short bones are designated as those bones that are as wide as they are long. Their primary function is to provide support and stability with little to no movement. They are one of five types of bones: long, short, flat, irregular and sesamoid. Examples of these bones include the tarsals in the foot and the carpals in the hand. A epithelium that is part of a intestinal villus. FMA:63587 intestinal villus epithelium uberon villous epithelium villus epithelium UBERON:0013636 epithelium of intestinal villus A epithelium that is part of a intestinal villus. OBOL:automatic intestinal villus epithelium FMA:63587 The prostate gland lobe that is located on the lateral side of the organ. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:29822 FMA:19577 MA:0003125 NCIT:C13092 lateral lobe of prostate lateral lobe of prostate gland uberon lateral prostate lateral ventral lobe of prostate gland UBERON:0013637 prostate gland lateral lobe The prostate gland lobe that is located on the lateral side of the organ. ncithesaurus:Lateral_Lobe_of_the_Prostate lateral lobe of prostate FMA:19577 lateral lobe of prostate gland FMA:19577 lateral ventral lobe of prostate gland MorphoBank:MorphoBank A gland that is part of the gular region (throat) uberon UBERON:0013645 gular gland A gland that is part of the gular region (throat) Anatomical space that is an opening in a bone of the skull. FMA:53165 foramen of skull cranial conduit cranial foramen uberon foramina of the skull UBERON:0013685 foramen of skull Anatomical space that is an opening in a bone of the skull. TAO:curator foramen of skull cranial conduit FMA:53165 foramina of the skull 2 2 An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 foramen space uberon UBERON:0013686 anatomical conduit space FMA An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 Lymphoid tissue located in the appendix. CALOHA:TS-1268 lymphatic tissue of appendix lymphatic tissue of vermiform appendix uberon appendix lymphoid UBERON:0013689 appendix lymphoid tissue Lymphoid tissue located in the appendix. CALOHA:TS-1268 lymphatic tissue of appendix OBOL:automatic lymphatic tissue of vermiform appendix OBOL:automatic appendix lymphoid CALOHA:TS-1268 Vascular endothelium found in blood vessels of the blood-brain-barrier. BTO:0001852 BTO:0003248 CALOHA:TS-0092 uberon cerebromicrovascular endothelium UBERON:0013694 brain endothelium Vascular endothelium found in blood vessels of the blood-brain-barrier. CALOHA:TS-0092 cerebromicrovascular endothelium CALOHA:TS-0092 Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 uberon colon endothelial cell colon endothelial cells colonic endothelial cell colonic endothelium colorectal endothelial cell colorectal endothelium UBERON:0013695 colon endothelium Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 colon endothelial cell CALOHA:TS-0162 colon endothelial cells CALOHA:TS-0162 colonic endothelial cell CALOHA:TS-0162 colonic endothelium CALOHA:TS-0162 colorectal endothelial cell CALOHA:TS-0162 colorectal endothelium CALOHA:TS-0162 The epithelium that forms the surface of the tonsil dips into the underlying connective tissue in numerous places, forming crypts kown as tonsillar crypts. Stratified squamous epithelium, that may be heavily infiltrated by lymphocytes. Epithelial cells are present in the germinal as well as in the periphery of the nodule. CALOHA:TS-2070 uberon epithelium of tonsil tonsil epithelial cell UBERON:0013696 tonsil epithelium The epithelium that forms the surface of the tonsil dips into the underlying connective tissue in numerous places, forming crypts kown as tonsillar crypts. Stratified squamous epithelium, that may be heavily infiltrated by lymphocytes. Epithelial cells are present in the germinal as well as in the periphery of the nodule. CALOHA:TS-2070 epithelium of tonsil CALOHA:TS-2070 tonsil epithelial cell CALOHA:TS-2070 Epithelium lining the exocrine pancreas. CALOHA:TS-2108 uberon epithelium of exocrine pancreas exocrine pancreas epithelial cell UBERON:0013697 exocrine pancreas epithelium Epithelium lining the exocrine pancreas. CALOHA:TS-2108 epithelium of exocrine pancreas CALOHA:TS-2108 exocrine pancreas epithelial cell CALOHA:TS-2108 Musculature of the head and neck, spine, and ribs. EHDAA2:0000159 EMAPA:18166 uberon UBERON:0013700 axial musculature Musculature of the head and neck, spine, and ribs. HP:0003327 A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. uberon UBERON:0013701 main body axis A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. The region of the organism associated with the visceral organs. Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 EMAPA:36031 FMA:231424 uberon body whole body UBERON:0013702 body proper AEO The region of the organism associated with the visceral organs. AEO:0000103 Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. FMA:231424 body AEO:0000103 whole body BTO:0001489 Anatomical projection that is part of the integumentl system. skin projection uberon UBERON:0013703 integumentary projection Anatomical projection that is part of the integumentl system. A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. FMA:293127 NCIT:C34230 UMLS:C1518428 uberon chordal canal UBERON:0013704 notochordal canal A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. UMLS:C1518428 ncithesaurus:Notochordal_Canal Fluid contained within the notochordal canal notochord fluid portion of notochordal fluid uberon UBERON:0013727 Distinct feature of coelocanths notochordal fluid Fluid contained within the notochordal canal A metaphysis that is part of a metaphysis. FMA:32830 diaphyseal end of humerus humeral metaphysis uberon UBERON:0013749 metaphysis of humerus A metaphysis that is part of a metaphysis. OBOL:automatic diaphyseal end of humerus FMA:32830 humeral metaphysis FMA:32830 A diaphysis that is part of a metacarpal bone. FMA:33804 body of metacarpal corpus ossis metacarpi metacarpal bone diaphysis shaft of metacarpal shaft of metacarpal bone uberon UBERON:0013752 diaphysis of metacarpal bone A diaphysis that is part of a metacarpal bone. OBOL:automatic body of metacarpal FMA:33804 corpus ossis metacarpi FMA:TA metacarpal bone diaphysis FMA:33804 shaft of metacarpal FMA:33804 shaft of metacarpal bone FMA:33804 A distal epiphysis that is part of a metacarpal bone. FMA:33798 caput ossis metacarpi distal end of metacarpal bone head of metacarpal bone lower end of metacarpal bone uberon UBERON:0013753 distal epiphysis of metacarpal bone A distal epiphysis that is part of a metacarpal bone. OBOL:automatic caput ossis metacarpi FMA:TA distal end of metacarpal bone FMA:33798 head of metacarpal bone FMA:33798 lower end of metacarpal bone FMA:33798 A organ component layer that is part of a integumental system. layer of skin skin layer uberon UBERON:0013754 integumentary system layer A organ component layer that is part of a integumental system. OBOL:automatic A blood that is part of a artery. FMA:83066 arterial blood blood in artery portion of arterial blood uberon UBERON:0013755 arterial blood A blood that is part of a artery. OBOL:automatic arterial blood FMA:83066 blood in artery FMA:83066 portion of arterial blood FMA:83066 A blood that is part of a vein. FMA:83067 blood in vein portion of venous blood venous blood uberon UBERON:0013756 venous blood A blood that is part of a vein. OBOL:automatic blood in vein FMA:83067 portion of venous blood FMA:83067 venous blood FMA:83067 A blood that is part of a capillary. FMA:263901 NCIT:C32212 blood in capillary portion of blood in capillary portion of capillary blood uberon UBERON:0013757 capillary blood A blood that is part of a capillary. OBOL:automatic portion of blood in capillary FMA:263901 One of two openings in the uterine cervix. FMA:20422 uberon cervical opening uterine cervix opening UBERON:0013758 cervical os One of two openings in the uterine cervix. Opening of uterine cervix into the body of the uterus. The internal orifice of the uterus (or internal orifice of the cervix uteri or internal os) is an interior narrowing of the uterine cavity. It corresponds to a slight constriction known as the isthmus that can be observed on the surface of the uterus about midway between the apex and base[Wikipedia:Internal_orifice_of_the_uterus]. FMA:17747 uberon internal orifice internal os UBERON:0013759 internal cervical os Opening of uterine cervix into the body of the uterus. The internal orifice of the uterus (or internal orifice of the cervix uteri or internal os) is an interior narrowing of the uterine cavity. It corresponds to a slight constriction known as the isthmus that can be observed on the surface of the uterus about midway between the apex and base[Wikipedia:Internal_orifice_of_the_uterus]. internal orifice internal os internal os FMA:17747 Opening of uterine cervix into the vagina. The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]. FMA:76836 NCIT:C32491 UMLS:C1512165 external os of uterus ostium uteri uberon external os ostium of uterus UBERON:0013760 external cervical os Opening of uterine cervix into the vagina. The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]. UMLS:C1512165 ncithesaurus:Ectocervical_Os external os of uterus FMA:76836 ostium uteri FMA:TA external os ostium of uterus The cavity formed by the walls of the cervix. BTO:0002249 FMA:17746 lumen of cervix of uterus uberon canal of the cervix cavity of cervix cervical canal cervical canal of uterus endocervical endocervical canal endocervix UBERON:0013761 cervical cavity The cavity formed by the walls of the cervix. lumen of cervix of uterus FMA:17746 canal of the cervix cavity of cervix BTO:0002249 cervical canal cervical canal of uterus BTO:0002249 endocervical endocervical canal endocervical canal BTO:0002249 endocervix Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 digestive organ digestive system organ uberon UBERON:0013765 digestive system element Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 MA:th Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. great vessel EMAPA:36460 great vessel of thorax uberon UBERON:0013768 Groupings may vary - typically pulmonary vessels and aorta and vena cavae great vessel of heart Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. A organ cavity that is part of a uterus. EMAPA:36273 FMA:17745 cavity of uterus uterine cavity uterine space uberon UBERON:0013769 uterine lumen A organ cavity that is part of a uterus. OBOL:automatic cavity of uterus FMA:17745 uterine cavity FMA:17745 A diaphysis that is part of a metatarsal bone. FMA:33826 diaphysis of metatarsal metatarsal bone diaphysis metatarsal diaphysis shaft of metatarsal bone uberon UBERON:0013774 diaphysis of metatarsal bone A diaphysis that is part of a metatarsal bone. OBOL:automatic metatarsal bone diaphysis FMA:33826 shaft of metatarsal bone FMA:33826 Embryonic structure that gives rise to the telencephalon. EHDAA2:0004424 EMAPA:36024 TAO:0000571 ZFA:0000571 presumptive telencephalon uberon UBERON:0014371 paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP] future telencephalon definitional Embryonic structure that gives rise to the telencephalon. ZFA:0000571 ZFA:curator presumptive telencephalon ZFA:0000571 A collection of hairs that is part of a craniocervical region. uberon UBERON:0014382 collection of hairs on head or neck A collection of hairs that is part of a craniocervical region. OBOL:automatic Mesenchyme that develops_from the neural crest[Automatically generated definition]. EMAPA:32735 FMA:293883 mesenchyme from neural crest neural crest derived mesenchyme neural crest mesenchyme uberon UBERON:0014387 mesenchyme derived from neural crest Mesenchyme that develops_from the neural crest[Automatically generated definition]. OBOL:automatic The simple cuboidal epithelium lining the lumen of kidney collecting ducts. In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis EMAPA:37885 collecting duct of renal tubule epithelium epithelium of collecting duct of renal tubule epithelium of renal collecting tubule uberon UBERON:0014388 kidney collecting duct epithelium The simple cuboidal epithelium lining the lumen of kidney collecting ducts. MGI:anna MP:0011843 EMAPA:37885 MA:th A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae. FMA:54822 gustatory papilla taste papilla uberon gustatory papillae taste papillae UBERON:0014389 gustatory papilla of tongue A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae. MGI:smb MP:0006256 gustatory papillae taste papillae A muscular coat that is part of a ileum. BTO:0005574 FMA:14958 muscularis externa of ileum uberon ileal smooth muscle muscularis propria of ileum smooth muscle of ileum UBERON:0014390 muscle layer of ileum A muscular coat that is part of a ileum. OBOL:automatic muscularis externa of ileum FMA:14958 ileal smooth muscle muscularis propria of ileum smooth muscle of ileum A proximal mesopodial endochondral element that is composed primarily of a bone tissue. uberon UBERON:0014395 proximal mesopodial bone A proximal mesopodial endochondral element that is composed primarily of a bone tissue. OBOL:automatic A anatomical space that is enclosed by a sinusoid. FMA:63133 lumen of sinusoid sinusoid lumen uberon UBERON:0014399 sinusoidal space A anatomical space that is enclosed by a sinusoid. OBOL:automatic lumen of sinusoid FMA:63133 sinusoid lumen FMA:63133 A sinusoidal space that is part of a hepatic sinusoid. FMA:262090 lumen of hepatic sinusoid uberon UBERON:0014400 hepatic sinusoidal space A sinusoidal space that is part of a hepatic sinusoid. OBOL:automatic lumen of hepatic sinusoid FMA:262090 Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta EMAPA:31450 MA:0002591 kidney venous blood vessel venous blood vessel of kidney uberon kidney venous system UBERON:0014401 renal venous blood vessel Any member of the network of tubes that return blood from the renal tissues to the systemic circulation. MGI:csmith we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta MA kidney venous blood vessel MA:0002591 kidney venous system EMAPA:31450 A taste bud that is located on the tongue, situated on a gustatory papilla. gustatory papilla taste bud gustatory papillae taste bud uberon UBERON:0014451 tongue taste bud A taste bud that is located on the tongue, situated on a gustatory papilla. gustatory papillae taste bud MP:0006260 A gustatory epithelium that is part of a tongue. BIRNLEX:4099 UMLS:C1179150 lingual gustatory epithelium uberon UBERON:0014452 gustatory epithelium of tongue A gustatory epithelium that is part of a tongue. OBOL:automatic UMLS:C1179150 BIRNLEX:4099 lingual gustatory epithelium Subcutaneous adipose tissue that is located in the peritoneal cavity. Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]. BTO:0004041 CALOHA:TS-2405 uberon abdominal fat intra-abdominal adipose tissue intra-abdominal fat organ fat visceral adipose tissue visceral fat UBERON:0014454 visceral abdominal adipose tissue Subcutaneous adipose tissue that is located in the peritoneal cavity. CALOHA:paula MGI:csmith Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]. BTO:0004041 abdominal fat BTO:0004041 intra-abdominal fat BTO:0004041 organ fat BTO:0004041 visceral adipose tissue BTO:0004041 visceral fat BTO:0004041 Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:TS-2406 abdominal subcutaneous adipose tissue subcutaneous abdominal fat subcutaneous fat of abdominal region uberon UBERON:0014455 subcutaneous abdominal adipose tissue Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:paula MGI:csmith FMA:75136 uberon UBERON:0014466 subarachnoid fissure Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. EHDAA2:0002013 FMA:77169 skeleton of thorax thoracic part of axial skeleton thoracic skeleton uberon UBERON:0014477 thoracic skeleton Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. thoracic skeleton EHDAA2:0002013 Subdivision of skeletal system that consists of all ribs and rib joints in an organism. In many vertebrates this consists of the combination of the rib cage and all rib joints, but some vertebrates have ribs outside the thoracic rib cage. FMA:265719 TAO:0002100 rib series uberon rib skeleton set of all ribs UBERON:0014478 rib skeletal system Subdivision of skeletal system that consists of all ribs and rib joints in an organism. In many vertebrates this consists of the combination of the rib cage and all rib joints, but some vertebrates have ribs outside the thoracic rib cage. rib series TAO:0002100 set of all ribs FMA:265719 A distal phalanx that is part of a digit 1 [Automatically generated definition]. digit 1 distal phalanx distal phalanx of digit I distal phalanx of first digit uberon digit I P3 first distal phalanx UBERON:0014483 distal phalanx of digit 1 A distal phalanx that is part of a digit 1 [Automatically generated definition]. digit 1 distal phalanx PHENOSCAPE:wd distal phalanx of digit I A distal phalanx that is part of a digit 5 [Automatically generated definition]. 5th digit distal phalanx digit 5 distal phalanx distal phalanx of 5th digit distal phalanx of digit V distal phalanx of fifth digit distal phalanx of little digit fifth digit distal phalanx fifth distal phalanx uberon digit V P3 UBERON:0014487 distal phalanx of digit 5 A distal phalanx that is part of a digit 5 [Automatically generated definition]. digit 5 distal phalanx PHENOSCAPE:wd distal phalanx of digit V A middle phalanx that is part of a digit 5 [Automatically generated definition]. 5th digit intermediate phalanx 5th digit middle phalanx 5th digit of intermediate phalanx 5th digit of middle phalanx digit 5 intermediate phalanx digit 5 middle phalanx fifth digit intermediate phalanx fifth digit middle phalanx fifth middle phalanx intermediate phalanx of 5th digit intermediate phalanx of digit 5 intermediate phalanx of fifth digit middle phalanx of 5th digit middle phalanx of digit V middle phalanx of fifth digit middle phalanx of little digit uberon digit V P2 UBERON:0014491 middle phalanx of digit 5 A middle phalanx that is part of a digit 5 [Automatically generated definition]. middle phalanx of digit V A proximal phalanx that is part of a autopod digit 1 [Automatically generated definition]. digit I P1 digit I-1 first proximal phalanx of autopod proximal phalanx of digit I proximal phalanx of first digit of autopod uberon UBERON:0014501 proximal phalanx of digit 1 A proximal phalanx that is part of a autopod digit 1 [Automatically generated definition]. digit I-1 PHENOSCAPE:wd proximal phalanx of digit I A proximal phalanx that is part of a autopod digit 5 [Automatically generated definition]. 5th digit of autopod proximal phalanx 5th digit proximal phalanx autopod digit 5 proximal phalanx digit V P1 digit V-1 fifth digit proximal phalanx fifth proximal phalanx of autopod proximal phalanx of 5th digit proximal phalanx of 5th digit of autopod proximal phalanx of digit V proximal phalanx of fifth digit proximal phalanx of fifth digit of autopod proximal phalanx of little digit uberon UBERON:0014505 proximal phalanx of digit 5 A proximal phalanx that is part of a autopod digit 5 [Automatically generated definition]. digit V-1 PHENOSCAPE:wd proximal phalanx of digit V A gray matter of spinal cord that is part of a cervical spinal cord. BIRNLEX:1521 UMLS:C0228610 cervical spinal cord gray matter uberon UBERON:0014613 cervical spinal cord gray matter A gray matter of spinal cord that is part of a cervical spinal cord. OBOL:automatic UMLS:C0228610 BIRNLEX:1521 cervical spinal cord gray matter BIRNLEX:1521 A gray matter of spinal cord that is part of a thoracic spinal cord. BIRNLEX:980 UMLS:C0228627 thoracic spinal cord gray matter uberon UBERON:0014636 thoracic spinal cord gray matter A gray matter of spinal cord that is part of a thoracic spinal cord. OBOL:automatic UMLS:C0228627 BIRNLEX:980 thoracic spinal cord gray matter BIRNLEX:980 FMA:35343 distal interphalangeal joint of little finger distal interphalangeal joint of manural digit V uberon UBERON:0014671 distal interphalangeal joint of manural digit 5 distal interphalangeal joint of little finger FMA:35343 distal interphalangeal joint of manural digit V FMA:35393 distal interphalangeal joint of fifth digit of foot distal interphalangeal joint of fifth toe distal interphalangeal joint of little toe distal interphalangeal joint of pedal digit V uberon UBERON:0014675 distal interphalangeal joint of pedal digit 5 distal interphalangeal joint of fifth digit of foot FMA:35393 distal interphalangeal joint of fifth toe FMA:35393 distal interphalangeal joint of little toe FMA:35393 distal interphalangeal joint of pedal digit V A distal interphalangeal joint that is part of a digit 5. NCIT:C102294 distal interphalangeal joint of digit V uberon distal interphalangeal joint 5 UBERON:0014680 distal interphalangeal joint of digit 5 A distal interphalangeal joint that is part of a digit 5. OBOL:automatic distal interphalangeal joint of digit V The deep auricular artery often arises in common with the anterior tympanic artery. It ascends in the substance of the parotid gland, behind the temporomandibular articulation, pierces the cartilaginous or bony wall of the external acoustic meatus, and supplies its cuticular lining and the outer surface of the tympanic membrane. It gives a branch to the temporomandibular joint. FMA:49689 uberon UBERON:0014695 deep auricular artery FMA The deep auricular artery often arises in common with the anterior tympanic artery. It ascends in the substance of the parotid gland, behind the temporomandibular articulation, pierces the cartilaginous or bony wall of the external acoustic meatus, and supplies its cuticular lining and the outer surface of the tympanic membrane. It gives a branch to the temporomandibular joint. A venous system that overlaps a umbilical cord and is part of a entire extraembryonic component. EHDAA2:0000479 EMAPA:16374 VHOG:0000282 uberon UBERON:0014699 extraembryonic venous system VHOG A venous system that overlaps a umbilical cord and is part of a entire extraembryonic component. OBOL:automatic A vascular system that overlaps a umbilical cord and is part of a entire extraembryonic component. EHDAA2:0000478 EMAPA:16370 VHOG:0001396 uberon UBERON:0014701 extraembryonic vascular system A vascular system that overlaps a umbilical cord and is part of a entire extraembryonic component. OBOL:automatic A epithelium that is part of a frontonasal prominence. EHDAA2:0004108 EMAPA:32918 uberon UBERON:0014702 frontonasal process epithelium EHDAA2 EHDAA2 A epithelium that is part of a frontonasal prominence. OBOL:automatic A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. EHDAA2:0004019 EMAPA:25040 uberon UBERON:0014703 anal membrane ectodermal component A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. OBOL:automatic A anatomical space that is enclosed by a pleuroperitoneal canal. EHDAA2:0004736 EMAPA:25034 pleuro-peritoneal canal cavity uberon UBERON:0014704 pleuroperitoneal canal lumen EHDAA2 A anatomical space that is enclosed by a pleuroperitoneal canal. OBOL:automatic pleuro-peritoneal canal cavity EMAPA:25034 A epithelium that is part of a median lingual swelling. EHDAA2:0001085 EMAPA:17188 uberon tuberculum impar epitheilium UBERON:0014705 median lingual swelling epithelium EHDAA2 EHDAA2 A epithelium that is part of a median lingual swelling. OBOL:automatic tuberculum impar epitheilium EMAPA:17188 EHDAA2:0001147 EMAPA:17646 metanephros primitive collecting ducts primitive collecting duct uberon UBERON:0014706 primitive renal collecting duct system EHDAA2 EHDAA2 metanephros primitive collecting ducts EHDAA2:0001147 primitive collecting duct EMAPA:17646 A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. NCIT:C32828 uberon UBERON:0014716 interlobular duct A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. ncithesaurus:Interlobular_Duct The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. FMA:86278 acinus of mucuous gland mucus acinus uberon UBERON:0014717 mucous acinus The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells. A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular uberon intralobular ductule UBERON:0014719 intralobular duct A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular A duct that is located between lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory. uberon intralobular ductule UBERON:0014720 interlobar duct A duct that is located between lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory. The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. EHDAA2:0000597 EMAPA:17703 VHOG:0001546 crural diaphragm uberon crura of the diaphragm crus of the diaphragm diaphragm crura diaphragmatic crura UBERON:0014765 Classification notes: May be considered an external sphincter[PMID:8224664] crus of diaphragm The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. crural diaphragm crura of the diaphragm crus of the diaphragm diaphragm crura diaphragmatic crura A crus of diaphragm that is in_the_right_side_of a diaphragm. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:58286 crus dextrum (Diaphragma) crus dextrum diaphragmatis external sphincter of esophagus right crus of diaphragm right crus of lumbar part of diaphragm uberon UBERON:0014766 right crus of diaphragm A crus of diaphragm that is in_the_right_side_of a diaphragm. OBOL:automatic crus dextrum (Diaphragma) FMA:58286 FMA:TA crus dextrum diaphragmatis FMA:58286 FMA:TA external sphincter of esophagus FMA:58286 right crus of diaphragm FMA:58286 right crus of lumbar part of diaphragm FMA:58286 A crus of diaphragm that is in_the_left_side_of a diaphragm. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:58287 crus sinistrum (Diaphragma) crus sinistrum diaphragmatis left crus of diaphragm left crus of lumbar part of diaphragm uberon UBERON:0014767 left crus of diaphragm A crus of diaphragm that is in_the_left_side_of a diaphragm. OBOL:automatic crus sinistrum (Diaphragma) FMA:58287 FMA:TA crus sinistrum diaphragmatis FMA:58287 FMA:TA left crus of diaphragm FMA:58287 left crus of lumbar part of diaphragm FMA:58287 A neuromere that is part of the presumptive forebrain forebrain segment segment of forebrain FMA:61996 forebrain neuromere uberon future prosencephalon UBERON:0014775 prosomere A neuromere that is part of the presumptive forebrain A neuromere that is part of the presumptive midbrain mesomere midbrain segment segment of midbrain EHDAA2:0004352 FMA:61997 mesomere of nervous system neuromere of mesomere group uberon future mesencephalon mesomere group UBERON:0014776 midbrain neuromere A neuromere that is part of the presumptive midbrain mesomere group EHDAA2:0004352 A neuromere that is part of the presumptive spinal cord TAO:0001332 ZFA:0001332 spinal cord metameric segment spinal neuromeres uberon spinal cord segment UBERON:0014777 spinal neuromere A neuromere that is part of the presumptive spinal cord spinal neuromeres TAO:0001332 spinal cord segment TAO:0001332 Any muscle organ that is part of a cloaca. uberon UBERON:0014783 cloacal muscle Any muscle organ that is part of a cloaca. OBOL:automatic The lingual septum consists of a vertical layer of fibrous tissue, extending throughout the entire length of the median plane of the tongue, though not quite reaching the dorsum. It is thicker behind than in front, and occasionally contains a small fibrocartilage, about 6 mm. in length. It is well displayed by making a vertical section across the organ. EMAPA:18274 FMA:54813 septum of tongue uberon median fibrous septum septum of tongue tongue septum UBERON:0014790 lingual septum The lingual septum consists of a vertical layer of fibrous tissue, extending throughout the entire length of the median plane of the tongue, though not quite reaching the dorsum. It is thicker behind than in front, and occasionally contains a small fibrocartilage, about 6 mm. in length. It is well displayed by making a vertical section across the organ. septum of tongue FMA:54813 median fibrous septum septum of tongue tongue septum Any collection of muscles that is part of the forelimb stylopod region [Automatically generated definition]. FMA:50202 uberon arm musculature muscle group of arm musculature of arm set of muscles of arm UBERON:0014791 musculature of forelimb stylopod Any collection of muscles that is part of the forelimb stylopod region [Automatically generated definition]. OBOL:automatic arm musculature FMA:50202 muscle group of arm FMA:50202 musculature of arm FMA:50202 set of muscles of arm FMA:50202 Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. currently defined by location rather than attachment EMAPA:37864 FMA:71297 muscles of lower limb musculature of lower limb musculi membri inferioris uberon UBERON:0014792 musculature of pelvic complex Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. OBOL:automatic EMAPA:37864 MA:th muscles of lower limb FMA:71297 musculature of lower limb FMA:71297 musculi membri inferioris FMA:TA Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin. currently defined by location rather than attachment EMAPA:37861 FMA:71296 muscles of upper limb musculature of upper limb musculi membri superioris set of muscles of upper limb upper limb musculature uberon UBERON:0014793 musculature of pectoral complex Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin. OBOL:automatic EMAPA:37861 MA:th muscles of upper limb FMA:71296 musculature of upper limb FMA:71296 musculi membri superioris FMA:TA set of muscles of upper limb FMA:71296 upper limb musculature FMA:71296 Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). uberon UBERON:0014794 pectoral appendage muscle prolog Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin). OBOL:automatic Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). uberon UBERON:0014795 pelvic appendage muscle prolog Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). OBOL:automatic A distal epiphysis that is part of a distal phalanx of pedal digit 1. FMA:33036 distal end of distal phalanx of big toe distal epiphysis of distal phalanx of big toe distal epiphysis of distal phalanx of pedal digit I head of distal phalanx of big toe head of distal phalanx of first digit of foot head of distal phalanx of great toe uberon ungual tuberosity of distal phalanx of big toe UBERON:0014871 distal epiphysis of distal phalanx of pedal digit 1 A distal epiphysis that is part of a distal phalanx of pedal digit 1. OBOL:automatic distal end of distal phalanx of big toe FMA:33036 distal epiphysis of distal phalanx of big toe FMA:33036 distal epiphysis of distal phalanx of pedal digit I head of distal phalanx of big toe FMA:33036 head of distal phalanx of first digit of foot FMA:33036 head of distal phalanx of great toe FMA:33036 ungual tuberosity of distal phalanx of big toe FMA:33036 A distal epiphysis that is part of a distal phalanx of pedal digit 5. FMA:33106 distal end of distal phalanx of little toe distal epiphysis of distal phalanx of little toe distal epiphysis of distal phalanx of pedal digit V head of distal phalanx of fifth digit of foot head of distal phalanx of fifth toe head of distal phalanx of little toe uberon ungual tuberosity of distal phalanx of fifth toe UBERON:0014875 distal epiphysis of distal phalanx of pedal digit 5 A distal epiphysis that is part of a distal phalanx of pedal digit 5. OBOL:automatic distal end of distal phalanx of little toe FMA:33106 distal epiphysis of distal phalanx of little toe FMA:33106 distal epiphysis of distal phalanx of pedal digit V head of distal phalanx of fifth digit of foot FMA:33106 head of distal phalanx of fifth toe FMA:33106 head of distal phalanx of little toe FMA:33106 ungual tuberosity of distal phalanx of fifth toe FMA:33106 distal end of distal phalanx of toe head of distal phalanx of digit of foot head of distal phalanx of digit of pes head of distal phalanx of toe uberon UBERON:0014876 distal epiphysis of distal phalanx of pedal digit A distal epiphysis that is part of a distal phalanx of manual digit 1. FMA:37609 distal end of phalanx of right thumb distal epiphysis of distal phalanx of manual digit I distal epiphysis of distal phalanx of thumb head of distal phalanx of first digit of hand head of distal phalanx of thumb uberon ungual tuberosity of distal phalanx of thumb UBERON:0014881 distal epiphysis of distal phalanx of manual digit 1 A distal epiphysis that is part of a distal phalanx of manual digit 1. OBOL:automatic distal end of phalanx of right thumb FMA:37609 distal epiphysis of distal phalanx of manual digit I distal epiphysis of distal phalanx of thumb FMA:37609 head of distal phalanx of first digit of hand FMA:37609 head of distal phalanx of thumb FMA:37609 ungual tuberosity of distal phalanx of thumb FMA:37609 A distal epiphysis that is part of a distal phalanx of manual digit 5. FMA:37657 distal end of distal phalanx of fifth finger distal end of distal phalanx of little finger distal epiphysis of distal phalanx of little finger distal epiphysis of distal phalanx of manual digit V head of distal phalanx of fifth digit of hand head of distal phalanx of fifth finger head of distal phalanx of little finger uberon ungual tuberosity of distal phalanx of little finger UBERON:0014885 distal epiphysis of distal phalanx of manual digit 5 A distal epiphysis that is part of a distal phalanx of manual digit 5. OBOL:automatic distal end of distal phalanx of fifth finger FMA:37657 distal end of distal phalanx of little finger FMA:37657 distal epiphysis of distal phalanx of little finger FMA:37657 distal epiphysis of distal phalanx of manual digit V head of distal phalanx of fifth digit of hand FMA:37657 head of distal phalanx of fifth finger FMA:37657 head of distal phalanx of little finger FMA:37657 ungual tuberosity of distal phalanx of little finger FMA:37657 distal end of distal phalanx of finger head of distal phalanx of digit of hand head of distal phalanx of digit of manus head of distal phalanx of finger uberon UBERON:0014886 distal epiphysis of distal phalanx of manual digit A distal epiphysis that is part of a distal phalanx. distal end of distal phalanx of digit head of distal phalanx head of distal phalanx of digit head of distal phalanx of digit of autopod uberon UBERON:0014887 distal epiphysis of distal phalanx of digit A distal epiphysis that is part of a distal phalanx. OBOL:automatic A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). skeletal muscle AAO:0011099 BTO:0001103 CALOHA:TS-0933 EFO:0000888 EHDAA:5035 EHDAA:5043 EHDAA:5978 EHDAA:5984 EMAPA:35988 EV:0100377 GAID:141 MA:0003148 MAT:0000302 MESH:D018482 MIAA:0000302 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA TAO:0005277 VHOG:0000319 XAO:0000174 ZFA:0005277 uberon UBERON:0014892 skeletal muscle organ A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). GOC:dos A portion of tissue that will develop into vasculature. EFO:0003708 TAO:0005076 ZFA:0005076 uberon UBERON:0014903 primordial vasculature A portion of tissue that will develop into vasculature. ZFA:0005076 ZFA:curator One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites. Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]. EFO:0003664 EMAPA:37389 TAO:0001285 XAO:0004075 ZFA:0001285 intersegmental vessel intersegmental vessels intersomitic blood vessel intersomitic vessels segmental vessel uberon UBERON:0014907 intersomitic vessel ZFA ZFA One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites. MGI:anna Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]. ZFA:0001285, ZFIN:ZDB-PUB-030908-4 EMAPA:37389 MA:th intersegmental vessel ZFA:0001285 intersegmental vessels ZFA:0001285 intersomitic blood vessel XAO:0004075 intersomitic vessels ZFA:0001285 segmental vessel ZFA:0001285 The space between a blood vessel and the pia mater. VRS NCIT:C83196 Virchow-Robin space perivascular region uberon perivascular spaces UBERON:0014930 VRS belonging to the subarachnoid space are continuous with VRS of the subpial space. The direct communication between VRS of the subarachnoid space and the subpial space is unique to the brain's arteries, as no leptomeningeal layers surround the brain's veins[WP] perivascular space https://static-content.springer.com/image/art%3A10.1007%2Fs11064-015-1581-6/MediaObjects/11064_2015_1581_Fig3_HTML.gif The space between a blood vessel and the pia mater. ncithesaurus:Perivascular_Space VRS Virchow-Robin space perivascular spaces these layers primarily refer to the mammalian future neocortex uberon UBERON:0014950 layer of developing cerebral cortex EMAPA A vertebral endochondral element in the cervical region of the vertebral column. cervical vertebra skeletal element cervical vertebra element uberon UBERON:0015007 cervical vertebra endochondral element A vertebral endochondral element in the cervical region of the vertebral column. cervical vertebra skeletal element cervical vertebra element A vertebral endochondral element in the thoracic region of the vertebral column. thoracic vertebra skeletal element thoracic vertebra element uberon UBERON:0015008 thoracic vertebra endochondral element A vertebral endochondral element in the thoracic region of the vertebral column. thoracic vertebra skeletal element thoracic vertebra element A lumbar vertebra bone or its cartilage or pre-cartilage precursor. lumbar vertebra skeletal element lumbar vertebra element uberon UBERON:0015009 lumbar vertebra endochondral element A lumbar vertebra bone or its cartilage or pre-cartilage precursor. lumbar vertebra skeletal element lumbar vertebra element A stapes bone or its cartilage or pre-cartilage precursor. stapes skeletal element stapes element uberon UBERON:0015016 stapes endochondral element A stapes bone or its cartilage or pre-cartilage precursor. stapes skeletal element stapes element A rib bone or its cartilage or pre-cartilage precursor. Humans have 24 ribs (12 pairs). The first seven sets of ribs, known as 'true ribs', are directly attached to the sternum through the costal cartilage. The following five sets are known as 'false ribs', three of these sharing a common cartilaginous connection to the sternum, while the last two (eleventh and twelfth ribs) are termed floating ribs (costae fluitantes) or vertebral ribs. They are attached to the vertebrae only, and not to the sternum or cartilage coming off of the sternum. Some people are missing one of the two pairs of floating ribs, while others have a third pair. Rib removal is the surgical excision of ribs for therapeutic or cosmetic reasons. In fish, there are often two sets of ribs attached to the vertebral column. One set, the dorsal ribs, are found in the dividing septum between the upper and lower parts of the main muscle segments, projecting roughly sideways from the vertebral column. The second set, of ventral ribs arise from the vertebral column just below the dorsal ribs, and enclose the lower body, often joining at the tips. Not all species possess both types of rib, with the dorsal ribs being most commonly absent. Sharks, for example, have no dorsal ribs, and only very short ventral ribs, while lampreys have no ribs at all. In some teleosts, there may be additional rib-like bones within the muscle mass. Tetrapods, however, only ever have a single set of ribs which are probably homologous with the dorsal ribs of fishes. In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. The sacral ribs were stout and short, since they formed part of the pelvis, connecting the backbone to the hip bones.[1] In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis.[1]. In birds, ribs are present as distinct bones only on the thoracic region, although small fused ribs are present on the cervical vertebrae. The thoracic ribs of birds possess a wide projection to the rear; this uncinate process is an attachment for the shoulder muscles.[1]. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals. rib skeletal element rib element uberon UBERON:0015019 rib endochondral element A rib bone or its cartilage or pre-cartilage precursor. rib skeletal element rib element A forelimb bone or its cartilage or pre-cartilage precursor. forelimb skeletal element uberon UBERON:0015021 forelimb endochondral element A forelimb bone or its cartilage or pre-cartilage precursor. forelimb skeletal element A hindlimb bone or its cartilage or pre-cartilage precursor. hindlimb bone skeletal element uberon UBERON:0015022 hindlimb endochondral element A hindlimb bone or its cartilage or pre-cartilage precursor. hindlimb bone skeletal element A phalanx bone or its cartilage or pre-cartilage precursor. phalanx skeletal element phalanx element uberon UBERON:0015023 phalanx endochondral element A phalanx bone or its cartilage or pre-cartilage precursor. phalanx skeletal element phalanx element A manual digit phalanx bone or its cartilage or pre-cartilage precursor. manual digit phalanx skeletal element manual digit phalanx element uberon UBERON:0015024 manual digit phalanx endochondral element A manual digit phalanx bone or its cartilage or pre-cartilage precursor. manual digit phalanx skeletal element manual digit phalanx element A manual digit 1 phalanx bone or its cartilage or pre-cartilage precursor. manual digit 1 phalanx skeletal element manual digit 1 phalanx element manual digit I phalanx endochondral element uberon UBERON:0015025 manual digit 1 phalanx endochondral element A manual digit 1 phalanx bone or its cartilage or pre-cartilage precursor. manual digit 1 phalanx skeletal element manual digit 1 phalanx element manual digit I phalanx endochondral element A manual digit 5 phalanx bone or its cartilage or pre-cartilage precursor. manual digit 5 phalanx skeletal element manual digit 5 phalanx element manual digit V phalanx endochondral element uberon UBERON:0015029 manual digit 5 phalanx endochondral element A manual digit 5 phalanx bone or its cartilage or pre-cartilage precursor. manual digit 5 phalanx skeletal element manual digit 5 phalanx element manual digit V phalanx endochondral element A pedal digit phalanx bone or its cartilage or pre-cartilage precursor. pedal digit phalanx skeletal element pedal digit phalanx element uberon UBERON:0015030 pedal digit phalanx endochondral element A pedal digit phalanx bone or its cartilage or pre-cartilage precursor. pedal digit phalanx skeletal element pedal digit phalanx element A pedal digit 1 phalanx bone or its cartilage or pre-cartilage precursor. pedal digit 1 phalanx skeletal element pedal digit 1 phalanx element pedal digit I phalanx endochondral element uberon UBERON:0015031 pedal digit 1 phalanx endochondral element A pedal digit 1 phalanx bone or its cartilage or pre-cartilage precursor. pedal digit 1 phalanx skeletal element pedal digit 1 phalanx element pedal digit I phalanx endochondral element A pedal digit 5 phalanx bone or its cartilage or pre-cartilage precursor. pedal digit 5 phalanx skeletal element pedal digit 5 phalanx element pedal digit V phalanx endochondral element uberon UBERON:0015035 pedal digit 5 phalanx endochondral element A pedal digit 5 phalanx bone or its cartilage or pre-cartilage precursor. pedal digit 5 phalanx skeletal element pedal digit 5 phalanx element pedal digit V phalanx endochondral element A pedal digit metatarsal bone or its cartilage or pre-cartilage precursor. pedal digit metatarsal skeletal element pedal digit metatarsal element uberon UBERON:0015036 pedal digit metatarsal endochondral element A pedal digit metatarsal bone or its cartilage or pre-cartilage precursor. pedal digit metatarsal skeletal element pedal digit metatarsal element A pedal digit 1 metatarsal bone or its cartilage or pre-cartilage precursor. pedal digit 1 metatarsal skeletal element pedal digit 1 metatarsal element pedal digit I metatarsal endochondral element uberon UBERON:0015037 pedal digit 1 metatarsal endochondral element A pedal digit 1 metatarsal bone or its cartilage or pre-cartilage precursor. pedal digit 1 metatarsal skeletal element pedal digit 1 metatarsal element pedal digit I metatarsal endochondral element A pedal digit 5 metatarsal bone or its cartilage or pre-cartilage precursor. pedal digit 5 metatarsal skeletal element pedal digit 5 metatarsal element pedal digit V metatarsal endochondral element uberon UBERON:0015041 pedal digit 5 metatarsal endochondral element A pedal digit 5 metatarsal bone or its cartilage or pre-cartilage precursor. pedal digit 5 metatarsal skeletal element pedal digit 5 metatarsal element pedal digit V metatarsal endochondral element A manual digit metacarpus bone or its cartilage or pre-cartilage precursor. manual digit metacarpus skeletal element manual digit metacarpus element uberon UBERON:0015042 manual digit metacarpus endochondral element A manual digit metacarpus bone or its cartilage or pre-cartilage precursor. manual digit metacarpus skeletal element manual digit metacarpus element A manual digit 1 metacarpus bone or its cartilage or pre-cartilage precursor. manual digit 1 metacarpus skeletal element manual digit 1 metacarpus element manual digit I metacarpus endochondral element uberon UBERON:0015043 manual digit 1 metacarpus endochondral element A manual digit 1 metacarpus bone or its cartilage or pre-cartilage precursor. manual digit 1 metacarpus skeletal element manual digit 1 metacarpus element manual digit I metacarpus endochondral element A manual digit 5 metacarpus bone or its cartilage or pre-cartilage precursor. manual digit 5 metacarpus skeletal element manual digit 5 metacarpus element manual digit V metacarpus endochondral element uberon UBERON:0015047 manual digit 5 metacarpus endochondral element A manual digit 5 metacarpus bone or its cartilage or pre-cartilage precursor. manual digit 5 metacarpus skeletal element manual digit 5 metacarpus element manual digit V metacarpus endochondral element A carpus bone or its cartilage or pre-cartilage precursor. carpus skeletal element carpus element uberon UBERON:0015049 carpus endochondral element A carpus bone or its cartilage or pre-cartilage precursor. carpus skeletal element carpus element A tarsus bone or its cartilage or pre-cartilage precursor. tarsus skeletal element tarsus element uberon UBERON:0015050 tarsus endochondral element A tarsus bone or its cartilage or pre-cartilage precursor. tarsus skeletal element tarsus element A femur bone or its cartilage or pre-cartilage precursor. femur skeletal element femur element uberon UBERON:0015052 femur endochondral element A femur bone or its cartilage or pre-cartilage precursor. femur skeletal element femur element A humerus bone or its cartilage or pre-cartilage precursor. humerus skeletal element humerus element uberon UBERON:0015053 humerus endochondral element A humerus bone or its cartilage or pre-cartilage precursor. humerus skeletal element humerus element A iliac bone or its cartilage or pre-cartilage precursor. iliac skeletal element iliac element uberon UBERON:0015054 iliac endochondral element A iliac bone or its cartilage or pre-cartilage precursor. iliac skeletal element iliac element A scapula bone or its cartilage or pre-cartilage precursor. scapula skeletal element scapula element uberon UBERON:0015057 scapula endochondral element A scapula bone or its cartilage or pre-cartilage precursor. scapula skeletal element scapula element A limb bone or its cartilage or pre-cartilage precursor. limb bone skeletal element limb bone endochondral element uberon UBERON:0015061 limb endochondral element A limb bone or its cartilage or pre-cartilage precursor. limb bone skeletal element limb bone endochondral element A endochondral element that is part of a autopod region. uberon UBERON:0015063 autopod endochondral element cjm A endochondral element that is part of a autopod region. OBOL:automatic A autopod endochondral element that is composed primarily of cartilage tissue. uberon UBERON:0015064 autopod cartilage A autopod endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A proximal mesopodial endochondral element that is part of a forelimb. proximal carpal element uberon proximal carpal UBERON:0015078 proximal carpal endochondral element A proximal mesopodial endochondral element that is part of a forelimb. OBOL:automatic proximal carpal element UBERON:cjm proximal carpal UBERON:cjm A proximal carpal endochondral element that is composed primarily of cartilage tissue. uberon UBERON:0015079 proximal carpal cartilage A proximal carpal endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A proximal carpal endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0015080 proximal carpal bone pre-cartilage condensation A proximal carpal endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A proximal mesopodial endochondral element that is part of a hindlimb. uberon proximal tarsal UBERON:0015081 proximal tarsal endochondral element A proximal mesopodial endochondral element that is part of a hindlimb. OBOL:automatic proximal tarsal UBERON:cjm A proximal tarsal endochondral element that is composed primarily of cartilage tissue. uberon UBERON:0015082 proximal tarsal cartilage A proximal tarsal endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A proximal tarsal endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0015083 proximal tarsal bone pre-cartilage condensation A proximal tarsal endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic consider merging into myocardial compact layer FMA:83105 perimysial connective tissue of subepicardium subepicardial connective tissue uberon UBERON:0015128 subepicardial layer of epicardium FMA perimysial connective tissue of subepicardium FMA:83105 subepicardial connective tissue FMA:83105 Visceral intrapericardial fat contiguous with the myocardial surface. FMA:9871 epicardial adipose tissue pericardial adipose tissue uberon UBERON:0015129 epicardial fat Visceral intrapericardial fat contiguous with the myocardial surface. A portion of connective tissue that is part of a prostate gland. FMA:74165 connective tissue of prostate uberon UBERON:0015130 connective tissue of prostate gland FMA A portion of connective tissue that is part of a prostate gland. OBOL:automatic connective tissue of prostate FMA:74165 A strand of hair that is part of a autopod region. hair of hand/foot hand/foot hair paw hair uberon UBERON:0015144 autopod hair A strand of hair that is part of a autopod region. OBOL:automatic A strand of hair that is part of a pes. foot hair hair of foot hind foot hair hind paw hair uberon UBERON:0015145 pes hair A strand of hair that is part of a pes. OBOL:automatic A strand of hair that is part of a manus. hair of hand hand hair front paw hair uberon UBERON:0015146 manus hair A strand of hair that is part of a manus. OBOL:automatic A strand of hair that is part of a pinna. uberon ear hair UBERON:0015147 pinna hair A strand of hair that is part of a pinna. OBOL:automatic A strand of hair that is part of a tail. EMAPA:37971 uberon UBERON:0015148 tail hair A strand of hair that is part of a tail. OBOL:automatic EMAPA:37971 MA:th A strand of hair that is part of a dorsum. FMA:54320 uberon back hair dorsal coat hair hair of back UBERON:0015150 dorsal hair A strand of hair that is part of a dorsum. OBOL:automatic hair of back FMA:54320 A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104] the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648] ocular gland uberon orbital gland UBERON:0015152 gland of ocular region inferred A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. A gland that is located in or around the ocular region, nearer the outer canthi. The class name or definition should not be taken to mean strictly in the lateral ocular region. We place the extraocular lacrimal glands, even though they are as the name suggests outside the ocular region. The class exists as the division between lateral vs medial (Harderian, nictitans) glands is standard, e.g. http://www.ncbi.nlm.nih.gov/pubmed/7559104 lateral ocular gland lateral orbital gland uberon UBERON:0015154 lateral gland of orbital region A gland that is located in or around the ocular region, nearer the outer canthi. An eye consisting of multiple light-sensing organs uberon UBERON:0015165 multi-unit eye An eye consisting of multiple light-sensing organs present on tentacular crown present on mantle edge in arcacean Bivalvia The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species A blood vessel that is part of a endometrium. blood vessel of endometrium uberon UBERON:0015172 endometrial blood vessel A blood vessel that is part of a endometrium. OBOL:automatic A region of somite adjacent to presomitic mesoderm. TAO:0001462 XAO:0004074 ZFA:0001462 uberon inter-somited border intersomitic boundary intersomitic fissure intersomitic junction segmental border somite boundary UBERON:0015178 somite border A region of somite adjacent to presomitic mesoderm. intersomitic junction XAO:0004074 somite boundary ZFA:0001462 Epithelium located in the intersomitic region. XAO:0004077 intersomitic epithelium intersomitic membrane uberon UBERON:0015179 somite boundary epithelium Epithelium located in the intersomitic region. XAO:0004077 XAO:EJS intersomitic epithelium XAO:0004077 intersomitic membrane XAO:0004077 The slightly constricted part of a tooth, between the crown and the root. FMA:55627 NCIT:C32346 cervix dentis cervix of tooth collumn dentis dental neck tooth neck uberon cervical margin of tooth cervical zone of tooth UBERON:0015181 neck of tooth The slightly constricted part of a tooth, between the crown and the root. cervix dentis FMA:TA cervix of tooth FMA:55627 collumn dentis ncithesaurus:Collum_Dentis dental neck tooth neck FMA:55627 cervical margin of tooth cervical zone of tooth Any structure that is placed on one side of the left-right axis of a bilaterian. This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. A ligament that is part of a diaphragm. EMAPA:19236 FMA:58280 uberon UBERON:0015214 arcuate ligament A ligament that is part of a diaphragm. OBOL:automatic A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart SPD:0000130 cardiac pump heart or heart like organ circulatory vessel uberon cardiac structure UBERON:0015228 circulatory organ A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. A cluster in the epithalamus that consists of the pineal body and any associated structures, such as the parapineal gland or the parietal organ. The complex is poorly developed in mammals. TAO:0001359 ZFA:0001359 uberon UBERON:0015238 pineal complex ZFA A cluster in the epithalamus that consists of the pineal body and any associated structures, such as the parapineal gland or the parietal organ. The complex is poorly developed in mammals. A zone of skin that is part of a digit [Automatically generated definition]. EMAPA:32615 MA:0003011 uberon UBERON:0015249 digit skin A zone of skin that is part of a digit [Automatically generated definition]. OBOL:automatic EMAPA:37680 MA:0003043 uberon UBERON:0015251 modified sebaceous gland MA EMAPA:37680 MA:th A pancreatic lobule that is in_the_left_side_of a exocrine pancreas. EMAPA:37711 MA:0000722 uberon UBERON:0015280 pancreas left lobe A pancreatic lobule that is in_the_left_side_of a exocrine pancreas. OBOL:automatic EMAPA:37711 MA:th A pancreatic lobule that is in_the_right_side_of a exocrine pancreas. EMAPA:37712 MA:0000723 uberon UBERON:0015281 pancreas right lobe A pancreatic lobule that is in_the_right_side_of a exocrine pancreas. OBOL:automatic EMAPA:37712 MA:th A basement membrane of epithelium that is part of a respiratory system. EMAPA:37570 MA:0001815 uberon UBERON:0015329 respiratory system basement membrane MA A basement membrane of epithelium that is part of a respiratory system. OBOL:automatic EMAPA:37570 MA:th EMAPA:37597 MA:0002449 heart/pericardium uberon UBERON:0015410 heart plus pericardium MA EMAPA:37597 MA:th heart/pericardium MA:0002449 A mesenchyme that is part of a urethra. EMAPA:37786 MA:0002648 uberon UBERON:0015418 urethra mesenchymal layer A mesenchyme that is part of a urethra. OBOL:automatic EMAPA:37786 MA:th A valve that is part of a ureter. EMAPA:37781 MA:0002658 ureteral valve valve or ureter uberon UBERON:0015420 ureteral valve A valve that is part of a ureter. OBOL:automatic EMAPA:37781 MA:th ureteral valve MA:0002658 A lymph node that is part of a hypodermis. MA:0003028 uberon UBERON:0015453 subcutaneous lymph node A lymph node that is part of a hypodermis. OBOL:automatic A zone of skin that is part of a external nose. EMAPA:37684 FMA:24763 MA:0003090 external nasal skin skin of external nose skin of nose uberon UBERON:0015476 nose skin A zone of skin that is part of a external nose. OBOL:automatic EMAPA:37684 MA:th external nasal skin FMA:24763 skin of external nose FMA:24763 skin of nose FMA:24763 A zone of skin that is part of a scrotum. EMAPA:36411 FMA:20432 MA:0003093 scrotal skin skin of scrotum uberon UBERON:0015479 scrotum skin A zone of skin that is part of a scrotum. OBOL:automatic skin of scrotum FMA:20432 A hepatic artery that is part of a left lobe of liver. EMAPA:37096 FMA:14779 MA:0003096 left branch of hepatic artery left part of hepatic artery proper ramus sinister (arteria hepatica propria) uberon UBERON:0015481 left hepatic artery FMA A hepatic artery that is part of a left lobe of liver. OBOL:automatic EMAPA:37096 MA:th left branch of hepatic artery FMA:14779 left part of hepatic artery proper FMA:14779 ramus sinister (arteria hepatica propria) FMA:14779 FMA:TA A hepatic artery that is part of a right lobe of liver. EMAPA:37376 FMA:14778 MA:0003097 ramus dexter (arteria hepatica propria) right branch of hepatic artery proper right part of hepatic artery proper uberon UBERON:0015482 right hepatic artery FMA A hepatic artery that is part of a right lobe of liver. OBOL:automatic EMAPA:37376 MA:th ramus dexter (arteria hepatica propria) FMA:14778 FMA:TA right branch of hepatic artery proper FMA:14778 right part of hepatic artery proper FMA:14778 hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla. EMAPA:37478 MA:0003108 choledochoduodenal junction uberon UBERON:0015485 choledocho-duodenal junction hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla. EMAPA:37478 MA:th choledochoduodenal junction MA:0003108 A epithelium that is part of a anal canal. EMAPA:18835 FMA:17511 anal canal epithelium epithelium of anal canal uberon UBERON:0015716 anal canal epithelium A epithelium that is part of a anal canal. OBOL:automatic anal canal epithelium FMA:17511 epithelium of anal canal FMA:17511 A smooth muscle tissue that is part of a ejaculatory duct. EMAPA:32289 FMA:19372 muscle layer of ejaculatory duct uberon UBERON:0015717 smooth muscle tissue layer of ejaculatory duct A smooth muscle tissue that is part of a ejaculatory duct. OBOL:automatic muscle layer of ejaculatory duct FMA:19372 FMA:62798 portion of heterogeneous tissue uberon UBERON:0015757 heterogeneous tissue FMA portion of heterogeneous tissue FMA:62798 A epithelium that is part of a duct of salivary gland. FMA:67682 epithelium of salivary duct salivary duct epithelium salivary ductal epithelium uberon UBERON:0015766 epithelium of duct of salivary gland FMA A epithelium that is part of a duct of salivary gland. OBOL:automatic epithelium of salivary duct FMA:67682 salivary duct epithelium FMA:67682 salivary ductal epithelium FMA:67682 A smooth muscle tissue that is part of a hypodermis. FMA:77862 muscle layer in fatty layer of subcutaneous tissue stratum musculosum panniculi adiposi telae subcutaneae uberon UBERON:0015783 smooth muscle layer in fatty layer of subcutaneous tissue A smooth muscle tissue that is part of a hypodermis. OBOL:automatic muscle layer in fatty layer of subcutaneous tissue FMA:77862 stratum musculosum panniculi adiposi telae subcutaneae FMA:77862 FMA:TA Any anatomical conduit which is part of the upper respiratory tract Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]. FMA:265132 uberon respiratory conduit UBERON:0015787 upper respiratory conduit Any anatomical conduit which is part of the upper respiratory tract Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]. FMA:265132 respiratory conduit FMA:265132 An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. FMA:265136 uberon UBERON:0015788 olfactory apparatus chamber An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present. see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper EMAPA:25133 MA:0000579 cranial/facial muscle uberon cranial-facial muscle cranio-facial muscle craniofacial muscle UBERON:0015789 cranial or facial muscle cranial/facial muscle MA:0000579 cranial-facial muscle EMAPA:25133 cranio-facial muscle EMAPA:25133 craniofacial muscle EMAPA:25133 A zone of skin that is part of a autopod region. EMAPA:32723 MA:0003120 uberon paw skin UBERON:0015790 autopod skin A zone of skin that is part of a autopod region. OBOL:automatic paw skin MA:0003120 A portion of connective tissue that is part of a digit. EMAPA:37290 MA:0003123 uberon UBERON:0015791 digit connective tissue A portion of connective tissue that is part of a digit. OBOL:automatic EMAPA:37290 MA:th A blood vessel that is part of a liver. EMAPA:35498 MA:0003137 uberon hepatic blood vessel UBERON:0015796 liver blood vessel A blood vessel that is part of a liver. OBOL:automatic hepatic blood vessel EMAPA:35498 A epithelium that is part of a ear. EMAPA:32800 MA:0003161 uberon UBERON:0015807 ear epithelium A epithelium that is part of a ear. OBOL:automatic A epithelium that is part of a camera-type eye. EMAPA:35957 MA:0003162 uberon UBERON:0015808 eye epithelium A epithelium that is part of a camera-type eye. OBOL:automatic A epithelium that is part of a middle ear. EMAPA:35673 MA:0003169 uberon UBERON:0015813 middle ear epithelium A epithelium that is part of a middle ear. OBOL:automatic A epithelium that is part of a external ear. EMAPA:35956 MA:0003170 uberon UBERON:0015814 outer ear epithelium A epithelium that is part of a external ear. OBOL:automatic A epithelium that is part of a foregut. EMAPA:32922 MA:0003204 uberon UBERON:0015833 foregut epithelium A epithelium that is part of a foregut. OBOL:automatic A lamina propria that is part of a duodenum. EMAPA:27255 FMA:15972 MA:0003209 duodenal lamina propria lamina propria mucosae of duodenum lamina propria of duodenum uberon UBERON:0015834 duodenum lamina propria FMA A lamina propria that is part of a duodenum. OBOL:automatic duodenal lamina propria FMA:15972 lamina propria mucosae of duodenum FMA:15972 lamina propria of duodenum FMA:15972 FMA:66178 uberon UBERON:0015860 visceral abdominal lymph node FMA A lymph node that is part of a head. FMA:61212 uberon UBERON:0015870 lymph node of head A lymph node that is part of a head. OBOL:automatic Any of the lymph nodes that are part of a face. In humans, these comprise three groups: (a) infraorbital or maxillary, scattered over the infraorbital region from the groove between the nose and cheek to the zygomatic arch; (b) buccinator, one or more placed on the Buccinator opposite the angle of the mouth; (c) supramandibular, on the outer surface of the mandible, in front of the Masseter and in contact with the external maxillary artery and anterior facial vein. FMA:61222 buccal lymph node uberon UBERON:0015871 facial lymph node Any of the lymph nodes that are part of a face. buccal lymph node FMA:61222 A lymph node that is located close to the surface. FMA:12767 NCIT:C102716 uberon UBERON:0015917 superficial lymph node A lymph node that is located close to the surface. A lymph node that is located deeper within the organism, further from the surface. FMA:12768 uberon UBERON:0015918 deep lymph node A lymph node that is located deeper within the organism, further from the surface. A lymph node that is part of a hindlimb. FMA:44310 uberon UBERON:0016398 lymph node of lower limb A lymph node that is part of a hindlimb. OBOL:automatic A lymph node that is part of a forelimb. FMA:44311 uberon UBERON:0016399 lymph node of upper limb A lymph node that is part of a forelimb. OBOL:automatic A capillary that is part of a lung. FMA:14121 capillary of lung uberon UBERON:0016405 pulmonary capillary A capillary that is part of a lung. OBOL:automatic capillary of lung FMA:14121 A breast that is part of a male organism. FMA:19901 NCIT:C33048 mamma masculina uberon UBERON:0016410 male breast A breast that is part of a male organism. OBOL:automatic mamma masculina FMA:19901 FMA:35324 uberon UBERON:0016426 proximal interphalangeal joint of little finger Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall. EMAPA:37233 FMA:50060 NCIT:C62484 uberon UBERON:0016435 chest wall Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall. FMA:50060 EMAPA:37233 MA:th A strand of hair that is part of a head. FMA:54241 hair of scalp head hair uberon UBERON:0016446 hair of head A strand of hair that is part of a head. OBOL:automatic hair of scalp FMA:54241 head hair FMA:54241 A strand of hair that is part of a trunk. FMA:54250 trunk hair uberon UBERON:0016447 hair of trunk A strand of hair that is part of a trunk. OBOL:automatic trunk hair FMA:54250 A hole in the diaphragm through which the esophagus passes FMA:58289 esophageal hiatus of diaphragm oesophageal aperture oesophageal hiatus uberon UBERON:0016458 esophageal hiatus A hole in the diaphragm through which the esophagus passes HP:0002036 esophageal hiatus of diaphragm FMA:58289 oesophageal aperture FMA:58289 oesophageal hiatus FMA:58289 A stroma that is part of a liver. FMA:17553 hepatic stroma stroma of liver uberon UBERON:0016478 liver stroma A stroma that is part of a liver. OBOL:automatic hepatic stroma FMA:17553 stroma of liver FMA:17553 A collagenous capsule covering the external surface of the liver. It consists of type III collagen and extends to the stroma of endothelial sinusoids. It is covered by a single layer of mesothelial cells. FMA:15813 capsula fibrosa perivascularis fibrous capsule of liver glisson's capsule hepatic capsule tunica fibrosa (hepar) tunica fibrosa hepatis uberon fibrous capsule of Glisson liver capsule UBERON:0016479 capsule of liver A collagenous capsule covering the external surface of the liver. capsula fibrosa perivascularis fibrous capsule of liver FMA:15813 glisson's capsule FMA:15813 hepatic capsule FMA:15813 tunica fibrosa (hepar) FMA:TA tunica fibrosa hepatis FMA:15813 FMA:TA fibrous capsule of Glisson liver capsule A lymph node that is part of a bronchus. MA:0003078 NCIT:C32232 uberon UBERON:0016481 bronchial lymph node A lymph node that is part of a bronchus. OBOL:automatic is the sensory system for the sense of hearing. Auditory system is general anatomical term in FMA EMAPA:36002 FMA:7192 MA:0002443 NCIT:C12889 NLXANAT:090817 OpenCyc:Mx4rvViwtJwpEbGdrcN5Y29ycA UMLS:C0587901 uberon UBERON:0016490 auditory system is the sensory system for the sense of hearing. NLXANAT:090817 Auditory system is general anatomical term in FMA FMA UMLS:C0587901 ncithesaurus:Auditory_System Skeletal element that functionally replaces the notochord[VSAP,modified]. Skeletal element that surrounds the notochord.[VSAO] the main cylindrical portion of the vertebra ventral to the vertebral canal The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification. centrum VSAO:0000183 centre vertébral@fr centrum of vertebra périchorde@fr uberon UBERON:0016491 vertebral centrum element VSAO VSAO Skeletal element that functionally replaces the notochord[VSAP,modified]. VSAO:0000183 VSAO:curator Skeletal element that surrounds the notochord.[VSAO] 2012-08-14 VSAO:0000183 VSAO VSAO:curator the main cylindrical portion of the vertebra ventral to the vertebral canal MP:0000141,ISBN:0-683-40008-8,PMID:10572046 centrum VSAO:0000183 centre vertébral@fr TAO:0000126 périchorde@fr TAO:0000126 Luminal space of the right ventricle of the heart. EMAPA:26047 FMA:9291 right ventricle lumen right ventricular cavity uberon UBERON:0016509 cavity of right ventricle Luminal space of the right ventricle of the heart. right ventricle lumen EMAPA:26047 right ventricular cavity FMA:FMA A epithelium that is part of a male urethra. EMAPA:30467 FMA:19684 male urethral epithelium urethral epithelium of male uberon UBERON:0016510 epithelium of male urethra A epithelium that is part of a male urethra. OBOL:automatic male urethral epithelium FMA:FMA urethral epithelium of male EMAPA:30467 A anatomical space that is part of a duodenum. EMAPA:19080 FMA:14589 doudenal lumen duodenal lumen uberon UBERON:0016512 lumen of duodenum A anatomical space that is part of a duodenum. OBOL:automatic doudenal lumen FMA:FMA duodenal lumen FMA:FMA luminal space of the left atrium of the heart. EMAPA:26011 FMA:9465 left atrial cavity left atrium lumen uberon UBERON:0016513 cavity of left atrium luminal space of the left atrium of the heart. left atrial cavity FMA:FMA left atrium lumen EMAPA:26011 luminal space of the left ventricle of the heart. EMAPA:26038 FMA:9466 left ventricular cavity uberon UBERON:0016514 cavity of left ventricle luminal space of the left ventricle of the heart. left ventricular cavity FMA:FMA A epithelium that is part of a female urethra. EMAPA:30470 FMA:19774 female urethral epithelium urethral epithelium of female uberon UBERON:0016520 epithelium of female urethra A epithelium that is part of a female urethra. OBOL:automatic female urethral epithelium FMA:FMA urethral epithelium of female EMAPA:30470 luminal space of the right atrium of the heart. EMAPA:26020 FMA:11359 right atrial cavity uberon UBERON:0016522 cavity of right atrium luminal space of the right atrium of the heart. right atrial cavity FMA:FMA Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border. Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though frontal region regio frontalis BAMS:Frontal_lobe BIRNLEX:928 BM:Tel-Cx-FR CALOHA:TS-0389 DHBA:12113 EFO:0000913 EV:0100167 FMA:61824 HBA:4009 MAT:0000505 MESH:A08.186.211.730.885.213.270 NCIT:C12352 OpenCyc:Mx4rv3OJ8JwpEbGdrcN5Y29ycA UMLS:C0016733 UMLS:C1268977 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=56 lobi frontales lobus frontalis frontal cortex uberon UBERON:0016525 frontal lobe FMA Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border. FMA:61824 Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though MM frontal region FMA:61824 regio frontalis FMA:61824 FMA:TA regio frontalis FMA:TA UMLS:C0016733 BIRNLEX:928 UMLS:C0016733 ncithesaurus:Frontal_Lobe UMLS:C1268977 BIRNLEX:928 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=56 BIRNLEX:928 lobi frontales NeuroNames:56 lobus frontalis frontal cortex FMA:61824 Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. UBERON:0000322 BIRNLEX:922 BTO:0000445 FMA:61823 cerebral hemisphere lobe cerebral lobe lobe of cerebral cortex lobe parts of cerebral cortex lobi cerebri uberon cerebral cortical segment lobes of the brain regional organ part of cerebral cortex segment of cerebral cortex UBERON:0016526 We use the term lobe broadly as a rough regional area, encompassing homologous regions in smooth-brained mammals. We subdivide the lobes into white matter and neocortical parts. lobe of cerebral hemisphere Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. FMA:61823 cerebral hemisphere lobe FMA:61823 cerebral lobe BTO:0000445 lobe of cerebral cortex BIRNLEX:922 lobe parts of cerebral cortex BIRNLEX:922 lobi cerebri FMA:77800 FMA:TA cerebral cortical segment FMA:68603 lobes of the brain BIRNLEX:922 regional organ part of cerebral cortex FMA:68603 segment of cerebral cortex BIRNLEX:922 Grey matter neocortex region of a lobe of the cerebral hemisphere. FMA:242197 cortex of cerebral hemisphere lobe cortex of lobe of cerebral hemisphere uberon gray matter of lobe of cerebral hemisphere neocortical part of cerebral hemisphere UBERON:0016529 cortex of cerebral lobe Grey matter neocortex region of a lobe of the cerebral hemisphere. cortex of cerebral hemisphere lobe FMA:242197 cortex of lobe of cerebral hemisphere FMA:242197 gray matter of lobe of cerebral hemisphere FMA:242197 Gray matter of the parietal region of the neocortex, located in the parietal lobe of gyrencephalic animals. It is continuous anteriorly with the frontal cortex, posteriorly with the occipital cortex and medially with the insular cortex and with the temporal cortex on the posterior/inferior border. DHBA:10208 DMBA:16016 EMAPA:35667 FMA:242203 MA:0000916 NLX:79282 cortex of parietal lobe parietal lobe cortex parietal neocortex uberon gray matter of parietal lobe UBERON:0016530 parietal cortex Gray matter of the parietal region of the neocortex, located in the parietal lobe of gyrencephalic animals. It is continuous anteriorly with the frontal cortex, posteriorly with the occipital cortex and medially with the insular cortex and with the temporal cortex on the posterior/inferior border. NLX:79282 cortex of parietal lobe FMA:242203 parietal lobe cortex FMA:242203 parietal neocortex DHBA:10208 gray matter of parietal lobe FMA:242203 Gray matter of the temporal region of the neocortex, located in the temporal lobe in gyrencephalic animals BM:Tel-Cx-Te DHBA:10235 DMBA:16044 FMA:242201 MA:0000941 NLX:94939 cortex of temporal lobe temporal lobe cortex temporal neocortex uberon gray matter of temporal lobe UBERON:0016538 temporal cortex Gray matter of the temporal region of the neocortex, located in the temporal lobe in gyrencephalic animals NLX:94939 cortex of temporal lobe FMA:242201 temporal lobe cortex FMA:242201 temporal neocortex DHBA:10235 gray matter of temporal lobe FMA:242201 The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. UBERON:2001379 TAO:0001379 ZFA:0001379 uberon UBERON:0016545 pharyngeal ectoderm The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. A layer of of the central nervous system that is part of gray matter. grey matter layer FMA:83142 CNS gray matter layer CNS grey matter layer gray matter layer of neuraxis grey matter layer of neuraxis uberon UBERON:0016548 central nervous system gray matter layer A layer of of the central nervous system that is part of gray matter. gray matter layer of neuraxis FMA:83142 mucus produced in the respiratory tract. NCIT:C93171 uberon UBERON:0016552 phlegm mucus produced in the respiratory tract. Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm). uberon UBERON:0016553 respiratory system mucus Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm). A blood vessel that is part of a cerebellum. uberon UBERON:0016565 cerebral blood vessel A blood vessel that is part of a cerebellum. OBOL:automatic An roughly circular indentation in a surface. AEO:0000204 uberon UBERON:0016566 pit An roughly circular indentation in a surface. AEO:0000204 AEO:JB FMA:68861 rexed lamina uberon UBERON:0016570 lamina of gray matter of spinal cord rexed lamina FMA:68861 A collection of protruberances derived from pharyngeal arch 1 that develop into the tragus, crus of the helix, and helix. uberon UBERON:0016611 auditory hillocks, pharyngeal arch 1 derived A collection of protruberances derived from pharyngeal arch 1 that develop into the tragus, crus of the helix, and helix. A collection of protruberances derived from pharyngeal arch 2 that develop into the concha, antihelix and antitragus. uberon UBERON:0016612 auditory hillocks, pharyngeal arch 2 derived A collection of protruberances derived from pharyngeal arch 2 that develop into the concha, antihelix and antitragus. A scent gland that is part of the skin cutaneous scent gland uberon UBERON:0016852 skin scent gland A scent gland that is part of the skin The dorsal region of the optic cup that gives rise to the dorsal part of the retina. dorsal optic cup dorsal region of optic cup uberon UBERON:0016854 dorsal part of optic cup The dorsal region of the optic cup that gives rise to the dorsal part of the retina. dorsal optic cup dorsal region of optic cup Primordium that develops into the central nervous system UBERON:3000469 future CNS presumptive central nervous system uberon UBERON:0016879 future central nervous system Primordium that develops into the central nervous system Primordium that develops into the nervous system UBERON:3000477 AAO:0000477 presumptive nervous system uberon UBERON:0016880 future nervous system Primordium that develops into the nervous system presumptive nervous system AAO:0000477 The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints joint of shoulder region uberon UBERON:0016884 shoulder joint definitional The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints Epithelium lining the distalmost portion of the digestive tract. BTO:0005445 WBbt:0005800 rectum epithelium uberon UBERON:0016885 epithelium of terminal part of digestive tract Epithelium lining the distalmost portion of the digestive tract. rectum epithelium BTO:0005445 Any muscle tissue of the distalmost portion of the digestive tract. rectum muscle rectum muscle structure uberon UBERON:0016886 muscle tissue of terminal part of digestive tract Any muscle tissue of the distalmost portion of the digestive tract. The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 EHDAA2:0000003 EMAPA:16042 extra-embryonic component extraembryonic component uberon UBERON:0016887 entire extraembryonic component AEO AEO The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 AEO:JB extraembryonic component AEO:0000195 An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 uberon UBERON:0016888 transitional anatomical structure AEO An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 AEO:JB The dorsal part of the body wall uberon UBERON:0017649 dorsal body wall The dorsal part of the body wall A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 uberon UBERON:0017650 developing mesenchymal structure A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 AEO:JB A primordium that has the potential to develop into a saliva-secreting gland. uberon UBERON:0017651 salivary gland primordium A primordium that has the potential to develop into a saliva-secreting gland. OBOL:automatic Any of the small racemose mucous glands in the mucous membrane lining the cheeks BTO:0005767 uberon cheek gland UBERON:0017654 buccal gland Any of the small racemose mucous glands in the mucous membrane lining the cheeks A viscus that is part of a abdomen. FMA:32413 FMA:67355 abdominal viscera abdominal viscera set set of abdominal viscera uberon UBERON:0017672 abdominal viscera A viscus that is part of a abdomen. OBOL:automatic abdominal viscera FMA:32413 abdominal viscera set FMA:32413 set of abdominal viscera FMA:32413 A mesopodial endochondral element that is in the most proximal part of the mesopodial skeleton, connected to the zeugopodial skeleton. awaiting approval by phenoscape curators uberon UBERON:0017750 proximal mesopodial endochondral element A mesopodial endochondral element that is in the most proximal part of the mesopodial skeleton, connected to the zeugopodial skeleton. A proximal mesopodial endochondral element that is composed primarily of cartilage tissue. uberon UBERON:0017751 proximal mesopodial cartilage element A proximal mesopodial endochondral element that is composed primarily of cartilage tissue. OBOL:automatic A muscle layer that is part of the rectum FMA:15035 muscular coat of rectum muscularis externa of rectum rectal muscularis propria tunica muscularis (rectum) tunica muscularis recti uberon UBERON:0018111 muscle layer of rectum A muscle layer that is part of the rectum muscular coat of rectum FMA:15035 muscularis externa of rectum FMA:15035 rectal muscularis propria FMA:15035 tunica muscularis (rectum) FMA:15035 tunica muscularis recti FMA:TA Any portion of smooth muscle tissue that is part of the rectum rectal smooth muscle tissue rectum smooth muscle smooth muscle of rectum uberon UBERON:0018112 rectum smooth muscle tissue Any portion of smooth muscle tissue that is part of the rectum A renal pelvis that is part of a left ureter. FMA:15579 pelvis of left ureter renal pelvis of left kidney uberon UBERON:0018115 left renal pelvis A renal pelvis that is part of a left ureter. OBOL:automatic pelvis of left ureter FMA:15579 renal pelvis of left kidney FMA:15579 A renal pelvis that is part of a right ureter. FMA:15578 pelvis of right kidney pelvis of right ureter uberon UBERON:0018116 right renal pelvis A renal pelvis that is part of a right ureter. OBOL:automatic pelvis of right kidney FMA:15578 pelvis of right ureter FMA:15578 FMA:83521 uberon UBERON:0018135 fibrocollagenous connective tissue Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx). UBERON:0015006 caudal vertebra element tail vertebra element coccygeal vertebra element coccyx vertebra element uberon UBERON:0018142 caudal vertebra endochondral element Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx). A transverse process that is part of a cervical vertebra May be homologous with the cervical ribs of some vertebrates FMA:23894 FMA:9913 uberon UBERON:0018143 transverse process of cervical vertebra A transverse process that is part of a cervical vertebra A rib that is attached to a cervical vertebra. Trunk, presacral and sacral ribs do not have a 'part of some region' asserted for them, we should add it to them[PHENOSCAPE:ad] May be homologous with the transverse processes of cervical vertebra EMAPA:37825 UBERONTEMP:d522e981-3a43-4cab-9862-4344b5c3ff22 uberon UBERON:0018144 cervical rib A rib that is attached to a cervical vertebra. EMAPA:37825 MA:th A rib that is attached to a lumbar vertebra. May be homologous with the transverse processes of lumbar vertebra uberon UBERON:0018145 lumbar rib A rib that is attached to a lumbar vertebra. A transverse process that is part of a lumbar vertebra May be homologous with the lumbar ribs of some vertebrates FMA:16080 FMA:65469 costa lumbalis lumbar transverse process uberon UBERON:0018146 transverse process of lumbar vertebra A transverse process that is part of a lumbar vertebra costa lumbalis FMA:65469 FMA:TA lumbar transverse process FMA:16080 A zone of skin that is part of a lower lip. FMA:24767 lower lip skin uberon UBERON:0018150 skin of lower lip A zone of skin that is part of a lower lip. OBOL:automatic lower lip skin FMA:24767 A ligament that is part of a middle ear. uberon UBERON:0018154 ligament of middle ear A ligament that is part of a middle ear. OBOL:automatic An organ system subdivision that is the part of the lymphoid system that includes the pulmonary lymphatic vessels. FMA:67999 pulmonary lymphatic chain uberon pulmonary lymphatic vasculature UBERON:0018226 pulmonary part of lymphatic system An organ system subdivision that is the part of the lymphoid system that includes the pulmonary lymphatic vessels. pulmonary lymphatic chain FMA:67999 A lymphatic vessel that is part of a lung. FMA:234006 lymphatic vessel of lung uberon UBERON:0018227 pulmonary lymphatic vessel A lymphatic vessel that is part of a lung. OBOL:automatic A stroma that is part of a pancreas. FMA:63121 pancreatic stroma uberon UBERON:0018234 stroma of pancreas A stroma that is part of a pancreas. OBOL:automatic pancreatic stroma FMA:63121 A capsule that divides the parenchyma of the pancreas into lobes and lobules typically thin but can thicken with age pancreatic capsule uberon UBERON:0018235 capsule of pancreas A capsule that divides the parenchyma of the pancreas into lobes and lobules ISBN:0123813611 A boundary delimiting a rhombomere. rhombomere junction uberon UBERON:0018239 rhombomere boundary A boundary delimiting a rhombomere. GO:0021654 A vein that supplies blood to the thymus. FMA:10647 thymic branch of internal thoracic artery uberon thymic arteries UBERON:0018243 The arteries supplying the thymus are derived from the internal thoracic artery, and from the superior thyroid artery and inferior thyroids.[WP] thymic artery FMA A vein that supplies blood to the thymus. thymic branch of internal thoracic artery FMA:10647 thymic arteries A vein that drains a thyroid gland. EMAPA:18648 uberon UBERON:0018246 thyroid vein A vein that drains a thyroid gland. OBOL:automatic An artery that supplies a cervical thymus. uberon UBERON:0018247 cervical thymic artery An artery that supplies a cervical thymus. One of the veins draining a meninix. In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault. FMA:50839 uberon UBERON:0018251 meningeal vein One of the veins draining a meninix. Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104 EHDAA2:0001842 EMAPA:35578 MA:0000165 uberon UBERON:0018254 skeletal musculature MA A vein that drains a lacrimal gland. FMA:51779 uberon UBERON:0018256 lacrimal vein A vein that drains a lacrimal gland. OBOL:automatic Any portion of submucosa that lines the digestive tract. uberon UBERON:0018257 submucosa of digestive tract Any portion of submucosa that lines the digestive tract. Any organ component layer that consists of muscle tissue. NCITA class may refer to smooth muscle only FMA:45634 NCIT:C75444 uberon UBERON:0018260 layer of muscle tissue Any organ component layer that consists of muscle tissue. NCITA class may refer to smooth muscle only NCIT A muscular coat that is part of a digestive tract. responsible for gut movement, such as peristalsis tunica muscularis of digestive tract uberon muscular layer of digestive tract muscularis externa of digestive tract tunica externa of digestive tract UBERON:0018261 muscular coat of digestive tract A muscular coat that is part of a digestive tract. OBOL:automatic Tissue that is part of some adrenal gland TODO - describe typology of adrenal gland tissue used in this ontology NCIT:C32051 UBERONTEMP:a7bf197b-0db2-467e-824e-be45b39e2672 adrenal gland tissue uberon UBERON:0018303 adrenal tissue Tissue that is part of some adrenal gland PHENOSCAPE:Alex adrenal gland tissue ncithesaurus:Adrenal_Gland_Tissue Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). UBERONTEMP:9ca0bda7-9111-4f59-bc72-5d47bc3d7d61 uberon UBERON:0018321 foramen for glossopharyngeal nerve Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). PHENOSCAPE:alex A skeletal ligament that is part of a hip joint. FMA:42868 hip joint ligament uberon UBERON:0018411 ligament of hip joint A skeletal ligament that is part of a hip joint. OBOL:automatic hip joint ligament FMA:42868 A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment . FMA:54952 canalis nervi facialis facial canal uberon fallopian canal UBERON:0018413 facial nerve canal A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment . canalis nervi facialis FMA:54952 FMA:TA facial canal FMA:54952 fallopian canal FMA:54952 The anatomical space within the intestine. see notes in inclusivity in class 'intestine' FMA:14586 TADS:0000495 WBbt:0005791 ZFA:0005807 intestinal lumen intestine lumen uberon gut lumen UBERON:0018543 lumen of intestine The anatomical space within the intestine. intestinal lumen FMA:14586 intestine lumen ZFA:0005807 gut lumen ZFA:0005807 Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscle innervated by the trigeminal nerve muscles innervated by the trigeminal nerve uberon UBERON:0018544 trigeminal nerve muscle Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscles innervated by the trigeminal nerve MFMO:0000072 FMA:83450 ventricular cardiac muscle tissue ventricular heart muscle uberon ventricular muscle UBERON:0018649 cardiac muscle tissue of ventricle ventricular cardiac muscle tissue ventricular heart muscle ventricular muscle the neck region of a bone organ. bone neck neck of bone uberon UBERON:0018664 neck of bone element https://github.com/obophenotype/uberon/wiki/Hidden-GCIs the neck region of a bone organ. FMA:23254 anatomical neck of scapula scapular neck uberon UBERON:0018667 neck of scapula anatomical neck of scapula FMA:23254 scapular neck FMA:23254 An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. FMA:73747 ZFA:0005811 cardiac vasculature uberon UBERON:0018674 heart vasculature An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. ZFA:0005811 ZFA:CVS cardiac vasculature FMA:73747 Thoracic splanchnic nerves are splanchnic nerves that arise from the sympathetic trunk in the thorax and travel inferiorly to provide sympathetic innervation to the abdomen. The nerves contain preganglionic sympathetic and general visceral afferent fibers. FMA:6280 uberon UBERON:0018679 thoracic splanchnic nerve FMA Thoracic splanchnic nerves are splanchnic nerves that arise from the sympathetic trunk in the thorax and travel inferiorly to provide sympathetic innervation to the abdomen. The nerves contain preganglionic sympathetic and general visceral afferent fibers. uberon UBERON:0018692 dorsal side of post-anal tail A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 bladder uberon UBERON:0018707 bladder organ A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 bladder BTO:0000123 BTO:0002439 genital mucosa uberon UBERON:0019042 reproductive system mucosa genital mucosa BTO:0002439 Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 uberon intramuscular fat UBERON:0019143 intramuscular adipose tissue Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 intramuscular fat BTO:0004043 BTO:0004626 uberon carotid endothelium carotid epithelium UBERON:0019189 carotid artery endothelium carotid endothelium BTO:0004626 BTO:0004638 FMA:13119 bronchial gland bronchial mucous gland peribronchial gland uberon UBERON:0019190 mucous gland of lung bronchial gland FMA:13119 bronchial mucous gland FMA:13119 peribronchial gland BTO:0004638 BTO:0004661 uberon UBERON:0019196 iliac artery endothelium Any region of epithelium that is part of a skin region. BTO:0004382 uberon UBERON:0019204 skin epithelium Any region of epithelium that is part of a skin region. EMAPA:35869 MA:0003178 uberon UBERON:0019206 tongue papilla epithelium The part of the eye that consists of both the retina and the optic choroid chorioretina choroid and retina retinachoroid retinachoroidal region uberon UBERON:0019207 chorioretinal region The part of the eye that consists of both the retina and the optic choroid UBERON:drseb Either of the outermost digits in a five-digit autopod, or their phylogenetic equivalent. uberon lateral digit outer digit outermost digit UBERON:0019221 digit 1 or 5 https://github.com/obophenotype/uberon/issues/592 Either of the outermost digits in a five-digit autopod, or their phylogenetic equivalent. UBERON:cjm lateral digit outer digit outermost digit uberon lateral finger lateral manual digit outer manual digit outermost manual digit UBERON:0019231 manual digit 1 or 5 https://github.com/obophenotype/uberon/issues/592 lateral finger lateral manual digit outer manual digit outermost manual digit uberon lateral pedal digit lateral toe outer pedal digit outermost pedal digit UBERON:0019241 pedal digit 1 or 5 https://github.com/obophenotype/uberon/issues/592 lateral pedal digit lateral toe outer pedal digit outermost pedal digit DHBA:10654 FMA:268630 gray matter of the hindbrain uberon UBERON:0019263 gray matter of hindbrain gray matter of the hindbrain DHBA:HGM DHBA:10157 FMA:268608 uberon UBERON:0019264 gray matter of forebrain DHBA:10649 FMA:83913 uberon UBERON:0019267 gray matter of midbrain FMA:83912 uberon UBERON:0019269 gray matter of diencephalon EMAPA:35952 MA:0003174 uberon UBERON:0019304 sensory organ epithelium EMAPA:35958 MA:0003171 uberon UBERON:0019306 nose epithelium Epithelial layer that is part of the external part of the nose. FMA:63143 epithelium of skin of external nose uberon UBERON:0019307 epithelium of external nose FMA Epithelial layer that is part of the external part of the nose. epithelium of skin of external nose FMA:63143 An exocrine gland that is part of a integumental system. integumental exocrine gland integumental system exocrine gland uberon UBERON:0019319 exocrine gland of integumental system An exocrine gland that is part of a integumental system. GOC:dos integumental exocrine gland integumental system exocrine gland The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. EMAPA:37067 FMA:83965 MA:0001033 accessory neural nucleus uberon accessory nucleus of anterior column of spinal cord nucleus accessorius columnae anterioris medullae spinalis nucleus nervi accessorii nucleus of accessory nerve nucleus of the accessory nerve nucleus of the spinal accessory nerve spinal accessory nucleus UBERON:0020358 See also: Wikipedia:Spinal_accessory_nucleus accessory XI nerve nucleus FMA The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. EMAPA:37067 MA:th accessory neural nucleus FMA:83965 accessory nucleus of anterior column of spinal cord NeuroNames:2003 nucleus accessorius columnae anterioris medullae spinalis NeuroNames:2003 nucleus nervi accessorii NeuroNames:2003 nucleus of accessory nerve NeuroNames:2003 nucleus of the accessory nerve NeuroNames:2003 nucleus of the spinal accessory nerve NeuroNames:2003 spinal accessory nucleus A blood vessel that supplies or drains an ear. EMAPA:37386 MA:0001226 uberon UBERON:0020550 auricular blood vessel A blood vessel that supplies or drains an ear. EMAPA:37386 MA:th FMA:53671 hair of external ear hair of tragus tragus hair uberon UBERON:0022279 strand of hair on external ear hair of external ear FMA:53671 hair of tragus FMA:53671 tragus hair FMA:53671 the single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland) in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe EMAPA:35464 uberon UBERON:0022284 lacrimal gland bud the single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland) MGI:anna FMA:58315 uberon surface of region of wall of eyeball UBERON:0022288 surface of eyeball surface of region of wall of eyeball FMA:58315 NCIT:C33596 uberon UBERON:0022292 splenic arteriole A portion of organism substance that is secreted by a reproductive gland. uberon genital fluid genital secretion reproductive system fluid reproductive system fluid/secretion reproductive system secretion UBERON:0022293 reproductive gland secretion A portion of organism substance that is secreted by a reproductive gland. UBERON:cjm Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer lamina layer NLX:149357 uberon UBERON:0022303 nervous system cell part layer Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. NLX:149357 lamina CUMBO:CUMBO layer CUMBO:CUMBO Serous membrane layer that is adjacent to and lines an organ. FMA:15860 visceral wall of serous membrane uberon UBERON:0022350 visceral serous membrane Serous membrane layer that is adjacent to and lines an organ. visceral wall of serous membrane FMA:15860 Serous membrane layer that lines to a body cavity. cavity lining FMA:15859 MA:0002448 parietal wall of serous membrane uberon UBERON:0022351 parietal serous membrane Serous membrane layer that lines to a body cavity. cavity lining MA:0002448 parietal wall of serous membrane FMA:15859 The layer of endometrial epithelium adjacent to the uterine cavity. FMA:86492 NCIT:C32189 pars basalis of endometrium stratum basalis of endometrium uberon UBERON:0022355 basal layer of endometrium The layer of endometrial epithelium adjacent to the uterine cavity. stratum basalis of endometrium FMA:86492 FMA:14652 ileal mesentery ileum mesentery mesoileum uberon UBERON:0022357 mesentery of ileum ileal mesentery FMA:14652 ileum mesentery FMA:14652 A blood vessel of the placenta. placental vessel uberon UBERON:0022358 placenta blood vessel A blood vessel of the placenta. GO:0060674 A specific region of the foregut into the area in which the lung will develop. lung field uberon UBERON:0022361 lung field A specific region of the foregut into the area in which the lung will develop. GOC:dph GOC:mtg_lung BIRNLEX:1624 lumbar spinal cord gray matter uberon UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter BIRNLEX:1624 lumbar spinal cord gray matter BIRNLEX:1624 An embryonic or larval epithelium that is committed to form part of the nervous system. neurepithelium AEO:0001008 BTO:0000314 EHDAA2_RETIRED:0004654 FMA:64807 embryonic neuroepithelium neuroepithelium uberon UBERON:0034705 developing neuroepithelium An embryonic or larval epithelium that is committed to form part of the nervous system. AEO:0001008 AEO:JB neurepithelium BTO:0000314 embryonic neuroepithelium neuroepithelium AEO:0001008 An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 uberon UBERON:0034706 proliferating neuroepithelium AEO An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 uberon UBERON:0034707 differentiating neuroepithelium AEO A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 In the cerebellum, some neuronal precursors enter the marginal zone to form clusters of neurons called nuclei[NBK10047] DHBA:12695 EHDAA2:0001152 EMAPA:17789 marginal zone of cerebellum uberon MZCB UBERON:0034708 cerebellum marginal layer marginal zone of cerebellum DHBA:12695 MZCB DHBA:12695 DHBA:12694 EMAPA:32916 marginal zone of hindbrain uberon MZH UBERON:0034709 hindbrain marginal layer marginal zone of hindbrain DHBA:12694 MZH DHBA:12694 EHDAA2:0001267 EMAPA:17585 spinal cord lateral wall ventricular layer uberon UBERON:0034710 spinal cord ventricular layer EHDAA2 spinal cord lateral wall ventricular layer EHDAA2:0001267 The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate. EMAPA:35261 uberon UBERON:0034711 cortical preplate The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate. Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain uberon cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain UBERON:0034713 cranial neuron projection bundle Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain ISBN:0471888893 cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain A cranial nerve fiber tract that innervates the parietal eye. uberon epiphyseal nerve UBERON:0034714 This should be classified as an evaginated sensory afferents rather than cranial nerves, as they are part of the CNS[ISBN:0471888893] epiphyseal tract A cranial nerve fiber tract that innervates the parietal eye. ISBN:0471888893 epiphyseal nerve ISBN:0471888893 A cranial nerve fiber tract that innervates the pineal body. FMA:77600 uberon pineal nerve UBERON:0034715 This should be classified as an evaginated sensory afferents rather than cranial nerves, as they are part of the CNS[ISBN:0471888893] pineal tract A cranial nerve fiber tract that innervates the pineal body. ISBN:0471888893 pineal nerve ISBN:0471888893 A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. uberon UBERON:0034717 integumental taste bud A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. A taste bud that is located on a lip. uberon UBERON:0034719 lip taste bud A taste bud that is located on a lip. A taste bud that is located on the skin of the head. uberon UBERON:0034720 head taste bud A taste bud that is located on the skin of the head. A taste bud that is located in the pharynx. uberon UBERON:0034721 pharyngeal taste bud A taste bud that is located in the pharynx. A taste bud that is located in the esophagus. uberon UBERON:0034724 esophageal taste bud A taste bud that is located in the esophagus. A taste bud that is located on the skin of the trunk. uberon UBERON:0034726 trunk taste bud A taste bud that is located on the skin of the trunk. The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. EMAPA:37957 FMA:5866 MESH:D017776 nervus visceralis visceral nerve uberon UBERON:0034728 autonomic nerve The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. EMAPA:37957 MA:th nervus visceralis FMA:5866 visceral nerve FMA:5866 EMAPA:37958 uberon UBERON:0034729 sympathetic nerve EMAPA:37958 MA:th A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. uberon UBERON:0034768 morphological feature A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. FMA:79770 NCIT:C41168 uberon UBERON:0034769 lymphomyeloid tissue FMA Any substance in the body or expelled from the body that is in a gaseous state. FMA:84580 gas in anatomical space portion of gas in anatomical space uberon UBERON:0034873 bodily gas Any substance in the body or expelled from the body that is in a gaseous state. portion of gas in anatomical space FMA:84580 Any portion of gas located in a part of the respiratory system that is composed primarily of air. FMA:84581 respiratory air respiratory system air uberon UBERON:0034874 air in respiratory system Any portion of gas located in a part of the respiratory system that is composed primarily of air. respiratory air FMA:84581 EHDAA2:0001472 EMAPA:32796 pituitary primordium uberon UBERON:0034875 future pituitary gland EMAPA Wikipedia pituitary primordium EHDAA2:0001472 the outgrowth of neuroectoderm located on the floor of the embryonic hypothalamus that gives rise to the neurohypophysis (posterior lobe) of the pituitary gland EMAPA:16647 EHDAA2:0004434 EMAPA:16647 uberon neurohypohysial region neurohypophyseal bud UBERON:0034876 future neurohypophysis EMAPA EMAPA the outgrowth of neuroectoderm located on the floor of the embryonic hypothalamus that gives rise to the neurohypophysis (posterior lobe) of the pituitary gland MP:0013339 neurohypohysial region EHDAA2:0004434 neurohypophyseal bud MP:0013339 the area of axial mesoderm that develops into the prechordal plate prechordal mesenchyme uberon UBERON:0034878 prechordal mesoderm the area of axial mesoderm that develops into the prechordal plate MGI:anna The cervical ganglia are paravertebral ganglia of the sympathetic nervous system. These emerging postganglionic nerves synapse with preganglionic nerves from the thoracic spinal cord. They consist of three paravertebral ganglia: superior cervical ganglion middle cervical ganglion inferior cervical ganglion. The inferior ganglion may be fused with the first thoracic ganglion to form a single structure, the stellate ganglion. Nerves emerging from cervical sympathetic ganglia contribute to the cardiac plexus, among other things. FMA:6261 cervical part of sympathetic trunk cervical sympathetic chain cervical sympathetic trunk uberon UBERON:0034901 cervical sympathetic nerve trunk The cervical ganglia are paravertebral ganglia of the sympathetic nervous system. These emerging postganglionic nerves synapse with preganglionic nerves from the thoracic spinal cord. They consist of three paravertebral ganglia: superior cervical ganglion middle cervical ganglion inferior cervical ganglion. The inferior ganglion may be fused with the first thoracic ganglion to form a single structure, the stellate ganglion. Nerves emerging from cervical sympathetic ganglia contribute to the cardiac plexus, among other things. cervical part of sympathetic trunk FMA:6261 cervical sympathetic chain FMA:6261 cervical sympathetic trunk FMA:6261 Endocardium that is part of the left atrium. Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein. FMA:7286 VHOG:0001226 endocardium of left atrium left atrial endocardium uberon left atrium endocardial tissue UBERON:0034903 left atrium endocardium Endocardium that is part of the left atrium. Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein. FMA:7286 endocardium of left atrium FMA:7286 left atrium endocardial tissue VHOG:0001226 lumen of gland uberon UBERON:0034905 gland lumen Parenchymal tissue that forms the pineal gland. NCIT:C41834 uberon UBERON:0034907 pineal parenchyma Parenchymal tissue that forms the pineal gland. Any of the muscles that are responsible for moving the scapula. In humans these are the levator scapulae, the infraspinatus muscle, the teres major, the teres minor, and the supraspinatus muscle. uberon UBERON:0034908 scapular muscle Any of the muscles that are responsible for moving the scapula. In humans these are the levator scapulae, the infraspinatus muscle, the teres major, the teres minor, and the supraspinatus muscle. HPO:curators An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 uberon anatomical cluster UBERON:0034921 multi organ part structure CARO An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 anatomical cluster CARO:0020001 A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 FMA:62807 uberon UBERON:0034922 cell cluster CARO A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 A collection of anatomical structures that are alike in terms of their morphology or developmental origin. resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected uberon UBERON:0034925 anatomical collection A collection of anatomical structures that are alike in terms of their morphology or developmental origin. An anatomical collection that is arranged in a line. resolve if this should be a subclass of or merged with aligned anatomical group. FBbt:00100152 uberon UBERON:0034926 anatomical row An anatomical collection that is arranged in a line. FMA:19623 dorsum of penis dorsum penis uberon UBERON:0034928 dorsal surface of penis dorsum of penis FMA:19623 dorsum penis FMA:TA A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. uberon UBERON:0034929 external soft tissue zone A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts. BTO:0001513 biliary system epithelium uberon biliary epithelium biliary tract epithelium UBERON:0034932 epithelium of biliary system The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts. BTO:0001513 MGI:cs biliary system epithelium biliary epithelium BTO:0001513 biliary tract epithelium Any organ component layer that consists of smooth muscle tissue. uberon UBERON:0034933 layer of smooth muscle tissue Any organ component layer that consists of smooth muscle tissue. FMA:55268 organ sector organ zonal region organ zone uberon organ region with floating fiat boundary UBERON:0034944 zone of organ organ sector FMA:55268 organ zone FMA:55268 organ region with floating fiat boundary FMA:55268 Any portion of gas located in a part of the respiratory system. respiratory gas respiratory system gas uberon UBERON:0034947 gas in respiratory system Any portion of gas located in a part of the respiratory system. A population of lymphatic endothelial cell precursors that will form the lymph vessels. NCIT:C34262 uberon primary lymph sac UBERON:0034953 embryonic lymph sac VHOG A population of lymphatic endothelial cell precursors that will form the lymph vessels. NCIT:C25787 uberon duct epithelium ductal epithelium UBERON:0034969 epithelial layer of duct DHBA:12682 EMAPA:32917 hindbrain mantle layer uberon UBERON:0034994 hindbrain cortical intermediate zone hindbrain mantle layer EMAPA:32917 Mesenchyme that is part of a developing jaw [Automatically generated definition]. EMAPA:32907 EMAPA:35454 uberon UBERON:0034995 jaw mesenchyme Mesenchyme that is part of a developing jaw [Automatically generated definition]. OBOL:automatic EMAPA:35702 uberon UBERON:0035004 preputial swelling EMAPA EMAPA:29220 uberon prepuce of male UBERON:0035005 preputial swelling of male EMAPA prepuce of male EMAPA:29220 EMAPA:30478 uberon prepuce of female UBERON:0035006 preputial swelling of female EMAPA prepuce of female EMAPA:30478 represented as a primordium in EMAPA - should be cartilage condensation EMAPA:35890 turbinal cartilage turbinate bone primordium turbinate cartilage condensation unossified nasal turbinal unossified nasal turbinate unossified turbinate uberon UBERON:0035007 nasal concha cartilage represented as a primordium in EMAPA - should be cartilage condensation EMAPA turbinate bone primordium EMAPA:35890 EMAPA:37798 FMA:18157 MA:0001151 left vagus neural trunk trunk of left vagus uberon anterior vagus X nerve trunk UBERON:0035020 left vagus X nerve trunk EMAPA:37798 MA:th left vagus neural trunk FMA:18157 trunk of left vagus FMA:18157 anterior vagus X nerve trunk MA:0001151 EMAPA:37799 FMA:18151 MA:0001152 right vagus neural trunk trunk of right vagus uberon posterior vagus X nerve trunk UBERON:0035021 right vagus X nerve trunk EMAPA:37799 MA:th right vagus neural trunk FMA:18151 trunk of right vagus FMA:18151 posterior vagus X nerve trunk MA:0001152 An epithelium that is part of a naris [Automatically generated definition]. EMAPA:35959 MA:0003172 uberon UBERON:0035036 naris epithelium An epithelium that is part of a naris [Automatically generated definition]. OBOL:automatic EMAPA:32904 MA:0003220 uberon UBERON:0035037 jaw epithelium hemorrhoidal artery uberon UBERON:0035039 rectal artery Any of the interlobular excretory ducts of a salivary gland which are found in the connective tissue septa and formed by the union of several intralobular striated (secretory) ducts[MP,generalized]. FMA:60052 uberon UBERON:0035049 excretory duct of salivary gland Any of the interlobular excretory ducts of a salivary gland which are found in the connective tissue septa and formed by the union of several intralobular striated (secretory) ducts[MP,generalized]. MP:0013750 uberon UBERON:0035050 excretory duct FMA:60053 uberon UBERON:0035053 interlobular duct of salivary gland FMA:71193 uberon lobe or lobule of thymus UBERON:0035075 thymus subunit A vertebra that has a transverse process. uberon TP vertebra pygal vertebra UBERON:0035083 transverse process-bearing vertebra A vertebra that has a transverse process. TP vertebra pygal vertebra A post-anal tail that attaches outside the tail. uberon UBERON:0035091 extrinsic post-anal tail muscle A post-anal tail that attaches outside the tail. A transverse process that is part of a caudal vertebra uberon UBERON:0035102 transverse process of caudal vertebra A transverse process that is part of a caudal vertebra Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat digestive tract contents uberon ingested material entity UBERON:0035118 material entity in digestive tract Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. digestive tract contents EMAPA:32631 hand cartilage condensation uberon UBERON:0035128 manus cartilage element EMAPA-modified hand cartilage condensation EMAPA:32631 EMAPA:32657 foot cartilage condensation uberon UBERON:0035129 pes cartilage element EMAPA-modified foot cartilage condensation EMAPA:32657 ossicle element auditory skeletal element middle ear ossicle element uberon ear ossicle element ear ossicles element middle ear skeletal element ossicle element of ear ossicle element of inner ear ossicular chain element UBERON:0035130 auditory ossicle endochondral element MA ossicle element EMAPA:17824 middle ear ossicle element MP:0005105 ear ossicles element ossicular chain element EMAPA:35979 ossicle cartilage condensation uberon UBERON:0035131 auditory ossicle cartilage element ossicle cartilage condensation EMAPA:35979 EMAPA:35982 ossicle pre-cartilage condensation uberon UBERON:0035132 auditory ossicle pre-cartilage element ossicle pre-cartilage condensation EMAPA:35982 Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 NCIT:C29667 surface of body uberon UBERON:0035159 entire surface of organism Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 surface of body FMA:61695 The flattened aspect of the prostate with a slight furrow facing the rectum and anus. FMA:19592 NCIT:C13095 facies posterior (prostatae) facies posterior prostatae posterior surface of prostate gland uberon UBERON:0035165 posterior surface of prostate lexical The flattened aspect of the prostate with a slight furrow facing the rectum and anus. ncithesaurus:Posterior_Surface_of_the_Prostate facies posterior (prostatae) FMA:19592 facies posterior prostatae FMA:19592 FMA:TA posterior surface of prostate gland FMA:19592 The organ of hearing located on the right side of the head. FMA:53641 NCIT:C81285 uberon UBERON:0035174 right ear The organ of hearing located on the right side of the head. ncithesaurus:Right_Ear The tubules that carry lymph throughout the body that are just beneath the surface of the skin. FMA:52011 NCIT:C33663 superficial lymph vessel uberon UBERON:0035198 superficial lymphatic vessel The tubules that carry lymph throughout the body that are just beneath the surface of the skin. ncithesaurus:Superficial_Lymphatic_Vessel superficial lymph vessel FMA:52011 FMA:70506 NCIT:C32837 internal carotid arterial subdivision subdivision of internal carotid artery uberon UBERON:0035237 branch of internal carotid artery internal carotid arterial subdivision FMA:70506 subdivision of internal carotid artery FMA:70506 FMA:55032 NCIT:C12240 uberon UBERON:0035240 posterior wall of oropharynx The narrowest portion of the gallbladder and distal to the cystic duct. FMA:14538 NCIT:C32649 cervix of gallbladder gallbladder neck uberon UBERON:0035267 neck of gallbladder The narrowest portion of the gallbladder and distal to the cystic duct. ncithesaurus:Gallbladder_Neck cervix of gallbladder FMA:14538 gallbladder neck FMA:14538 FMA:55008 NCIT:C12239 uberon UBERON:0035286 lateral wall of oropharynx The organ of hearing located on the left side of the head[ncit,modified]. FMA:53642 NCIT:C81259 uberon UBERON:0035295 left ear The organ of hearing located on the left side of the head[ncit,modified]. ncithesaurus:Left_Ear FMA:55063 NCIT:C12249 posterior wall of hypopharynx uberon UBERON:0035313 posterior wall of laryngopharynx posterior wall of hypopharynx FMA:55063 The membrane the surrounds the prostate gland. FMA:19583 NCIT:C13086 capsule of prostate capsule of prostate gland uberon UBERON:0035316 prostatic capsule The membrane the surrounds the prostate gland. ncithesaurus:Capsule_of_the_Prostate capsule of prostate FMA:19583 capsule of prostate gland FMA:19583 FMA:14765 NCIT:C33474 trunk of right common iliac arterial tree uberon UBERON:0035322 right common iliac artery trunk of right common iliac arterial tree FMA:14765 FMA:54908 NCIT:C12244 lateral nasopharynx uberon UBERON:0035383 lateral wall of nasopharynx lateral nasopharynx FMA:54908 FMA:70505 NCIT:C32552 external carotid arterial subdivision subdivision of external carotid artery uberon UBERON:0035398 branch of external carotid artery external carotid arterial subdivision FMA:70505 subdivision of external carotid artery FMA:70505 FMA:54907 NCIT:C12243 posterior nasopharynx uberon UBERON:0035401 posterior wall of nasopharynx posterior nasopharynx FMA:54907 An artery that supplies the pituitary gland. uberon UBERON:0035403 hypophysial artery An artery that supplies the pituitary gland. The parietal pleura that lines the mediastinum. FMA:9736 NCIT:C94820 mediastinal part of parietal pleura pars mediastinalis (pleurae) pars mediastinalis pleurae parietalis uberon UBERON:0035431 mediastinal pleura FMA FMA The parietal pleura that lines the mediastinum. ncithesaurus:Mediastinal_Pleura mediastinal part of parietal pleura FMA:9736 pars mediastinalis (pleurae) FMA:9736 pars mediastinalis pleurae parietalis FMA:9736 FMA:TA A vein that drains blood from the right adrenal gland into the inferior vena cava. FMA:14343 NCIT:C53131 vena suprarenalis (adrenalis) dextra uberon UBERON:0035435 right suprarenal vein A vein that drains blood from the right adrenal gland into the inferior vena cava. ncithesaurus:Right_Suprarenal_Vein vena suprarenalis (adrenalis) dextra FMA:14343 A space inside the uterus lined by a layer of mucus membranes called the endometrium. FMA:18076 NCIT:C32514 cavity of body of uterus endometrial cavity endometrial lumen intrauterine cavity uberon UBERON:0035465 endometrial cavity A space inside the uterus lined by a layer of mucus membranes called the endometrium. ncithesaurus:Endometrial_Cavity cavity of body of uterus FMA:18076 endometrial cavity FMA:18076 intrauterine cavity FMA:18076 FMA:15590 NCIT:C32895 facies posterior (Ren) facies posterior renis uberon UBERON:0035471 posterior surface of kidney facies posterior (Ren) FMA:15590 facies posterior renis FMA:15590 FMA:TA The external portion of the prostate including the anterior, inferolateral, lateral and posterior surfaces. FMA:19590 NCIT:C13091 prostatic surface surface of prostate gland uberon UBERON:0035480 surface of prostate The external portion of the prostate including the anterior, inferolateral, lateral and posterior surfaces. ncithesaurus:Surface_of_the_Prostate prostatic surface FMA:19590 surface of prostate gland FMA:19590 A vein that drains blood from the left adrenal gland into the left renal artery. FMA:14349 NCIT:C53138 uberon UBERON:0035483 left suprarenal vein A vein that drains blood from the left adrenal gland into the left renal artery. ncithesaurus:Left_Suprarenal_Vein The aspect of the prostate facing the pubic symphysis. FMA:19591 NCIT:C13089 anterior surface of prostate gland facies anterior (prostatae) facies anterior prostatae uberon UBERON:0035523 anterior surface of prostate lexical The aspect of the prostate facing the pubic symphysis. ncithesaurus:Anterior_Surface_of_the_Prostate anterior surface of prostate gland FMA:19591 facies anterior (prostatae) FMA:19591 facies anterior prostatae FMA:19591 FMA:TA FMA:14766 NCIT:C32957 trunk of left common iliac arterial tree uberon UBERON:0035529 left common iliac artery trunk of left common iliac arterial tree FMA:14766 Any of several arteries that arise from the aorta and supply blood to the esophagus. FMA:4149 NCIT:C32535 aortic esophageal artery oesophageal artery uberon UBERON:0035539 esophageal artery FMA FMA Any of several arteries that arise from the aorta and supply blood to the esophagus. ncithesaurus:Esophageal_Artery aortic esophageal artery FMA:4149 oesophageal artery FMA:4149 The tubules that carry lymph throughout the body that are in the interior of the body or limbs. FMA:52012 NCIT:C32439 deep lymph vessel uberon UBERON:0035545 deep lymphatic vessel The tubules that carry lymph throughout the body that are in the interior of the body or limbs. ncithesaurus:Deep_Lymphatic_Vessel deep lymph vessel FMA:52012 FMA:51797 ciliary vein uberon UBERON:0035546 uveal vein ciliary vein FMA:51797 uberon UBERON:0035548 colic artery The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. FMA:225275 superficial part of circulatory system superficial vasculature dermis vasculature hypodermis vasculature uberon skin vasculature subcutaneous vasculature vasculature of skin UBERON:0035549 vasculature of integument The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. vasculature of skin FMA:225275 Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. FMA:76719 NCIT:C33666 uberon superfical vein superficial veins superficial vessels UBERON:0035550 superficial vein Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. ncithesaurus:Superficial_Vein superfical vein superficial veins superficial vessels The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. deep part of circulatory system uberon UBERON:0035551 deep vasculature The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. FMA:76718 NCIT:C32444 uberon deep veins deep vessels UBERON:0035552 deep vein A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. ncithesaurus:Deep_Vein deep veins deep vessels Any chamber of the left side of the heart FMA:7166 uberon UBERON:0035553 left cardiac chamber Any chamber of the left side of the heart Any chamber of the right side of the heart FMA:7165 uberon UBERON:0035554 right cardiac chamber Any chamber of the right side of the heart An embryonic structure positioned halfway between the prospective eye and ear, adjacent to the future midbrain-hindbrain boundary. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. XAO:0004093 ophthalmic lobe of trigeminal placode ophthalmic lobe of trigeminal placode complex ophthalmic placode profundus placode uberon UBERON:0035597 profundal placode An embryonic structure positioned halfway between the prospective eye and ear, adjacent to the future midbrain-hindbrain boundary. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. XAO:0004093 ophthalmic lobe of trigeminal placode NCBIBook:NBK53171 ophthalmic lobe of trigeminal placode complex NCBIBook:NBK53171 ophthalmic placode profundus placode XAO:0004093 FMA:61298 cartilage of acoustic meatus cartilage of auditory canal cartilago meatus acustici external acoustic meatus cartilage uberon UBERON:0035606 cartilage of external acoustic meatus cartilage of acoustic meatus FMA:61298 cartilage of auditory canal FMA:61298 cartilago meatus acustici FMA:TA external acoustic meatus cartilage FMA:61298 Any lymph vessel that is located in the dura mater of the brain. while Louveau et al (DOI:10.1038/nature14432) state this is within the CNS (thus overturning dogma about the presence of lymphatics in the CNS), in this ontology the dura dural lymph vessel uberon dural lymph vasculature UBERON:0035608 Louveau et al (DOI:10.1038/nature14432) claim the discovery of lymphatics in the cerebral dura mater, but this is disputed by Bucchieri et al (DOI:10.1111/joa.12381) dura mater lymph vessel Any lymph vessel that is located in the dura mater of the brain. A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning. consult http://www.ncbi.nlm.nih.gov/pubmed/25312359 to add missing structures, e.g. ectoturbinals unossified in dinosaurs[http://palaeos.com/vertebrates/bones/braincase/ethmoid.html] nasal turbinal nasal turbinal element nasal turbinate turbinal turbinate uberon concha conchae nasales nasal concha UBERON:0035612 nasal turbinal ISBN:0073040584 A skeletal element of the ethmoid region with complex morphology that are lined with mucuous membranes involved in either olfaction or air conditioning. UBERON:cjm turbinal concha EMAPA:25093 conchae nasales The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva FMA:76554 NCIT:C32574 adnexa oculi uberon accessory parts of orbital region accessory visual structures accessory visual structures set adnexal parts of orbital region appendage of eye appendages of the eye eye adnexa set of accessory visual structures structurae oculi accessoriae UBERON:0035639 ocular adnexa The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva HPO:pr UBERON:cjm adnexa oculi accessory visual structures accessory visual structures FMA:76554 accessory visual structures set FMA:76554 appendage of eye appendages of the eye set of accessory visual structures FMA:76554 structurae oculi accessoriae Any nerve that innervates the larynx. MESH:A08.800.050.050.925.450 uberon UBERON:0035642 laryngeal nerve Any nerve that innervates the larynx. UBERON:cjm Any nerve that innervates the pinna. EMAPA:36513 MA:0001232 auricular nerve uberon UBERON:0035648 nerve innervating pinna FMA Any nerve that innervates the pinna. UBERON:cjm auricular nerve MA:0001232 Any nerve that innervates the penis. EMAPA:35057 penile nerve penis nerve uberon UBERON:0035649 nerve of penis Any nerve that innervates the penis. UBERON:cjm Any nerve that innervates the clitoris. EMAPA:35044 clitoral nerve clitoris nerve uberon UBERON:0035650 nerve of clitoris Any nerve that innervates the clitoris. UBERON:cjm uberon UBERON:0035651 glans EHDAA2:0004181 FMA:9464 cardiac chamber cavity heart cavity heart lumen uberon UBERON:0035763 cavity of cardiac chamber FMA cardiac chamber cavity FMA:9464 heart cavity FMA:9464 heart lumen EHDAA2:0004181 FMA:5968 intrapulmonary lymph node pulmonary node uberon UBERON:0035764 pulmonary lymph node intrapulmonary lymph node FMA:5968 pulmonary node FMA:5968 FMA:223208 NCIT:C12930 uberon UBERON:0035767 intrapulmonary bronchus The primordial mouth region of the developing head. FMA:293105 primitive mouth primordial mouth uberon UBERON:0035804 future mouth The primordial mouth region of the developing head. MP:0003119 primitive mouth FMA:293105 A muscle layer that is part of the sigmoid colon FMA:15028 muscularis externa of sigmoid colon muscularis propria of sigmoid colon sigmoid colon muscularis propria uberon sigmoideum muscularis tunica muscularis colon sigmoideum UBERON:0035805 muscle layer of sigmoid colon A muscle layer that is part of the sigmoid colon muscularis externa of sigmoid colon FMA:15028 FMA:12241 uberon UBERON:0035809 serous cavity The sum of epicardial and paracardial fat deposits. ZFA:0005765 uberon UBERON:0035814 pericardial fat The sum of epicardial and paracardial fat deposits. Fat deposits in the mediastinum outside the parietal pericardium . intrathoracic fat uberon UBERON:0035815 paracardial fat Fat deposits in the mediastinum outside the parietal pericardium . intrathoracic fat Any fat deposit surrounding a visceral organ. uberon UBERON:0035818 visceral fat Any fat deposit surrounding a visceral organ. UBERON:cjm The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. FMA:12267 cavitas abdominis et pelvis uberon UBERON:0035819 abdominopelvic cavity The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. UBERON:cjm cavitas abdominis et pelvis FMA:TA A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. EMAPA:16137 FMA:9908 MA:0000054 uberon peritoneal component UBERON:0035820 peritoneal sac A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. peritoneal component EMAPA:16137 the thick outer layer of the adrenal gland that is in the left side of the abdomen FMA:69089 cortex of left adrenal gland cortex of left suprarenal gland left adrenal cortex uberon UBERON:0035825 left adrenal gland cortex true the thick outer layer of the adrenal gland that is in the left side of the abdomen cortex of left adrenal gland FMA:69089 cortex of left suprarenal gland FMA:69089 left adrenal cortex FMA:69089 the adrenal gland medulla that is in the left side of the abdomen FMA:69092 left adrenal medulla medulla of left adrenal gland medulla of left suprarenal gland uberon UBERON:0035826 left adrenal gland medulla true the adrenal gland medulla that is in the left side of the abdomen left adrenal medulla FMA:69092 medulla of left adrenal gland FMA:69092 medulla of left suprarenal gland FMA:69092 the thick outer layer of the adrenal gland that is in the right side of the abdomen FMA:69088 cortex of right adrenal gland cortex of right suprarenal gland right adrenal cortex uberon UBERON:0035827 right adrenal gland cortex true the thick outer layer of the adrenal gland that is in the right side of the abdomen cortex of right adrenal gland FMA:69088 cortex of right suprarenal gland FMA:69088 right adrenal cortex FMA:69088 the adrenal gland medulla that is in the right side of the abdomen FMA:69091 medulla of right adrenal gland medulla of right suprarenal gland right adrenal medulla uberon UBERON:0035828 right adrenal gland medulla true the adrenal gland medulla that is in the right side of the abdomen medulla of right adrenal gland FMA:69091 medulla of right suprarenal gland FMA:69091 right adrenal medulla FMA:69091 The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. FMA:58277 costal part of diaphragm pars costalis diaphragmatis uberon UBERON:0035831 costal diaphragm The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. costal part of diaphragm FMA:58277 pars costalis diaphragmatis FMA:TA The lumen of the epididymis FMA:18274 epididymis lumen lumen of epididymis uberon UBERON:0035956 epididymal lumen FMA The lumen of the epididymis GOC:DOS epididymis lumen FMA:18274 lumen of epididymis FMA:18274 BTO:0004378 EMAPA:37987 FMA:67473 blood vessel wall uberon vascular wall UBERON:0035965 wall of blood vessel EMAPA:37987 MA:th blood vessel wall FMA:67473 vascular wall BTO:0004378 The lower portion of the larynx, extending from just beneath the vocal cords down to the top of the trachea. the structures in the subglottis are implicated in the regulation of the temperature of the breath EMAPA:37969 FMA:55477 NCIT:C12280 infraglottic part of larynx subglottic larynx subglottic region uberon UBERON:0036068 subglottis The lower portion of the larynx, extending from just beneath the vocal cords down to the top of the trachea. MP:0030000 ORCID:orcid.org/0000-0002-6490-7723 EMAPA:37969 MA:th infraglottic part of larynx FMA:55477 subglottic larynx FMA:55477 subglottic region MP:0030000 EHDAA2:0004070 uberon UBERON:0036072 respiratory primordium epithelium EHDAA2 EHDAA2:0004071 respiratory primordium associated mesenchyme uberon UBERON:0036073 respiratory primordium mesenchyme EHDAA2 respiratory primordium associated mesenchyme EHDAA2:0004071 An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. uberon UBERON:0036146 cardiopharyngeal field An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. BGEE:ann An organ subunit in the skin that gives rise to cutaneous appendage. follicle cutaneous appendage follicle skin follicle uberon UBERON:0036150 skin appendage follicle An organ subunit in the skin that gives rise to cutaneous appendage. UBERON:cjm An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 uberon rectosigmoid region UBERON:0036214 rectosigmoid junction An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 rectosigmoid region NCIT:C54188 Material anatomical entity that forms the outermost boundary of an anatomical structure. AAO:0010270 AEO:0000154 ZFA:0005594 uberon UBERON:0036215 anatomical surface region Material anatomical entity that forms the outermost boundary of an anatomical structure. A bodily fluid that is located in the coelom. he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid] BTO:0001708 uberon UBERON:0036217 coelomic fluid A bodily fluid that is located in the coelom. Any gland that is part os the respiratory system. uberon UBERON:0036225 respiratory system gland Any gland that is part os the respiratory system. UBERON:cjm A notochord that has persisted beyond the embryonic stage. uberon UBERON:0036242 post-embryonic notochord A notochord that has persisted beyond the embryonic stage. UBERON:cjm Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands. uberon vaginal discharge vaginal secretion UBERON:0036243 vaginal fluid Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands. A transudate found in the serous sac. serous fluid FMA:20932 serous sac fluid uberon UBERON:0036244 secretion of serous membrane A transudate found in the serous sac. FMA:20932 serous fluid FMA:20932 Any synovial joint that connects auditory ossicles. FMA:60063 auditory ossicle joint auditory ossicles joint joint of auditory ossicles uberon UBERON:0036248 joint of auditory ossicle Any synovial joint that connects auditory ossicles. UBERON:cjm auditory ossicles joint FMA:60063 joint of auditory ossicles FMA:60063 FMA:53133 cranial orifice skull orifice uberon UBERON:0036253 orifice of skull cranial orifice FMA:53133 skull orifice FMA:53133 Any of the eight ligaments pertaining to the uterus including the anterior, posterior, lateral, sacro-uterine and round ligaments. NCIT:C61360 uberon UBERON:0036262 uterine ligament Any of the eight ligaments pertaining to the uterus including the anterior, posterior, lateral, sacro-uterine and round ligaments. NCIT:C61360 The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. FMA:52972 ramus zygomaticotemporalis (Nervus zygomaticus) ramus zygomaticotemporalis nervus zygomatici zygomaticotemporal branch of zygomatic nerve uberon zygomaticotemporal zygomaticotemporal branch UBERON:0036264 zygomaticotemporal nerve The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. ramus zygomaticotemporalis (Nervus zygomaticus) FMA:52972 ramus zygomaticotemporalis nervus zygomatici FMA:TA zygomaticotemporal branch of zygomatic nerve FMA:52972 zygomaticotemporal zygomaticotemporal branch uberon UBERON:0036267 vulval vein uberon UBERON:0036268 pelvic vein EMAPA:30807 uberon penis vasculature vasculature of penis UBERON:0036269 penis blood vessel vasculature of penis EMAPA:30807 Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall pared del ventrC-culo izquierdo@es uberon UBERON:0036285 wall of left ventricle FMA FMA Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall FMA:9556 pared del ventrC-culo izquierdo@es FMA:9556 Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 pared del ventrC-culo derecho@es right ventricular wall uberon UBERON:0036286 wall of right ventricle FMA FMA Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 pared del ventrC-culo derecho@es FMA:9533 right ventricular wall FMA:9533 FMA:9560 uberon UBERON:0036288 anterior wall of left ventricle Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 uberon UBERON:0036289 anterior wall of right ventricle Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 FMA:87177 uberon UBERON:0036290 myocardium of anterior wall of left ventricle FMA:260877 uberon UBERON:0036291 myocardium of anterior wall of right ventricle A mucosa that is part of a lip region [Automatically generated definition]. NCIT:C12226 labial mucosa uberon UBERON:0036294 mucosa of lip A mucosa that is part of a lip region [Automatically generated definition]. OBOL:automatic labial mucosa UBERON:cjm The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 renal pelvis and ureter renal pelvis plus ureter uberon UBERON:0036295 renal pelvis/ureter NCIT The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 FMA:225251 uberon UBERON:0036301 vasculature of spleen FMA uberon UBERON:0036302 vasculature of central nervous system plus retina FMA:259905 uberon UBERON:0036303 vasculature of central nervous system An anatomical structure that is located along the line dividing two regions of an anatomical structure. uberon UBERON:0036304 anatomical border An anatomical structure that is located along the line dividing two regions of an anatomical structure. UBERON:cjm FMA:14621 appendix wall wall of vermiform appendix uberon UBERON:0036337 wall of appendix FMA appendix wall FMA:14621 wall of vermiform appendix FMA:14621 FMA:14657 gallbladder wall uberon UBERON:0036343 wall of gallbladder FMA gallbladder wall FMA:14657 FMA:15090 subclavian arterial wall uberon UBERON:0036352 wall of subclavian artery FMA FMA subclavian arterial wall FMA:15090 FMA:15704 anal canal wall uberon UBERON:0036362 wall of anal canal FMA anal canal wall FMA:15704 FMA:15889 right ureteral wall uberon UBERON:0036375 wall of right ureter FMA FMA right ureteral wall FMA:15889 FMA:15890 left ureteral wall uberon UBERON:0036376 wall of left ureter FMA FMA left ureteral wall FMA:15890 FMA:18211 pulmonary arterial wall uberon UBERON:0036422 wall of pulmonary artery FMA FMA pulmonary arterial wall FMA:18211 FMA:18303 uterine tube wall wall of fallopian tube wall of oviduct uberon UBERON:0036441 wall of uterine tube FMA FMA uterine tube wall FMA:18303 wall of fallopian tube FMA:18303 wall of oviduct FMA:18303 FMA:19779 urethral wall uberon UBERON:0036521 wall of urethra FMA FMA urethral wall FMA:19779 FMA:19971 vaginal wall uberon UBERON:0036523 wall of vagina FMA FMA vaginal wall FMA:19971 FMA:231590 uberon UBERON:0036553 wall of synovial tendon sheath FMA FMA FMA:242772 uberon UBERON:0036654 wall of lateral ventricle FMA FMA:242778 uberon UBERON:0036657 wall of fourth ventricle FMA FMA:242841 uberon UBERON:0036661 wall of ventricular system of brain FMA FMA FMA:58098 eyeball wall uberon UBERON:0036925 wall of eyeball FMA FMA eyeball wall FMA:58098 FMA:66284 common carotid arterial wall uberon UBERON:0037094 wall of common carotid artery FMA FMA common carotid arterial wall FMA:66284 wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall uberon UBERON:0037144 wall of heart FMA FMA FMA FMA wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall FMA:7274 FMA:85375 lacrimal ductal wall uberon UBERON:0037237 wall of lacrimal duct FMA FMA lacrimal ductal wall FMA:85375 FMA:19676 male urethral wall uberon UBERON:0037447 wall of male urethra FMA FMA male urethral wall FMA:19676 FMA:19780 female urethral wall uberon UBERON:0037455 wall of female urethra FMA FMA female urethral wall FMA:19780 A collection of hairs that grows on the external ear. uberon external ear hair UBERON:1000004 collection of hair on external ear A collection of hairs that grows on the external ear. UBERON:EJS A zone of skin that is part of the face. eriks 2012-02-05T05:23:01Z EMAPA:36657 FMA:24758 NCIT:C33561 UMLS:C0222084 face skin uberon facial skin UBERON:1000021 skin of face A zone of skin that is part of the face. UBERON:EJS UMLS:C0222084 ncithesaurus:Skin_of_the_Face face skin EMAPA:36657 FMA:24758 A parenchyma that is part of a spleen. FMA:16029 splenic parenchyma uberon UBERON:1000024 parenchyma of spleen A parenchyma that is part of a spleen. OBOL:automatic splenic parenchyma FMA:16029 EFO:0003612 TAO:0001053 ZFA:0001053 PICA primitive internal carotid artery uberon UBERON:2001053 future internal carotid artery EHDAA2 PICA TAO:0001053 primitive internal carotid artery ZFA:0001053 This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon teleost_anatomy_curators ZFA:0001073 uberon/phenoscape-anatomy axial vasculature Cartilage which is part of the axial skeleton. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon teleost_anatomy_curators ZFA:0001457 uberon/phenoscape-anatomy postcranial axial cartilage Cartilage which is part of the axial skeleton. ZFIN:curator Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA]. fenestrated blood vessel endothelium FMA:63196 NCIT:C32595 TAO:0005260 UMLS:C1179615 ZFA:0005260 fenestrated capillary vessel uberon UBERON:2005260 fenestrated capillary FMA ZFA Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse fenestrated blood vessel endothelium ZFA:0005260 UMLS:C1179615 ncithesaurus:Fenestrated_Capillary fenestrated capillary vessel FMA:63196 Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon teleost_anatomy_curators ZFA:0007013 uberon/phenoscape-anatomy preplacodal ectoderm Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. ZFIN:curator Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon/phenoscape-anatomy Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 external integument structure Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the external head integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon/phenoscape-anatomy head external integument structure Dermal, epidermal, glandular and pigment structures of the external head integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the body integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon/phenoscape-anatomy body external integument structure Dermal, epidermal, glandular and pigment structures of the body integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the limb integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon/phenoscape-anatomy limb external integument structure Dermal, epidermal, glandular and pigment structures of the limb integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the tail integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon/phenoscape-anatomy tail external integument structure Dermal, epidermal, glandular and pigment structures of the tail integument. AAO:EJS Blood vessels in respiratory skin. Modified from the original AAO source amphibian_anatomy_curators uberon/phenoscape-anatomy vasculature of respiratory integument Blood vessels in respiratory skin. AAO:EJS Skeletal tissue that is mineralized. mineralized tissue VSAO:0000013 XAO:0004039 uberon UBERON:4000013 mineralized skeletal tissue Skeletal tissue that is mineralized. XAO:0004039 XAO:EJS mineralized tissue VSAO:0000013 Anatomical projection that is composed of bone or cartilage tissue. none skeletal element projection FMA:23356 NCIT:C33164 collum anatomicum (Humerus) collum anatomicum humeri humeral neck none uberon anatomic neck of humerus UBERON:4200172 neck of humerus collum anatomicum (Humerus) FMA:23356 collum anatomicum humeri FMA:23356 FMA:TA anatomic neck of humerus FMA:23356 An anatomical surface that is part of a bone bone surface surface of bone Mesenchyme that is part of a forelimb bud. WD forelimb bud mesenchyme Mesenchyme that is part of a hindlimb bud. WD hindlimb bud mesenchyme A subdivision of the autopod consisting of manual digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. manual digit 1 manual digit 1 ( phalanges plus metapodial) plus soft tissue manual digit 1 digitopodial subdivision manual digit 1 ray manual digit I plus metapodial segment uberon UBERON:5001463 manual digit 1 plus metapodial segment A subdivision of the autopod consisting of manual digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. manual digit 1 manual digit 1 ( phalanges plus metapodial) plus soft tissue manual digit 1 digitopodial subdivision manual digit 1 ray manual digit I plus metapodial segment A subdivision of the autopod consisting of pedal digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. pedal digit pedal digit ( phalanges plus metapodial) plus soft tissue pedal digit digitopodial subdivision pedal digit ray uberon UBERON:5001466 pedal digit plus metapodial segment A subdivision of the autopod consisting of pedal digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. pedal digit pedal digit ( phalanges plus metapodial) plus soft tissue pedal digit digitopodial subdivision pedal digit ray A subdivision of the autopod consisting of manual digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. manual digit manual digit ( phalanges plus metapodial) plus soft tissue manual digit digitopodial subdivision manual digit ray uberon UBERON:5002389 manual digit plus metapodial segment A subdivision of the autopod consisting of manual digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. manual digit manual digit ( phalanges plus metapodial) plus soft tissue manual digit digitopodial subdivision manual digit ray A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. digit digit ( phalanges plus metapodial) plus soft tissue digit digitopodial subdivision digit ray uberon UBERON:5002544 digit plus metapodial segment A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. digit digit ( phalanges plus metapodial) plus soft tissue digit digitopodial subdivision digit ray A subdivision of the autopod consisting of manual digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. manual digit 5 manual digit 5 ( phalanges plus metapodial) plus soft tissue manual digit 5 digitopodial subdivision manual digit 5 ray manual digit V plus metapodial segment uberon UBERON:5003625 manual digit 5 plus metapodial segment A subdivision of the autopod consisting of manual digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. manual digit 5 manual digit 5 ( phalanges plus metapodial) plus soft tissue manual digit 5 digitopodial subdivision manual digit 5 ray manual digit V plus metapodial segment A subdivision of the autopod consisting of pedal digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. pedal digit 1 pedal digit 1 ( phalanges plus metapodial) plus soft tissue pedal digit 1 digitopodial subdivision pedal digit 1 ray pedal digit I plus metapodial segment uberon UBERON:5003631 pedal digit 1 plus metapodial segment A subdivision of the autopod consisting of pedal digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. pedal digit 1 pedal digit 1 ( phalanges plus metapodial) plus soft tissue pedal digit 1 digitopodial subdivision pedal digit 1 ray pedal digit I plus metapodial segment A subdivision of the autopod consisting of pedal digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. pedal digit 5 pedal digit 5 ( phalanges plus metapodial) plus soft tissue pedal digit 5 digitopodial subdivision pedal digit 5 ray pedal digit V plus metapodial segment uberon UBERON:5003635 pedal digit 5 plus metapodial segment A subdivision of the autopod consisting of pedal digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. pedal digit 5 pedal digit 5 ( phalanges plus metapodial) plus soft tissue pedal digit 5 digitopodial subdivision pedal digit 5 ray pedal digit V plus metapodial segment A subdivision of the autopod consisting of digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. digit 1 digit 1 ( phalanges plus metapodial) plus soft tissue digit 1 digitopodial subdivision digit 1 ray digit I plus metapodial segment uberon UBERON:5006048 digit 1 plus metapodial segment A subdivision of the autopod consisting of digit 1 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. digit 1 digit 1 ( phalanges plus metapodial) plus soft tissue digit 1 digitopodial subdivision digit 1 ray digit I plus metapodial segment A subdivision of the autopod consisting of digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. digit 5 digit 5 ( phalanges plus metapodial) plus soft tissue digit 5 digitopodial subdivision digit 5 ray digit V plus metapodial segment uberon UBERON:5006052 digit 5 plus metapodial segment A subdivision of the autopod consisting of digit 5 plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. digit 5 digit 5 ( phalanges plus metapodial) plus soft tissue digit 5 digitopodial subdivision digit 5 ray digit V plus metapodial segment A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 1 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. manual digit I digitopodial skeleton uberon manual digit 1 manual digit 1 skeleton UBERON:5101463 manual digit 1 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 1 plus the associated metapodial element. manual digit I digitopodial skeleton manual digit 1 manual digit 1 skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. uberon pedal digit pedal digit skeleton UBERON:5101466 pedal digit digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit plus the associated metapodial element. pedal digit pedal digit skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. uberon manual digit manual digit skeleton UBERON:5102389 manual digit digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit plus the associated metapodial element. manual digit manual digit skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. uberon digit digit skeleton UBERON:5102544 individual digit of digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element. digit digit skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 5 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. manual digit V digitopodial skeleton uberon manual digit 5 manual digit 5 skeleton UBERON:5103625 manual digit 5 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit 5 plus the associated metapodial element. manual digit V digitopodial skeleton manual digit 5 manual digit 5 skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 1 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. pedal digit I digitopodial skeleton uberon pedal digit 1 pedal digit 1 skeleton UBERON:5103631 pedal digit 1 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 1 plus the associated metapodial element. pedal digit I digitopodial skeleton pedal digit 1 pedal digit 1 skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 5 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. pedal digit V digitopodial skeleton uberon pedal digit 5 pedal digit 5 skeleton UBERON:5103635 pedal digit 5 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit 5 plus the associated metapodial element. pedal digit V digitopodial skeleton pedal digit 5 pedal digit 5 skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of digit 1 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. digit I digitopodial skeleton uberon digit 1 digit 1 skeleton UBERON:5106048 digit 1 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of digit 1 plus the associated metapodial element. digit I digitopodial skeleton digit 1 digit 1 skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of digit 5 plus the associated metapodial element. this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. digit V digitopodial skeleton uberon digit 5 digit 5 skeleton UBERON:5106052 digit 5 digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of digit 5 plus the associated metapodial element. digit V digitopodial skeleton digit 5 digit 5 skeleton Outermost point of a tail. https://orcid.org/0000-0003-2699-3066 uberon UBERON:7500035 tip of tail Outermost point of a tail. The posterior-most point of a foot. https://orcid.org/0000-0003-2699-3066 uberon UBERON:7500039 posterior of pes The posterior-most point of a foot. The distal-most point of a cutaneous appendage. https://orcid.org/0000-0003-2699-3066 uberon UBERON:7500040 tip of nail The distal-most point of a cutaneous appendage. The distal-most point of a digit. https://orcid.org/0000-0003-2699-3066 uberon UBERON:7500041 tip of digit The distal-most point of a digit. The proximal-most point of the head of a femur. https://orcid.org/0000-0003-2699-3066 uberon UBERON:7500046 proximal-most point of head of femur The proximal-most point of the head of a femur. Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. http://orcid.org/0000-0001-5208-3432 uberon UBERON:8000006 left side of back Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. http://orcid.org/0000-0001-5208-3432 uberon UBERON:8000007 right side of back Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. A forelimb that is on the right side of a pectoral complex. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern http://orcid.org/0000-0001-9897-3238 FMA:7185 uberon UBERON:8300001 right forelimb A forelimb that is on the right side of a pectoral complex. UBERONREF:0000003 A forelimb that is on the left side of a pectoral complex. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern http://orcid.org/0000-0001-9897-3238 FMA:7186 uberon UBERON:8300002 left forelimb A forelimb that is on the left side of a pectoral complex. UBERONREF:0000003 A hindlimb that is on the right side of a pelvic complex. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern http://orcid.org/0000-0001-9897-3238 FMA:7187 uberon UBERON:8300003 right hindlimb A hindlimb that is on the right side of a pelvic complex. UBERONREF:0000003 A hindlimb that is on the left side of a pelvic complex. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern http://orcid.org/0000-0001-9897-3238 FMA:7188 uberon UBERON:8300004 left hindlimb A hindlimb that is on the left side of a pelvic complex. UBERONREF:0000003 length unit A unit which is a standard measure of the distance between two points. length unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit temperature unit temperature unit substance unit substance unit concentration unit concentration unit volume unit volume unit frequency unit frequency unit volumetric flow rate unit volumetric flow rate unit rate unit rate unit The quantitative measurement of liver enzymes in the blood, which is useful in assessing the functional state of a patient's liver. Liver function tests include the measurement of albumin, alanine transaminase, aspartate transaminase, alkaline phosphatase, bilirubin, and gamma glutamyl transferase. 2019-01-15T19:35:59Z NCIT:C74954 LFT liver function assessment liver function testing The quantitative measurement of liver enzymes in the blood, which is useful in assessing the functional state of a patient's liver. Liver function tests include the measurement of albumin, alanine transaminase, aspartate transaminase, alkaline phosphatase, bilirubin, and gamma glutamyl transferase. NCIT:C74954 LFT example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release term created to ease viewing/sort terms for development purpose, and will not be included in a release PERSON:Alan Ruttenberg organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion Transformation-ML Transformation-ML file describing parameter transformations used in a GvHD experiment. Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf Transformation-ML ACS d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment. ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/) person:Jennifer Fostel web-page:http://www.isac-net.org/content/view/607/150/ ACS XML RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/) person:Jennifer Fostel web-page:http://www.w3.org/XML/ XML RDF A FOAF file, a SKOS file, an OWL file. RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/) person:Jennifer Fostel web-page:http://www.w3.org/RDF/ RDF zip MagicDraw MDZIP archive, Java JAR file. zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/) person:Jennifer Fostel web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/ zip tar Example.tar file. tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/) person:Jennifer Fostel web-page:http://www.gnu.org/software/tar/manual/ tar FCS d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment. FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/) person:Jennifer Fostel web-page:http://www.fcspress.com/ FCS Compensation-ML compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf) person:Jennifer Fostel web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf Compensation-ML Gating-ML foogate.xml, Gating-ML file describing gates used in a GvHD experiment. Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/) person:Jennifer Fostel web-page:http://www.flowcyt.org/gating/ Gating-ML OWL OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file. OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/) person:Jennifer Fostel web-page:http://www.w3.org/2004/OWL/ OWL Affymetrix Affymetrix supplied microarray An organization which supplies technology, tools and protocols for use in high throughput applications Affymetrix Thermo Philippe Rocca-Serra Thermo Waters Philippe Rocca-Serra Waters BIO-RAD Philippe Rocca-Serra BIO-RAD GenePattern hierarchical clustering James Malone GenePattern hierarchical clustering Ambion Philippe Rocca-Serra Ambion Helicos Philippe Rocca-Serra Helicos Roche Philippe Rocca-Serra Roche Illumina Philippe Rocca-Serra Illumina GenePattern PCA GenePattern PCA GenePattern module SVM GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation. James Malone Ryan Brinkman GenePattern module SVM GenePattern k-nearest neighbors James Malone GenePattern k-nearest neighbors GenePattern LOOCV GenePattern LOOCV GenePattern k-means clustering James Malone GenePattern k-means clustering Agilent Philippe Rocca-Serra Agilent GenePattern module KMeansClustering GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation. James Malone PERSON: James Malone GenePattern module KMeansClustering GenePattern CART James Malone GenePattern CART GenePattern module CARTXValidation GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations. GenePattern module CARTXValidation Li-Cor Philippe Rocca-Serra Li-Cor Bruker Corporation Philippe Rocca-Serra Bruker Corporation GenePattern module KNNXValidation GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations. James Malone PERSON: James Malone GenePattern module KNNXValidation GenePattern module PeakMatch GenePattern module PeakMatch GenePattern module KNN GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation. James Malone GenePattern module KNN GenePattern module HierarchicalClustering GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation. James Malone PERSON: James Malone GenePattern module HierarchicalClustering GenePattern SVM James Malone GenePattern SVM Applied Biosystems Philippe Rocca-Serra Applied Biosystems GenePattern module PCA GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation. James Malone PERSON: James Malone GenePattern module PCA GenePattern peak matching James Malone Ryan Brinkman GenePattern peak matching Bruker Daltonics Philippe Rocca-Serra Bruker Daltonics GenePattern HeatMapViewer data visualization The GenePattern process of generating Heat Maps from clustered data. James Malone GenePattern HeatMapViewer data visualization GenePattern HierarchicalClusteringViewer data visualization The GenePattern process of generating hierarchical clustering visualization from clustered data. James Malone GenePattern HierarchicalClusteringViewer data visualization GenePattern module HeatMapViewer A GenePattern software module which is used to generate a heatmap view of data. James Malone GenePattern module HeatMapViewer GenePattern module HierarchicalClusteringViewer A GenePattern software module which is used to generate a view of data that has been hierarchically clustered. James Malone GenePattern module HierarchicalClusteringViewer Sysmex Corporation, Kobe, Japan WEB:http://www.sysmex.com/@2009/08/06 Sysmex Corporation, Kobe, Japan U.S. Food and Drug Administration FDA U.S. Food and Drug Administration right handed right handed ambidexterous ambidexterous left handed left handed Edingburgh handedness inventory The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities. PERSON:Alan Ruttenberg PERSON:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edingburgh handedness inventory eBioscience A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.ebioscience.com/@2011/04/11 eBioscience Cytopeia A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.cytopeia.com/@2011/04/11 Cytopeia Exalpha Biological A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.exalpha.com/@2011/04/11 Exalpha Biological Apogee Flow Systems A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.apogeeflow.com/@2011/04/11 Apogee Flow Systems Exbio Antibodies A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.exbio.cz/@2011/04/11 Exbio Antibodies Becton Dickinson (BD Biosciences) A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.bdbiosciences.com/@2011/04/11 Becton Dickinson (BD Biosciences) Dako Cytomation A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.dakousa.com/@2011/04/11 Dako Cytomation Millipore A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.guavatechnologies.com/@2011/04/11 Millipore Antigenix A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.antigenix.com/@2011/04/11 Antigenix Partec A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.partec.de/@2011/04/11 Partec Beckman Coulter A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.beckmancoulter.com/@2011/04/11 Beckman Coulter Advanced Instruments Inc. (AI Companies) A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.aicompanies.com/@2011/04/11 Advanced Instruments Inc. (AI Companies) Miltenyi Biotec A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.miltenyibiotec.com/@2011/04/11 Miltenyi Biotec AES Chemunex A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.aeschemunex.com/@2011/04/11 AES Chemunex Bentley Instruments A supplier of flow cytometry analyzers Karin Breuer WEB:http://bentleyinstruments.com/@2011/04/11 Bentley Instruments Invitrogen A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.invitrogen.com/@2011/04/11 Invitrogen Luminex A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.luminexcorp.com/@2011/04/11 Luminex CytoBuoy A supplier of flow cytometry analyzers Karin Breuer WEB:http://www.cytobuoy.com/@2011/04/11 CytoBuoy Nimblegen An organization that focuses on manufacturing target enrichment probe pools for DNA sequencing. Person: Jie Zheng Nimblegen Pacific Biosciences An organization that supplies tools for studying the synthesis and regulation of DNA, RNA and protein. It developed a powerful technology platform called single molecule real-time (SMRT) technology which enables real-time analysis of biomolecules with single molecule resolution. Person: Jie Zheng Pacific Biosciences NanoString Technologies An organization that supplies life science tools for translational research and molecular diagnostics based on a novel digital molecular barcoding technology. The NanoString platform can provide simple, multiplexed digital profiling of single molecules. NanoString Technologies Thermo Fisher Scientific An organization that is an American multinational, biotechnology product development company, created in 2006 by the merger of Thermo Electron and Fisher Scientific. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Thermo_Fisher_Scientific Thermo Fisher Scientific G1: Well differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells and the organization of the tumor tissue appear close to normal. Chris Stoeckert, Helena Ellis G1 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G1: Well differentiated G2: Moderately differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are moderately differentiated and reflect an intermediate grade. Chris Stoeckert, Helena Ellis G2 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G2: Moderately differentiated G3: Poorly differentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are poorly differentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G3 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G3: Poorly differentiated G4: Undifferentiated A histologic grade according to AJCC 7th edition indicating that the tumor cells are undifferentiated and do not look like normal cells and tissue. Chris Stoeckert, Helena Ellis G4 https://www.cancer.gov/about-cancer/diagnosis-staging/prognosis/tumor-grade-fact-sheet NCI BBRB G4: Undifferentiated G1 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are round, uniform, approximately 10um and that nucleoli are inconspicuous or absent. Chris Stoeckert, Helena Ellis Grade 1 NCI BBRB, OBI NCI BBRB G1 (Fuhrman) G2 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are slightly irregular, approximately 15um and nucleoli are evident. Chris Stoeckert, Helena Ellis Grade 2 NCI BBRB, OBI NCI BBRB G2 (Fuhrman) G3 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei are very irregular, approximately 20um and nucleoli large and prominent. Chris Stoeckert, Helena Ellis Grade 3 NCI BBRB, OBI NCI BBRB G3 (Fuhrman) G4 (Fuhrman) A histologic grade according to the Fuhrman Nuclear Grading System indicating that nuclei arei bizarre and multilobulated, 20um or greater and nucleoli are prominent and chromatin clumped. Chris Stoeckert, Helena Ellis Grade 4 NCI BBRB, OBI NCI BBRB G4 (Fuhrman) Low grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is low grade. Chris Stoeckert, Helena Ellis Low grade NCI BBRB, OBI NCI BBRB Low grade ovarian tumor High grade ovarian tumor A histologic grade for ovarian tumor according to a two-tier grading system indicating that the tumor is high grade. Chris Stoeckert, Helena Ellis High grade NCI BBRB, OBI NCI BBRB High grade ovarian tumor G1 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is well differentiated. Chris Stoeckert, Helena Ellis G1 NCI BBRB, OBI NCI BBRB G1 (WHO) G2 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is moderately differentiated. Chris Stoeckert, Helena Ellis G2 NCI BBRB, OBI NCI BBRB G2 (WHO) G3 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is poorly differentiated. Chris Stoeckert, Helena Ellis G3 NCI BBRB, OBI NCI BBRB G3 (WHO) G4 (WHO) A histologic grade for ovarian tumor according to the World Health Organization indicating that the tumor is undifferentiated. Chris Stoeckert, Helena Ellis G4 NCI BBRB, OBI NCI BBRB G4 (WHO) pT0 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT0 (colon) pTis (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating carcinoma in situ (intraepithelial or invasion of lamina propria). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pTis (colon) pT1 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades submucosa. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT1 (colon) pT2 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades muscularis propria. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT2 (colon) pT3 (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor invades subserosa or into non-peritionealized pericolic or perirectal tissues. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT3 (colon) pT4a (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor perforates visceral peritoneum. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4a (colon) pT4b (colon) A pathologic primary tumor stage for colon and rectum according to AJCC 7th edition indicating that the tumor directly invades other organs or structures. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_t/ NCI BBRB pT4b (colon) pT0 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT0 (lung) pTis (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating carcinoma in situ. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pTis (lung) pT1 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 3 cm or less in greatest dimension, surrounded by lung or visceral pleura without bronchoscopic evidence of invasion more proximal than the lobar bronchus (i.e., not in the main bronchus). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1 (lung) pT1a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1a (lung) pT1b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 2 cm but not more than 3 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT1b (lung) pT2 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 7 cm or the tumor has any of the following features: involves main bronchus, 2 cm or more distal to the carina, invades visceral pleura, associated with atelectasis or obstructive pneumonitis that extends to the hilar region but does not involve the entire lung. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2 (lung) pT2a (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 3 cm but not more than 5 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2a (lung) pT2b (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 5 cm but not more than 7 cm in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT2b (lung) pT3 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor is more than 7 cm or one that directly invades any of: parietal pleura, chest wall (including superior sulcus tumors), diaphragm, phrenic nerve, mediastinal pleura, parietal pericardiu or the tumor is in the main bronchus less than 2 cm distal to the carina but without involvement of the carina or there is associated atelectasis or obstructive pneumonitis of the entire lung or there is separate tumor nodule(s) in the same lobe as the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT3 (lung) pT4 (lung) A pathologic primary tumor stage for lung according to AJCC 7th edition indicating that the tumor of any size that invades any of the following: mediastinum, heart, great vessels, trachea, recurrent laryngeal nerve, esophagus, vertebral body, carina or there is separate tumor nodule(s) in a different ipsilateral lobe to that of the primary. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_t/ NCI BBRB pT4 (lung) pT0 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT0 (kidney) pT1 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 7 cm or less in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1 (kidney) pT1a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is 4 cm or less. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1a (kidney) pT1b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 4 cm but not more than 7 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT1b (kidney) pT2 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm in greatest dimension and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2 (kidney) pT2a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 7 cm but not more than 10 cm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2a (kidney) pT2b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor is more than 10 cm and limited to the kidney. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT2b (kidney) pT3 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor extends into major veins or perinephric tissues but not into the ipsilateral adrenal gland and not beyond the Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3 (kidney) pT3a (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into the renal vein or its segmental (muscle containing) branches, or the tumor invades perirenal and/or renal sinus fat (peripelvic) fat but not beyond Gerota fascia. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3a (kidney) pT3b (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava below diaphragm. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3b (kidney) pT3c (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor grossly extends into vena cava above the diaphragm or Invades the wall of the vena cava. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT3c (kidney) pT4 (kidney) A pathologic primary tumor stage for kidney according to AJCC 7th edition indicating that the tumor invades beyond Gerota fascia (including contiguous extension into the ipsilateral adrenal gland). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_t/ NCI BBRB pT4 (kidney) pT0 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that there is no evidence of primary tumor. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT0 (ovary) pT1 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to the ovaries (one or both). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1 (ovary) pT1a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one ovary; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1a (ovary) pT1b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to both ovaries; capsule intact, no tumor on ovarian surface and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1b (ovary) pT1c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor is limited to one or both ovaries with capsule ruptured, tumor on ovarian surface, or malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT1c (ovary) pT2 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with pelvic extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2 (ovary) pT2a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension and/or implants on uterus and/or tube(s) and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2a (ovary) pT2b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has extension to other pelvic tissues and no malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2b (ovary) pT2c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has pelvic extension with malignant cells in ascites or peritoneal washings. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT2c (ovary) pT3 (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor involves one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3 (ovary) pT3a (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has microscopic peritoneal metastasis beyond pelvis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3a (ovary) pT3b (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has macroscopic peritoneal, metastatasis beyond pelvis, 2 cm or less in greatest dimension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3b (ovary) pT3c (ovary) A pathologic primary tumor stage for ovary according to AJCC 7th edition indicating that the tumor has peritoneal metastasis beyond pelvis, more than 2 cm in greatest dimension and/or regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_t/ NCI BBRB pT3c (ovary) pN0 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating no regional lymph node metastsis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN0 (colon) pN1 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1 (colon) pN1a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 1 regional lymph node. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1a (colon) pN1b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 2-3 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1b (colon) pN1c (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating tumor deposit(s), i.e., satellites in the subserosa, or in non-peritonealized pericolic or perirectal soft tissue without regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN1c (colon) pN2 (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2 (colon) pN2a (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 4 to 6 regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2a (colon) pN2b (colon) A pathologic lymph node stage for colon and rectum according to AJCC 7th edition indicating metastasis in 7 or more regional lymph nodes. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_n/ NCI BBRB pN2b (colon) pN0 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN0 (lung) pN1 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral peribronchial and/or ipsilateral hilar lymph nodes and intrapulmonary nodes, including involvement by direct extension. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN1 (lung) pN2 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in ipsilateral mediastinal and/or subcarinal lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN2 (lung) pN3 (lung) A pathologic lymph node stage for lung according to AJCC 7th edition indicating metastasis in contralateral mediastinal, contralateral hilar, ipsilateral or contralateral scalene, or supraclavicular lymph node(s). Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_n/ NCI BBRB pN3 (lung) pN0 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN0 (kidney) pN1 (kidney) A pathologic lymph node stage for kidney according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_n/ NCI BBRB pN1 (kidney) pN0 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is no regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN0 (ovary) pN1 (ovary) A pathologic lymph node stage for ovary according to AJCC 7th edition indicating that there is regional lymph node metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_n/ NCI BBRB pN1 (ovary) cM0 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there are no symptoms or signs of distant metastasis. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM0 (colon) cM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is clinical evidence of distant metastases by history, physical examination, imaging studies, or invasive procedures, but without microscopic evidence of the presumed distant metastases. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Cancer_staging#Pathological_M_Categorization_.28cM_and_pM.29 NCI BBRB cM1 (colon) cM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1a (colon) cM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB cM1b (colon) pM1 (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that there is microscopic evidence confirming distant metastatic disease. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1 (colon) pM1a (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is confined to one organ and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1a (colon) pM1b (colon) A pathologic distant metastases stage for colon according to AJCC 7th edition indicating that metastasis is in more than one organ or the peritoneum and histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/colon/path_m/ NCI BBRB pM1b (colon) cM0 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM0 (lung) cM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1 (lung) cM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is based on clinical assessment and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1a (lung) cM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB cM1b (lung) pM1 (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1 (lung) pM1a (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that metastasis is histologically confirmed and a separate tumor nodule(s) in a contralateral lobe; tumor with pleural nodules OR malignant pleural or pericardial effusion. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1a (lung) pM1b (lung) A pathologic distant metastases stage for lung according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed and associated with distant lymph nodes or carcinomatosis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/lung/path_m/ NCI BBRB pM1b (lung) cM0 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM0 (kidney) cM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there are distant metastases based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB cM1 (kidney) pM1 (kidney) A pathologic distant metastases stage for kidney according to AJCC 7th edition indicating that there is a distant metastases that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/kidney_parenchyma/path_m/ NCI BBRB pM1 (kidney) cM0 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is no distant metastasis. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM0 (ovary) cM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis based on clinical assessment. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB cM1 (ovary) pM1 (ovary) A pathologic distant metastases stage for ovary according to AJCC 7th edition indicating that there is distant metastasis except peritoneal metastasis that is histologically confirmed. Chris Stoeckert, Helena Ellis https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_m/ NCI BBRB pM1 (ovary) Occult Carcinoma (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a small carcinoma, either asymptomatic or giving rise to metastases without symptoms due to the primary carcinoma. Chris Stoeckert, Helena Ellis Occult Carcinoma http://www.medilexicon.com/dictionary/14371 NCI BBRB Occult Carcinoma (AJCC 7th) Stage 0 (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating a carcinoma in situ (or melanoma in situ for melanoma of the skin or germ cell neoplasia in situ for testicular germ cell tumors) and generally is considered to have no metastatic potential. Chris Stoeckert, Helena Ellis Stage 0 https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage 0 (AJCC 7th) Stage I (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers that are smaller or less deeply invasive without regional disease or nodes. Chris Stoeckert, Helena Ellis Stage I https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage I (AJCC 7th) Stage IIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIB and IIC. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIA (AJCC 7th) Stage IIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIC. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIB (AJCC 7th) Stage IIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent but less than in Stage III and with differing characteristics from IIA and IIB. Chris Stoeckert, Helena Ellis Stage IIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIC (AJCC 7th) Stage IIIA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIB and IIIC. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIA (AJCC 7th) Stage IIIB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIC. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIB (AJCC 7th) Stage IIIC (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers with increasing tumor or nodal extent greater than in Stage II and with differing characteristics from IIIA and IIIB. Chris Stoeckert, Helena Ellis Stage IIIC https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IIIC (AJCC 7th) Stage IVA (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVB. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVA (AJCC 7th) Stage IVB (AJCC 7th) A clinical tumor stage group according to AJCC 7th edition indicating cancers in patients who present with distant metastases at diagnosis and with differing characteristics from IVA. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cancer_staging NCI BBRB Stage IVB (AJCC 7th) Stage IA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating invasive carcinoma which can be diagnosed only by microscopy, with deepest invasion <5 mm and the largest extension <7 mm. Chris Stoeckert, Helena Ellis Stage IA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA (FIGO) Stage IA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of <3.0 mm in depth and extension of <7.0 mm. Chris Stoeckert, Helena Ellis Stage IA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA1 (FIGO) Stage IA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating measured stromal invasion of >3.0 mm and not >5.0 mm with an extension of not >7.0 mm. Chris Stoeckert, Helena Ellis Stage IA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IA2 (FIGO) Stage IB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesions limited to the cervix uteri or pre-clinical cancers greater than stage IA Chris Stoeckert, Helena Ellis Stage IB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB (FIGO) Stage IB1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB1 (FIGO) Stage IB2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating clinically visible lesion limited to the cervix uteri or pre-clinical cancers greater than stage IA >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IB2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IB2 (FIGO) Stage IIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA (FIGO) Stage IIA1 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion <4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA1 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA1 (FIGO) Stage IIA2 (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina without parametrial invasion and clinically visible lesion >4.0 cm in greatest dimension. Chris Stoeckert, Helena Ellis Stage IIA2 https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIA2 (FIGO) Stage IIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating cervical carcinoma invades beyond the uterus, but not to the pelvic wall or to the lower third of the vagina with obvious parametrial invasion. Chris Stoeckert, Helena Ellis Stage IIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIB (FIGO) Stage IIIA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating tumour involves lower third of the vagina, with no extension to the pelvic wall. Chris Stoeckert, Helena Ellis Stage IIIA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIA (FIGO) Stage IIIB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating extension to the pelvic wall and/or hydronephrosis or non-functioning kidney. Chris Stoeckert, Helena Ellis Stage IIIB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IIIB (FIGO) Stage IVA (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread of the growth to adjacent organs. Chris Stoeckert, Helena Ellis Stage IVA https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVA (FIGO) Stage IVB (FIGO) An International Federation of Gynecology and Obstetrics cervical cancer stage value specification indicating spread to distant organs. Chris Stoeckert, Helena Ellis Stage IVB https://en.wikipedia.org/wiki/Cervical_cancer_staging NCI BBRB Stage IVB (FIGO) Stage 1 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1 (FIGO) Stage 1A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1A (FIGO) Stage 1B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1B (FIGO) Stage 1C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T1c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 1C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 1C (FIGO) Stage 2 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2 (FIGO) Stage 2A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2a, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2A (FIGO) Stage 2B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2b, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2B (FIGO) Stage 2C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T2c, N0, and M0. Chris Stoeckert, Helena Ellis Stage 2C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 2C (FIGO) Stage 3 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3, N0, and M0) or (T3,3a,3b, NX, and M0). Chris Stoeckert, Helena Ellis Stage 3 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3 (FIGO) Stage 3A (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3a, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3A https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3A (FIGO) Stage 3B (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of T3b, N0, and M0 . Chris Stoeckert, Helena Ellis Stage 3B https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3B (FIGO) Stage 3C (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T3c, N0,X and M0) or (any T, N1 and M0). Chris Stoeckert, Helena Ellis Stage 3C https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 3C (FIGO) Stage 4 (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of any T, any N, and M1. Chris Stoeckert, Helena Ellis Stage 4 https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage 4 (FIGO) Stage Unknown (FIGO) A International Federation of Gynecology and Obstetrics ovarian cancer stage value specification associated with TNM stage values of (T0, N0, and M0) or (T1,1a-1c,2,2a-2c, NX, and M0) or (TX, N0,X, M0). Chris Stoeckert, Helena Ellis Stage Unknown https://staging.seer.cancer.gov/tnm/input/1.0/ovary/path_stage_group_direct/ NCI BBRB Stage Unknown (FIGO) 3: symptomatic in bed more than 50% of the day but not bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and in bed for more than 50% of the day but is not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 3: symptomatic in bed more than 50% of the day but not bed ridden 2: symptomatic but in bed less than 50% of the day An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is in bed for less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 2: symptomatic but in bed less than 50% of the day 4: bed ridden An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic and is bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 4: bed ridden 0: asymptomatic An Eastern Cooperative Oncology Group score value specification indicating a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 0: asymptomatic 1: symptomatic but fully ambulatory An Eastern Cooperative Oncology Group score value specification indicating a patient is symptomatic but is fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 1: symptomatic but fully ambulatory 100: asymptomatic A Karnofsky score vaue specification indicating that a patient is asymptomatic. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 100: asymptomatic 80-90: symptomatic but fully ambulatory A Karnofsky score vaue specification indicating that a patient is symptomatic but fully ambulatory. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 80-90: symptomatic but fully ambulatory 60-70: symptomatic but in bed less than 50% of the day A Karnofsky score vaue specification indicating that a patient is symptomatic but in bed less than 50% of the day. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 60-70: symptomatic but in bed less than 50% of the day 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden A Karnofsky score vaue specification indicating that a patient is symptomatic, in bed more than 50% of the day, but not bed ridden. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden Oxford Nanopore Technologies An organization that is developing and selling nanopore sequencing products and is based in the UK. James A. Overton https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies Oxford Nanopore Technologies meter A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second. m meter kilogram A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France. kg kilogram second A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom. s sec second centimeter A length unit which is equal to one hundredth of a meter or 10^[-2] m. cm centimeter millimeter A length unit which is equal to one thousandth of a meter or 10^[-3] m. mm millimeter micrometer A length unit which is equal to one millionth of a meter or 10^[-6] m. um micrometer nanometer A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m. nm nanometer angstrom A length unit which is equal to 10 [-10] m. angstrom gram A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg. g gram milligram A mass unit which is equal to one thousandth of a gram or 10^[-3] g. mg milligram microgram A mass unit which is equal to one millionth of a gram or 10^[-6] g. ug microgram nanogram A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g. ng nanogram picogram A mass unit which is equal to 10^[-12] g. pg picogram degree Celsius A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K. C degree C degree Celsius minute A time unit which is equal to 60 seconds. min minute hour A time unit which is equal to 3600 seconds or 60 minutes. h hr hour day A time unit which is equal to 24 hours. day week A time unit which is equal to 7 days. week month A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which in science is taken to be equal to 30 days. month year A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days. year micromole A substance unit equal to a millionth of a mol or 10^[-6] mol. umol micromole nanomole A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol. nmol nanomole picomole A substance unit equal to 10^[-12] mol. pmol picomole molar A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L). M molar millimolar A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M. mM millimolar micromolar A unit of molarity which is equal to one millionth of a molar or 10^[-6] M. uM micromolar nanomolar A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M. nM nanomolar picomolar A unit of molarity which is equal to 10^[-12] M. pM picomolar cubic centimeter A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml. cc cubic centimeter milliliter A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter. ml milliliter liter A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter. L liter cubic decimeter A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L. cubic decimeter microliter A volume unit which is equal to one millionth of a liter or 10^[-6] L. ul microliter nanoliter A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L. nl nanoliter picoliter A volume unit which is equal to 10^[-12] L. pl picoliter hertz A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second. hertz mass percentage A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture. % w/w percent weight pr weight mass percentage mass volume percentage A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture. % w/v percent vol per vol mass volume percentage volume percentage A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution. % v/v percent vol per vol volume percentage gram per liter A mass unit density which is equal to mass of an object in grams divided by the volume in liters. g per L g/L gram per liter milligram per milliliter A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters. mg per ml mg/ml milligram per milliliter degree Fahrenheit A temperature unit which is equal to 5/9ths of a kelvin. Negative 40 degrees Fahrenheit is equal to negative 40 degrees Celsius. degree Fahrenheit pH A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+). pH milliliter per liter A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution. ml per L ml/l milliliter per liter gram per deciliter A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters. g/dl gram per deciliter colony forming unit per volume A concentration unit which a measure of viable bacterial numbers in a given volume. colony forming unit per volume microliters per minute A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute. microliters per minute count per nanomolar second A rate unit which is equal to one over one nanomolar second. count per nanomolar second count per molar second A rate unit which is equal to one over one molar second. count per molar second count per nanomolar A rate unit which is equal to one over one nanomolar. count per nanomolar count per molar A rate unit which is equal to one over one molar. count per molar microgram per liter A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters. ng/ml ug/L microgram per liter 2019-07-12T14:23:27Z avoided excessive intake of food 2 2 1 2 true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP From ligand activity to has_ligand This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction From has_ligand to ligand activity effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).